Starting phenix.real_space_refine on Sat Feb 24 22:50:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f66_28876/02_2024/8f66_28876_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f66_28876/02_2024/8f66_28876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f66_28876/02_2024/8f66_28876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f66_28876/02_2024/8f66_28876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f66_28876/02_2024/8f66_28876_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f66_28876/02_2024/8f66_28876_neut.pdb" } resolution = 2.28 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= 0.015 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 196 5.16 5 C 29470 2.51 5 N 7868 2.21 5 O 8974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "E TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 179": "OE1" <-> "OE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 206": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "F GLU 179": "OE1" <-> "OE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 206": "OE1" <-> "OE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "G GLU 159": "OE1" <-> "OE2" Residue "G GLU 179": "OE1" <-> "OE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "G GLU 206": "OE1" <-> "OE2" Residue "G GLU 227": "OE1" <-> "OE2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H GLU 23": "OE1" <-> "OE2" Residue "H PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I GLU 23": "OE1" <-> "OE2" Residue "I PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J GLU 23": "OE1" <-> "OE2" Residue "J PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K GLU 77": "OE1" <-> "OE2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L GLU 23": "OE1" <-> "OE2" Residue "L PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L GLU 77": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M GLU 23": "OE1" <-> "OE2" Residue "M PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 62": "OE1" <-> "OE2" Residue "M GLU 64": "OE1" <-> "OE2" Residue "M GLU 77": "OE1" <-> "OE2" Residue "M GLU 121": "OE1" <-> "OE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N GLU 23": "OE1" <-> "OE2" Residue "N PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 62": "OE1" <-> "OE2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "N GLU 77": "OE1" <-> "OE2" Residue "N GLU 121": "OE1" <-> "OE2" Residue "O GLU 159": "OE1" <-> "OE2" Residue "O GLU 179": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "O GLU 205": "OE1" <-> "OE2" Residue "O GLU 206": "OE1" <-> "OE2" Residue "O GLU 227": "OE1" <-> "OE2" Residue "P GLU 159": "OE1" <-> "OE2" Residue "P GLU 179": "OE1" <-> "OE2" Residue "P GLU 202": "OE1" <-> "OE2" Residue "P GLU 205": "OE1" <-> "OE2" Residue "P GLU 206": "OE1" <-> "OE2" Residue "P GLU 227": "OE1" <-> "OE2" Residue "Q GLU 159": "OE1" <-> "OE2" Residue "Q GLU 179": "OE1" <-> "OE2" Residue "Q GLU 202": "OE1" <-> "OE2" Residue "Q GLU 205": "OE1" <-> "OE2" Residue "Q GLU 206": "OE1" <-> "OE2" Residue "Q GLU 227": "OE1" <-> "OE2" Residue "R GLU 159": "OE1" <-> "OE2" Residue "R GLU 179": "OE1" <-> "OE2" Residue "R GLU 202": "OE1" <-> "OE2" Residue "R GLU 205": "OE1" <-> "OE2" Residue "R GLU 206": "OE1" <-> "OE2" Residue "R GLU 227": "OE1" <-> "OE2" Residue "S GLU 159": "OE1" <-> "OE2" Residue "S GLU 179": "OE1" <-> "OE2" Residue "S GLU 202": "OE1" <-> "OE2" Residue "S GLU 205": "OE1" <-> "OE2" Residue "S GLU 206": "OE1" <-> "OE2" Residue "S GLU 227": "OE1" <-> "OE2" Residue "T GLU 159": "OE1" <-> "OE2" Residue "T GLU 179": "OE1" <-> "OE2" Residue "T GLU 202": "OE1" <-> "OE2" Residue "T GLU 205": "OE1" <-> "OE2" Residue "T GLU 206": "OE1" <-> "OE2" Residue "T GLU 227": "OE1" <-> "OE2" Residue "U GLU 159": "OE1" <-> "OE2" Residue "U GLU 179": "OE1" <-> "OE2" Residue "U GLU 202": "OE1" <-> "OE2" Residue "U GLU 205": "OE1" <-> "OE2" Residue "U GLU 206": "OE1" <-> "OE2" Residue "U GLU 227": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V GLU 23": "OE1" <-> "OE2" Residue "V PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V GLU 64": "OE1" <-> "OE2" Residue "V GLU 77": "OE1" <-> "OE2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W GLU 23": "OE1" <-> "OE2" Residue "W PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 62": "OE1" <-> "OE2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "W GLU 77": "OE1" <-> "OE2" Residue "W GLU 121": "OE1" <-> "OE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X GLU 23": "OE1" <-> "OE2" Residue "X PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 62": "OE1" <-> "OE2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 121": "OE1" <-> "OE2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y GLU 23": "OE1" <-> "OE2" Residue "Y PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 62": "OE1" <-> "OE2" Residue "Y GLU 64": "OE1" <-> "OE2" Residue "Y GLU 77": "OE1" <-> "OE2" Residue "Y GLU 121": "OE1" <-> "OE2" Residue "Z GLU 17": "OE1" <-> "OE2" Residue "Z GLU 23": "OE1" <-> "OE2" Residue "Z PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 62": "OE1" <-> "OE2" Residue "Z GLU 64": "OE1" <-> "OE2" Residue "Z GLU 77": "OE1" <-> "OE2" Residue "Z GLU 121": "OE1" <-> "OE2" Residue "a GLU 17": "OE1" <-> "OE2" Residue "a GLU 23": "OE1" <-> "OE2" Residue "a PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 62": "OE1" <-> "OE2" Residue "a GLU 64": "OE1" <-> "OE2" Residue "a GLU 77": "OE1" <-> "OE2" Residue "a GLU 121": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "b GLU 23": "OE1" <-> "OE2" Residue "b PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 62": "OE1" <-> "OE2" Residue "b GLU 64": "OE1" <-> "OE2" Residue "b GLU 77": "OE1" <-> "OE2" Residue "b GLU 121": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 46508 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "B" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "C" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "D" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "E" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "F" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "G" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "H" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "I" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "J" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "K" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "L" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "M" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "N" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "O" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "P" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "Q" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "R" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "S" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "T" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "U" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "V" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "W" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "X" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "Y" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "Z" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "a" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "b" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Time building chain proxies: 23.88, per 1000 atoms: 0.51 Number of scatterers: 46508 At special positions: 0 Unit cell: (133.523, 132.89, 170.226, 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 196 16.00 O 8974 8.00 N 7868 7.00 C 29470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.86 Conformation dependent library (CDL) restraints added in 8.7 seconds 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11060 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 70 sheets defined 40.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.26 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'B' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA B 30 " --> pdb=" O TYR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 185 through 199 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.503A pdb=" N ALA C 30 " --> pdb=" O TYR C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 104 Processing helix chain 'C' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'D' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 185 through 199 Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 123 removed outlier: 3.972A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'E' and resid 185 through 199 Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'F' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA F 30 " --> pdb=" O TYR F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 Processing helix chain 'F' and resid 185 through 199 Processing helix chain 'F' and resid 225 through 231 Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 180 Processing helix chain 'G' and resid 185 through 199 Processing helix chain 'G' and resid 225 through 231 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 147 through 166 Processing helix chain 'H' and resid 188 through 200 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'I' and resid 188 through 200 Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 147 through 166 Processing helix chain 'J' and resid 188 through 200 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.836A pdb=" N VAL K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 Processing helix chain 'K' and resid 147 through 166 Processing helix chain 'K' and resid 188 through 200 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.836A pdb=" N VAL L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 Processing helix chain 'L' and resid 147 through 166 Processing helix chain 'L' and resid 188 through 200 Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 90 removed outlier: 3.836A pdb=" N VAL M 90 " --> pdb=" O MET M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 147 through 166 Processing helix chain 'M' and resid 188 through 200 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 142 Processing helix chain 'N' and resid 147 through 166 Processing helix chain 'N' and resid 188 through 200 Processing helix chain 'O' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA O 30 " --> pdb=" O TYR O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 104 Processing helix chain 'O' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 180 Processing helix chain 'O' and resid 185 through 199 Processing helix chain 'O' and resid 225 through 231 Processing helix chain 'P' and resid 21 through 32 removed outlier: 3.503A pdb=" N ALA P 30 " --> pdb=" O TYR P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 104 Processing helix chain 'P' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU P 112 " --> pdb=" O ASN P 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 180 Processing helix chain 'P' and resid 185 through 199 Processing helix chain 'P' and resid 225 through 231 Processing helix chain 'Q' and resid 21 through 32 removed outlier: 3.503A pdb=" N ALA Q 30 " --> pdb=" O TYR Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 104 Processing helix chain 'Q' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU Q 112 " --> pdb=" O ASN Q 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 180 Processing helix chain 'Q' and resid 185 through 199 Processing helix chain 'Q' and resid 225 through 231 Processing helix chain 'R' and resid 21 through 32 removed outlier: 3.503A pdb=" N ALA R 30 " --> pdb=" O TYR R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 104 Processing helix chain 'R' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU R 112 " --> pdb=" O ASN R 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 180 Processing helix chain 'R' and resid 185 through 199 Processing helix chain 'R' and resid 225 through 231 Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA S 30 " --> pdb=" O TYR S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 104 Processing helix chain 'S' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR S 123 " --> pdb=" O GLN S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 180 Processing helix chain 'S' and resid 185 through 199 Processing helix chain 'S' and resid 225 through 231 Processing helix chain 'T' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA T 30 " --> pdb=" O TYR T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 104 Processing helix chain 'T' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU T 112 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 180 Processing helix chain 'T' and resid 185 through 199 Processing helix chain 'T' and resid 225 through 231 Processing helix chain 'U' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA U 30 " --> pdb=" O TYR U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU U 112 " --> pdb=" O ASN U 108 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 180 Processing helix chain 'U' and resid 185 through 199 Processing helix chain 'U' and resid 225 through 231 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 Processing helix chain 'V' and resid 147 through 166 Processing helix chain 'V' and resid 188 through 200 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.836A pdb=" N VAL W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'W' and resid 188 through 200 Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL X 90 " --> pdb=" O MET X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 142 Processing helix chain 'X' and resid 147 through 166 Processing helix chain 'X' and resid 188 through 200 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 142 Processing helix chain 'Y' and resid 147 through 166 Processing helix chain 'Y' and resid 188 through 200 Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 142 Processing helix chain 'Z' and resid 147 through 166 Processing helix chain 'Z' and resid 188 through 200 Processing helix chain 'a' and resid 48 through 71 Processing helix chain 'a' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL a 90 " --> pdb=" O MET a 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 142 Processing helix chain 'a' and resid 147 through 166 Processing helix chain 'a' and resid 188 through 200 Processing helix chain 'b' and resid 48 through 71 Processing helix chain 'b' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL b 90 " --> pdb=" O MET b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 142 Processing helix chain 'b' and resid 147 through 166 Processing helix chain 'b' and resid 188 through 200 Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 165 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN A 158 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN B 158 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN C 158 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 162 through 165 Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN D 158 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 162 through 165 Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN E 158 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 162 through 165 Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.795A pdb=" N ASN F 158 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.793A pdb=" N ASN G 158 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 124 through 127 Processing sheet with id=AB7, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AB8, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL H 110 " --> pdb=" O ASP H 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 124 through 127 Processing sheet with id=AC1, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AC2, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.414A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL I 110 " --> pdb=" O ASP I 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 124 through 127 Processing sheet with id=AC4, first strand: chain 'J' and resid 20 through 21 Processing sheet with id=AC5, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL J 110 " --> pdb=" O ASP J 122 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 124 through 127 Processing sheet with id=AC7, first strand: chain 'K' and resid 20 through 21 Processing sheet with id=AC8, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL K 110 " --> pdb=" O ASP K 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 124 through 127 Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 21 Processing sheet with id=AD2, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL L 110 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 124 through 127 Processing sheet with id=AD4, first strand: chain 'M' and resid 20 through 21 Processing sheet with id=AD5, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL M 110 " --> pdb=" O ASP M 122 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 124 through 127 Processing sheet with id=AD7, first strand: chain 'N' and resid 20 through 21 Processing sheet with id=AD8, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.414A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL N 110 " --> pdb=" O ASP N 122 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 162 through 165 Processing sheet with id=AE1, first strand: chain 'O' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN O 158 " --> pdb=" O ASP O 150 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 162 through 165 Processing sheet with id=AE3, first strand: chain 'P' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN P 158 " --> pdb=" O ASP P 150 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 162 through 165 Processing sheet with id=AE5, first strand: chain 'Q' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN Q 158 " --> pdb=" O ASP Q 150 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 162 through 165 Processing sheet with id=AE7, first strand: chain 'R' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN R 158 " --> pdb=" O ASP R 150 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 162 through 165 Processing sheet with id=AE9, first strand: chain 'S' and resid 67 through 69 removed outlier: 3.795A pdb=" N ASN S 158 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 162 through 165 Processing sheet with id=AF2, first strand: chain 'T' and resid 67 through 69 removed outlier: 3.793A pdb=" N ASN T 158 " --> pdb=" O ASP T 150 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AF4, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN U 158 " --> pdb=" O ASP U 150 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 124 through 127 Processing sheet with id=AF6, first strand: chain 'V' and resid 20 through 21 Processing sheet with id=AF7, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL V 110 " --> pdb=" O ASP V 122 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 124 through 127 Processing sheet with id=AF9, first strand: chain 'W' and resid 20 through 21 Processing sheet with id=AG1, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.414A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL W 110 " --> pdb=" O ASP W 122 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'X' and resid 124 through 127 Processing sheet with id=AG3, first strand: chain 'X' and resid 20 through 21 Processing sheet with id=AG4, first strand: chain 'X' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL X 110 " --> pdb=" O ASP X 122 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 124 through 127 Processing sheet with id=AG6, first strand: chain 'Y' and resid 20 through 21 Processing sheet with id=AG7, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL Y 110 " --> pdb=" O ASP Y 122 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 124 through 127 Processing sheet with id=AG9, first strand: chain 'Z' and resid 20 through 21 Processing sheet with id=AH1, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL Z 110 " --> pdb=" O ASP Z 122 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'a' and resid 124 through 127 Processing sheet with id=AH3, first strand: chain 'a' and resid 20 through 21 Processing sheet with id=AH4, first strand: chain 'a' and resid 34 through 38 removed outlier: 6.414A pdb=" N THR a 41 " --> pdb=" O ILE a 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL a 110 " --> pdb=" O ASP a 122 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 124 through 127 Processing sheet with id=AH6, first strand: chain 'b' and resid 20 through 21 Processing sheet with id=AH7, first strand: chain 'b' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR b 41 " --> pdb=" O ILE b 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL b 110 " --> pdb=" O ASP b 122 " (cutoff:3.500A) 2772 hydrogen bonds defined for protein. 7896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.78 Time building geometry restraints manager: 17.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8034 1.31 - 1.43: 10958 1.43 - 1.56: 27754 1.56 - 1.68: 0 1.68 - 1.81: 378 Bond restraints: 47124 Sorted by residual: bond pdb=" C THR O 13 " pdb=" N VAL O 14 " ideal model delta sigma weight residual 1.330 1.265 0.065 1.26e-02 6.30e+03 2.67e+01 bond pdb=" C THR F 13 " pdb=" N VAL F 14 " ideal model delta sigma weight residual 1.330 1.266 0.065 1.26e-02 6.30e+03 2.64e+01 bond pdb=" C THR C 13 " pdb=" N VAL C 14 " ideal model delta sigma weight residual 1.330 1.266 0.065 1.26e-02 6.30e+03 2.64e+01 bond pdb=" C THR D 13 " pdb=" N VAL D 14 " ideal model delta sigma weight residual 1.330 1.266 0.065 1.26e-02 6.30e+03 2.63e+01 bond pdb=" C THR P 13 " pdb=" N VAL P 14 " ideal model delta sigma weight residual 1.330 1.266 0.065 1.26e-02 6.30e+03 2.63e+01 ... (remaining 47119 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.01: 644 105.01 - 111.61: 20894 111.61 - 118.21: 15116 118.21 - 124.82: 26613 124.82 - 131.42: 335 Bond angle restraints: 63602 Sorted by residual: angle pdb=" CA ASP T 84 " pdb=" CB ASP T 84 " pdb=" CG ASP T 84 " ideal model delta sigma weight residual 112.60 119.20 -6.60 1.00e+00 1.00e+00 4.36e+01 angle pdb=" CA ASP E 84 " pdb=" CB ASP E 84 " pdb=" CG ASP E 84 " ideal model delta sigma weight residual 112.60 119.17 -6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" CA ASP P 84 " pdb=" CB ASP P 84 " pdb=" CG ASP P 84 " ideal model delta sigma weight residual 112.60 119.17 -6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" CA ASP R 84 " pdb=" CB ASP R 84 " pdb=" CG ASP R 84 " ideal model delta sigma weight residual 112.60 119.16 -6.56 1.00e+00 1.00e+00 4.31e+01 angle pdb=" CA ASP S 84 " pdb=" CB ASP S 84 " pdb=" CG ASP S 84 " ideal model delta sigma weight residual 112.60 119.15 -6.55 1.00e+00 1.00e+00 4.29e+01 ... (remaining 63597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 24639 17.64 - 35.29: 2801 35.29 - 52.93: 924 52.93 - 70.58: 252 70.58 - 88.22: 196 Dihedral angle restraints: 28812 sinusoidal: 11480 harmonic: 17332 Sorted by residual: dihedral pdb=" CA MET V 93 " pdb=" C MET V 93 " pdb=" N PRO V 94 " pdb=" CA PRO V 94 " ideal model delta harmonic sigma weight residual -180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA MET K 93 " pdb=" C MET K 93 " pdb=" N PRO K 94 " pdb=" CA PRO K 94 " ideal model delta harmonic sigma weight residual -180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA MET a 93 " pdb=" C MET a 93 " pdb=" N PRO a 94 " pdb=" CA PRO a 94 " ideal model delta harmonic sigma weight residual -180.00 -156.14 -23.86 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 28809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 5578 0.044 - 0.089: 1180 0.089 - 0.133: 564 0.133 - 0.178: 56 0.178 - 0.222: 28 Chirality restraints: 7406 Sorted by residual: chirality pdb=" CA PRO Q 17 " pdb=" N PRO Q 17 " pdb=" C PRO Q 17 " pdb=" CB PRO Q 17 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA PRO O 17 " pdb=" N PRO O 17 " pdb=" C PRO O 17 " pdb=" CB PRO O 17 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA PRO U 17 " pdb=" N PRO U 17 " pdb=" C PRO U 17 " pdb=" CB PRO U 17 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 7403 not shown) Planarity restraints: 8162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 13 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C THR B 13 " -0.071 2.00e-02 2.50e+03 pdb=" O THR B 13 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL B 14 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 13 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR G 13 " 0.071 2.00e-02 2.50e+03 pdb=" O THR G 13 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL G 14 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR U 13 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR U 13 " 0.071 2.00e-02 2.50e+03 pdb=" O THR U 13 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL U 14 " -0.025 2.00e-02 2.50e+03 ... (remaining 8159 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 11112 2.80 - 3.32: 43008 3.32 - 3.85: 80244 3.85 - 4.37: 95995 4.37 - 4.90: 158233 Nonbonded interactions: 388592 Sorted by model distance: nonbonded pdb=" OH TYR O 123 " pdb=" OH TYR U 126 " model vdw 2.269 2.440 nonbonded pdb=" OH TYR D 126 " pdb=" OH TYR E 123 " model vdw 2.271 2.440 nonbonded pdb=" ND1 HIS I 28 " pdb=" OD2 ASP J 122 " model vdw 2.283 2.520 nonbonded pdb=" OH TYR T 126 " pdb=" OH TYR U 123 " model vdw 2.293 2.440 nonbonded pdb=" NE2 GLN P 97 " pdb=" OE2 GLU V 64 " model vdw 2.295 2.520 ... (remaining 388587 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 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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: 7.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 29.370 Check model and map are aligned: 0.880 Set scattering table: 0.450 Process input model: 120.610 Find NCS groups from input model: 3.600 Set up NCS constraints: 0.490 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:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 47124 Z= 0.256 Angle : 0.741 12.389 63602 Z= 0.474 Chirality : 0.046 0.222 7406 Planarity : 0.005 0.041 8162 Dihedral : 19.003 88.223 17752 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.76 % Favored : 95.53 % Rotamer: Outliers : 3.94 % Allowed : 20.67 % Favored : 75.39 % 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: 0.82 (0.11), residues: 5950 helix: 1.33 (0.10), residues: 2380 sheet: 0.72 (0.13), residues: 1582 loop : -0.47 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 109 PHE 0.036 0.002 PHE X 25 TYR 0.013 0.001 TYR O 8 ARG 0.005 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 893 time to evaluate : 5.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 197 outliers final: 44 residues processed: 1057 average time/residue: 2.0097 time to fit residues: 2516.1932 Evaluate side-chains 732 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 688 time to evaluate : 5.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 205 GLU Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 205 GLU Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain S residue 205 GLU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 205 GLU Chi-restraints excluded: chain T residue 207 LEU Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain b residue 120 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 0.9990 chunk 445 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 460 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 280 optimal weight: 4.9990 chunk 343 optimal weight: 0.0970 chunk 533 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN E 44 ASN F 44 ASN F 219 ASN G 219 ASN H 69 GLN H 89 GLN I 89 GLN I 141 GLN I 191 GLN J 30 ASN J 89 GLN J 191 GLN K 30 ASN K 69 GLN K 89 GLN L 30 ASN L 69 GLN L 89 GLN L 141 GLN M 89 GLN M 141 GLN N 30 ASN N 69 GLN N 89 GLN O 98 GLN O 122 GLN O 219 ASN P 98 GLN P 219 ASN ** Q 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN R 219 ASN ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 219 ASN U 98 GLN V 30 ASN V 89 GLN W 69 GLN W 89 GLN W 141 GLN X 30 ASN X 89 GLN Y 89 GLN Y 141 GLN Z 30 ASN Z 89 GLN Z 141 GLN Z 191 GLN a 89 GLN a 141 GLN b 30 ASN b 69 GLN b 89 GLN b 141 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 47124 Z= 0.238 Angle : 0.575 8.863 63602 Z= 0.322 Chirality : 0.045 0.189 7406 Planarity : 0.003 0.030 8162 Dihedral : 6.736 59.800 6694 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.71 % Allowed : 2.87 % Favored : 96.42 % Rotamer: Outliers : 4.40 % Allowed : 21.27 % Favored : 74.33 % 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: 1.61 (0.11), residues: 5950 helix: 2.58 (0.10), residues: 2338 sheet: 1.18 (0.13), residues: 1428 loop : -0.72 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS a 109 PHE 0.039 0.002 PHE Z 25 TYR 0.011 0.001 TYR M 184 ARG 0.004 0.000 ARG V 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 652 time to evaluate : 6.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7101 (t80) REVERT: B 221 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.7109 (t80) REVERT: D 221 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7121 (t80) REVERT: G 68 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.7005 (mm110) REVERT: L 96 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7243 (mtp) REVERT: O 221 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7024 (t80) REVERT: P 68 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6909 (mm110) REVERT: Q 221 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.7091 (t80) REVERT: R 221 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7092 (t80) REVERT: S 221 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7120 (t80) REVERT: U 221 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.7155 (t80) REVERT: a 96 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7226 (mtp) outliers start: 220 outliers final: 39 residues processed: 829 average time/residue: 1.8353 time to fit residues: 1827.0624 Evaluate side-chains 650 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 599 time to evaluate : 5.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 205 GLU Chi-restraints excluded: chain O residue 219 ASN Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 122 GLN Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain a residue 96 MET Chi-restraints excluded: chain b residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 444 optimal weight: 8.9990 chunk 363 optimal weight: 0.2980 chunk 147 optimal weight: 9.9990 chunk 534 optimal weight: 3.9990 chunk 577 optimal weight: 3.9990 chunk 476 optimal weight: 0.9990 chunk 530 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 429 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN B 122 GLN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN E 122 GLN G 122 GLN J 191 GLN L 191 GLN N 30 ASN O 122 GLN ** Q 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN S 111 ASN S 122 GLN ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 219 ASN U 219 ASN V 30 ASN V 191 GLN W 89 GLN X 30 ASN Y 141 GLN Y 191 GLN Z 141 GLN Z 191 GLN a 89 GLN a 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 47124 Z= 0.183 Angle : 0.531 10.453 63602 Z= 0.297 Chirality : 0.045 0.332 7406 Planarity : 0.003 0.031 8162 Dihedral : 5.624 57.898 6656 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.24 % Favored : 96.05 % Rotamer: Outliers : 3.40 % Allowed : 20.59 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.11), residues: 5950 helix: 2.85 (0.10), residues: 2338 sheet: 0.79 (0.13), residues: 1582 loop : -0.65 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 109 PHE 0.038 0.001 PHE a 25 TYR 0.009 0.001 TYR X 66 ARG 0.003 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 609 time to evaluate : 5.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6932 (mm-40) REVERT: A 221 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7130 (t80) REVERT: B 221 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.7085 (t80) REVERT: D 68 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6859 (mm-40) REVERT: D 221 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7127 (t80) REVERT: E 221 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6870 (t80) REVERT: F 68 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6912 (mm110) REVERT: G 68 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6938 (mm110) REVERT: I 32 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7720 (tttt) REVERT: L 96 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7207 (mtp) REVERT: P 68 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6882 (mm110) REVERT: Q 221 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.7139 (t80) REVERT: R 221 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7129 (t80) REVERT: S 68 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6902 (mm110) REVERT: S 221 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7063 (t80) REVERT: U 221 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.7193 (t80) outliers start: 170 outliers final: 34 residues processed: 750 average time/residue: 1.9753 time to fit residues: 1763.2208 Evaluate side-chains 648 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 598 time to evaluate : 5.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 205 GLU Chi-restraints excluded: chain O residue 219 ASN Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 219 ASN Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 219 ASN Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain a residue 23 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 8.9990 chunk 402 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 255 optimal weight: 2.9990 chunk 359 optimal weight: 2.9990 chunk 536 optimal weight: 1.9990 chunk 568 optimal weight: 6.9990 chunk 280 optimal weight: 2.9990 chunk 508 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 62 ASN B 111 ASN D 62 ASN E 122 GLN F 122 GLN G 122 GLN H 191 GLN I 89 GLN J 191 GLN K 191 GLN L 30 ASN O 122 GLN O 219 ASN P 122 GLN Q 62 ASN Q 122 GLN R 62 ASN S 62 ASN T 62 ASN U 219 ASN V 30 ASN V 191 GLN W 89 GLN X 89 GLN X 191 GLN Y 141 GLN Y 191 GLN Z 89 GLN b 191 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 47124 Z= 0.277 Angle : 0.546 9.121 63602 Z= 0.304 Chirality : 0.045 0.228 7406 Planarity : 0.004 0.034 8162 Dihedral : 5.553 59.295 6645 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.16 % Favored : 96.37 % Rotamer: Outliers : 3.08 % Allowed : 21.51 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.11), residues: 5950 helix: 2.83 (0.10), residues: 2338 sheet: 1.25 (0.13), residues: 1428 loop : -0.75 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS a 109 PHE 0.041 0.002 PHE V 25 TYR 0.012 0.001 TYR a 184 ARG 0.003 0.000 ARG V 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 597 time to evaluate : 5.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6963 (mm-40) REVERT: A 221 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.7010 (t80) REVERT: B 221 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.7056 (t80) REVERT: C 68 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6923 (mm110) REVERT: D 221 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.7150 (t80) REVERT: E 221 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.6953 (t80) REVERT: F 68 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6971 (mm110) REVERT: G 68 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.7021 (mm110) REVERT: I 32 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7741 (tttt) REVERT: K 201 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8256 (mt) REVERT: L 96 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7252 (mtp) REVERT: O 221 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6889 (t80) REVERT: P 68 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6986 (mm110) REVERT: Q 68 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6950 (mm-40) REVERT: R 221 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.7083 (t80) REVERT: S 68 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6969 (mm110) REVERT: S 221 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.7063 (t80) REVERT: U 221 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7150 (t80) outliers start: 154 outliers final: 40 residues processed: 725 average time/residue: 1.8999 time to fit residues: 1645.6344 Evaluate side-chains 643 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 585 time to evaluate : 5.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 205 GLU Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 219 ASN Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 219 ASN Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 219 ASN Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 199 SER Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 5.9990 chunk 322 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 423 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 485 optimal weight: 5.9990 chunk 392 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 510 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 ASN I 89 GLN J 191 GLN K 191 GLN L 30 ASN M 191 GLN ** O 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 122 GLN P 219 ASN Q 122 GLN R 219 ASN T 219 ASN U 219 ASN V 30 ASN V 89 GLN V 191 GLN Y 191 GLN b 191 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 47124 Z= 0.506 Angle : 0.619 7.780 63602 Z= 0.343 Chirality : 0.049 0.189 7406 Planarity : 0.004 0.046 8162 Dihedral : 5.633 46.646 6636 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.75 % Favored : 95.78 % Rotamer: Outliers : 3.12 % Allowed : 21.25 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.11), residues: 5950 helix: 2.52 (0.10), residues: 2338 sheet: 1.16 (0.13), residues: 1428 loop : -0.81 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS J 28 PHE 0.046 0.002 PHE a 25 TYR 0.015 0.002 TYR Y 184 ARG 0.003 0.000 ARG W 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 583 time to evaluate : 5.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7042 (mm-40) REVERT: B 221 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.6944 (t80) REVERT: F 64 ILE cc_start: 0.5536 (OUTLIER) cc_final: 0.5300 (mt) REVERT: F 68 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.7052 (mm110) REVERT: G 68 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7079 (mm110) REVERT: P 68 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7091 (mm110) REVERT: Q 68 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7061 (mm-40) REVERT: S 68 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7044 (mm110) REVERT: S 221 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.6963 (t80) REVERT: U 68 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7043 (mm110) outliers start: 156 outliers final: 48 residues processed: 729 average time/residue: 1.8843 time to fit residues: 1647.7586 Evaluate side-chains 636 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 578 time to evaluate : 5.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 219 ASN Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 199 SER Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 68 GLN Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 199 SER Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 4.9990 chunk 511 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 333 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 568 optimal weight: 3.9990 chunk 472 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN C 219 ASN H 89 GLN H 191 GLN L 30 ASN M 191 GLN N 30 ASN O 44 ASN R 44 ASN T 219 ASN U 219 ASN X 30 ASN X 141 GLN b 191 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 47124 Z= 0.189 Angle : 0.533 10.292 63602 Z= 0.296 Chirality : 0.047 0.404 7406 Planarity : 0.003 0.048 8162 Dihedral : 5.052 39.235 6630 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.34 % Favored : 96.18 % Rotamer: Outliers : 2.26 % Allowed : 22.45 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.11), residues: 5950 helix: 2.77 (0.10), residues: 2338 sheet: 1.21 (0.13), residues: 1428 loop : -0.81 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS W 28 PHE 0.038 0.001 PHE N 25 TYR 0.010 0.001 TYR Y 184 ARG 0.001 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 589 time to evaluate : 5.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.7073 (t80) REVERT: B 68 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6977 (mm-40) REVERT: B 221 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7078 (t80) REVERT: D 64 ILE cc_start: 0.5474 (OUTLIER) cc_final: 0.5243 (mt) REVERT: D 221 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7181 (t80) REVERT: E 221 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.6936 (t80) REVERT: F 68 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6989 (mm110) REVERT: G 68 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.7046 (mm110) REVERT: L 197 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.7089 (mtp180) REVERT: O 221 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.6871 (t80) REVERT: P 68 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.7012 (mm110) REVERT: Q 68 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.7005 (mm-40) REVERT: R 64 ILE cc_start: 0.5344 (OUTLIER) cc_final: 0.5116 (mt) REVERT: R 221 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.7068 (t80) REVERT: S 68 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7002 (mm110) REVERT: S 221 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7107 (t80) REVERT: U 221 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7159 (t80) outliers start: 113 outliers final: 28 residues processed: 689 average time/residue: 1.9345 time to fit residues: 1590.4860 Evaluate side-chains 624 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 579 time to evaluate : 5.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain L residue 197 ARG Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 219 ASN Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 415 optimal weight: 7.9990 chunk 321 optimal weight: 10.0000 chunk 478 optimal weight: 5.9990 chunk 317 optimal weight: 7.9990 chunk 566 optimal weight: 7.9990 chunk 354 optimal weight: 10.0000 chunk 345 optimal weight: 4.9990 chunk 261 optimal weight: 0.0570 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 ASN H 191 GLN I 89 GLN L 30 ASN ** O 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 219 ASN Y 191 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 47124 Z= 0.392 Angle : 0.585 8.977 63602 Z= 0.324 Chirality : 0.048 0.334 7406 Planarity : 0.004 0.047 8162 Dihedral : 5.271 41.525 6630 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.43 % Favored : 96.10 % Rotamer: Outliers : 2.08 % Allowed : 22.75 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.11), residues: 5950 helix: 2.62 (0.10), residues: 2338 sheet: 1.14 (0.13), residues: 1428 loop : -0.84 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS a 109 PHE 0.046 0.002 PHE a 25 TYR 0.013 0.002 TYR a 184 ARG 0.002 0.000 ARG M 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 575 time to evaluate : 5.507 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7009 (mm110) REVERT: A 221 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.6981 (t80) REVERT: B 68 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7017 (mm-40) REVERT: B 221 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6976 (t80) REVERT: D 64 ILE cc_start: 0.5495 (OUTLIER) cc_final: 0.5252 (mt) REVERT: F 68 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7052 (mm110) REVERT: G 68 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7055 (mm110) REVERT: K 201 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8341 (mt) REVERT: L 197 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7130 (mtp180) REVERT: O 221 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.6893 (t80) REVERT: P 68 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7070 (mm110) REVERT: Q 68 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7047 (mm-40) REVERT: R 64 ILE cc_start: 0.5435 (OUTLIER) cc_final: 0.5174 (mt) REVERT: R 221 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.6962 (t80) REVERT: S 68 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7019 (mm110) REVERT: S 221 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.6991 (t80) outliers start: 104 outliers final: 46 residues processed: 669 average time/residue: 1.9195 time to fit residues: 1534.5000 Evaluate side-chains 632 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 570 time to evaluate : 5.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain L residue 197 ARG Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 199 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 64 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 199 SER Chi-restraints excluded: chain T residue 219 ASN Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 199 SER Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 4.9990 chunk 226 optimal weight: 0.5980 chunk 338 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 360 optimal weight: 8.9990 chunk 386 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 445 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN N 30 ASN S 111 ASN U 219 ASN X 30 ASN Y 89 GLN Y 191 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 47124 Z= 0.198 Angle : 0.524 8.958 63602 Z= 0.290 Chirality : 0.045 0.288 7406 Planarity : 0.003 0.046 8162 Dihedral : 4.913 38.021 6630 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.66 % Favored : 95.87 % Rotamer: Outliers : 1.74 % Allowed : 23.43 % Favored : 74.83 % 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: 1.69 (0.11), residues: 5950 helix: 2.80 (0.10), residues: 2338 sheet: 1.16 (0.13), residues: 1428 loop : -0.85 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS Y 109 PHE 0.038 0.001 PHE Y 25 TYR 0.010 0.001 TYR Z 66 ARG 0.002 0.000 ARG X 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 577 time to evaluate : 5.113 Fit side-chains revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.7147 (t80) REVERT: B 68 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6983 (mm-40) REVERT: B 221 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.7085 (t80) REVERT: D 64 ILE cc_start: 0.5346 (OUTLIER) cc_final: 0.5101 (mt) REVERT: D 221 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.7156 (t80) REVERT: E 221 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.6920 (t80) REVERT: G 68 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.7042 (mm110) REVERT: O 221 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.6931 (t80) REVERT: P 68 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.7016 (mm110) REVERT: Q 68 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6990 (mm-40) REVERT: R 64 ILE cc_start: 0.5326 (OUTLIER) cc_final: 0.5076 (mt) REVERT: R 221 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7141 (t80) REVERT: S 68 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6983 (mm110) REVERT: S 221 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7104 (t80) REVERT: U 221 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7142 (t80) outliers start: 87 outliers final: 34 residues processed: 659 average time/residue: 1.9930 time to fit residues: 1564.7965 Evaluate side-chains 621 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 572 time to evaluate : 5.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 167 SER Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 4.9990 chunk 542 optimal weight: 2.9990 chunk 495 optimal weight: 4.9990 chunk 528 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 414 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 477 optimal weight: 7.9990 chunk 499 optimal weight: 0.9980 chunk 526 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 ASN H 89 GLN H 191 GLN ** O 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 219 ASN U 219 ASN Y 191 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 47124 Z= 0.291 Angle : 0.549 8.558 63602 Z= 0.303 Chirality : 0.046 0.273 7406 Planarity : 0.004 0.049 8162 Dihedral : 5.021 39.488 6630 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.58 % Favored : 95.95 % Rotamer: Outliers : 1.70 % Allowed : 23.67 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.11), residues: 5950 helix: 2.73 (0.10), residues: 2338 sheet: 1.12 (0.13), residues: 1428 loop : -0.83 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 109 PHE 0.039 0.002 PHE Z 25 TYR 0.012 0.001 TYR Y 184 ARG 0.002 0.000 ARG W 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 569 time to evaluate : 5.421 Fit side-chains revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7028 (t80) REVERT: B 68 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6978 (mm-40) REVERT: B 221 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.7044 (t80) REVERT: D 64 ILE cc_start: 0.5387 (OUTLIER) cc_final: 0.5147 (mt) REVERT: D 221 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7123 (t80) REVERT: E 221 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.6963 (t80) REVERT: G 68 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.7027 (mm110) REVERT: L 197 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7107 (mtp180) REVERT: O 221 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.6887 (t80) REVERT: P 68 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7043 (mm110) REVERT: Q 68 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.7018 (mm-40) REVERT: R 64 ILE cc_start: 0.5353 (OUTLIER) cc_final: 0.5096 (mt) REVERT: R 221 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7016 (t80) REVERT: S 68 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6994 (mm110) REVERT: S 221 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7056 (t80) REVERT: U 221 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.7112 (t80) outliers start: 85 outliers final: 41 residues processed: 646 average time/residue: 2.0709 time to fit residues: 1608.9210 Evaluate side-chains 626 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 569 time to evaluate : 5.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain L residue 197 ARG Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 167 SER Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 0.9990 chunk 558 optimal weight: 5.9990 chunk 340 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 388 optimal weight: 4.9990 chunk 585 optimal weight: 4.9990 chunk 539 optimal weight: 0.4980 chunk 466 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 360 optimal weight: 0.6980 chunk 286 optimal weight: 7.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN I 89 GLN T 219 ASN U 219 ASN Y 191 GLN Z 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 47124 Z= 0.245 Angle : 0.536 8.552 63602 Z= 0.295 Chirality : 0.046 0.267 7406 Planarity : 0.003 0.049 8162 Dihedral : 4.928 38.626 6630 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.66 % Favored : 95.87 % Rotamer: Outliers : 1.38 % Allowed : 23.93 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.11), residues: 5950 helix: 2.77 (0.10), residues: 2338 sheet: 1.13 (0.13), residues: 1428 loop : -0.85 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 109 PHE 0.037 0.002 PHE Z 25 TYR 0.011 0.001 TYR I 66 ARG 0.004 0.000 ARG L 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 572 time to evaluate : 5.421 Fit side-chains revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7053 (t80) REVERT: B 68 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6958 (mm-40) REVERT: B 221 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7065 (t80) REVERT: C 68 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6939 (mm110) REVERT: D 64 ILE cc_start: 0.5334 (OUTLIER) cc_final: 0.5100 (mt) REVERT: D 221 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.7136 (t80) REVERT: E 221 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.6968 (t80) REVERT: G 68 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.7018 (mm110) REVERT: O 221 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.6905 (t80) REVERT: P 68 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.7036 (mm110) REVERT: Q 68 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.7005 (mm-40) REVERT: R 221 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.7111 (t80) REVERT: S 68 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6986 (mm110) REVERT: S 221 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7078 (t80) REVERT: U 221 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7121 (t80) outliers start: 69 outliers final: 44 residues processed: 639 average time/residue: 1.9902 time to fit residues: 1511.9646 Evaluate side-chains 631 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 572 time to evaluate : 5.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 167 SER Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 1.9990 chunk 496 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 430 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 467 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 479 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 191 GLN K 191 GLN ** O 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 219 ASN U 219 ASN Y 191 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.078525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.055888 restraints weight = 80754.182| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 2.55 r_work: 0.2422 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2290 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 47124 Z= 0.330 Angle : 0.561 8.187 63602 Z= 0.309 Chirality : 0.047 0.262 7406 Planarity : 0.004 0.049 8162 Dihedral : 5.067 40.302 6630 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.45 % Favored : 96.08 % Rotamer: Outliers : 1.40 % Allowed : 23.87 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.11), residues: 5950 helix: 2.69 (0.10), residues: 2338 sheet: 1.10 (0.13), residues: 1428 loop : -0.87 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS M 28 PHE 0.038 0.002 PHE N 25 TYR 0.012 0.001 TYR Y 184 ARG 0.002 0.000 ARG W 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24933.97 seconds wall clock time: 441 minutes 6.51 seconds (26466.51 seconds total)