Starting phenix.real_space_refine on Sun Apr 7 05:17:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfe_21160/04_2024/6vfe_21160.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfe_21160/04_2024/6vfe_21160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfe_21160/04_2024/6vfe_21160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfe_21160/04_2024/6vfe_21160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfe_21160/04_2024/6vfe_21160.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfe_21160/04_2024/6vfe_21160.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 165 5.16 5 C 38709 2.51 5 N 11187 2.21 5 O 11847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 87": "OD1" <-> "OD2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E ASP 87": "OD1" <-> "OD2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 63": "OD1" <-> "OD2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "G PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 15": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 63": "OD1" <-> "OD2" Residue "G TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 171": "OE1" <-> "OE2" Residue "G GLU 179": "OE1" <-> "OE2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 234": "OD1" <-> "OD2" Residue "H ASP 63": "OD1" <-> "OD2" Residue "H ASP 234": "OD1" <-> "OD2" Residue "I GLU 15": "OE1" <-> "OE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 63": "OD1" <-> "OD2" Residue "I GLU 192": "OE1" <-> "OE2" Residue "I PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 63": "OD1" <-> "OD2" Residue "J ASP 155": "OD1" <-> "OD2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 169": "OE1" <-> "OE2" Residue "J GLU 192": "OE1" <-> "OE2" Residue "K PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 15": "OE1" <-> "OE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K GLU 192": "OE1" <-> "OE2" Residue "K PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 169": "OE1" <-> "OE2" Residue "L GLU 171": "OE1" <-> "OE2" Residue "M PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 63": "OD1" <-> "OD2" Residue "M ASP 87": "OD1" <-> "OD2" Residue "N TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 95": "OE1" <-> "OE2" Residue "O TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 63": "OD1" <-> "OD2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P ASP 234": "OD1" <-> "OD2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 63": "OD1" <-> "OD2" Residue "Q ASP 87": "OD1" <-> "OD2" Residue "Q ASP 228": "OD1" <-> "OD2" Residue "R GLU 95": "OE1" <-> "OE2" Residue "R GLU 162": "OE1" <-> "OE2" Residue "R GLU 169": "OE1" <-> "OE2" Residue "R GLU 171": "OE1" <-> "OE2" Residue "R ASP 234": "OD1" <-> "OD2" Residue "S TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 169": "OE1" <-> "OE2" Residue "S GLU 192": "OE1" <-> "OE2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 95": "OE1" <-> "OE2" Residue "T GLU 169": "OE1" <-> "OE2" Residue "T GLU 171": "OE1" <-> "OE2" Residue "U GLU 15": "OE1" <-> "OE2" Residue "U ASP 63": "OD1" <-> "OD2" Residue "U TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 162": "OE1" <-> "OE2" Residue "V PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 15": "OE1" <-> "OE2" Residue "V TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 63": "OD1" <-> "OD2" Residue "V GLU 136": "OE1" <-> "OE2" Residue "V GLU 192": "OE1" <-> "OE2" Residue "W TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 63": "OD1" <-> "OD2" Residue "W TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 171": "OE1" <-> "OE2" Residue "W GLU 192": "OE1" <-> "OE2" Residue "X TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "X TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 87": "OD1" <-> "OD2" Residue "X TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 192": "OE1" <-> "OE2" Residue "X ASP 234": "OD1" <-> "OD2" Residue "Y PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 162": "OE1" <-> "OE2" Residue "Y PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 63": "OD1" <-> "OD2" Residue "Z GLU 162": "OE1" <-> "OE2" Residue "Z GLU 169": "OE1" <-> "OE2" Residue "Z GLU 192": "OE1" <-> "OE2" Residue "Z PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 234": "OD1" <-> "OD2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 63": "OD1" <-> "OD2" Residue "a ASP 228": "OD1" <-> "OD2" Residue "b GLU 162": "OE1" <-> "OE2" Residue "b GLU 169": "OE1" <-> "OE2" Residue "b GLU 192": "OE1" <-> "OE2" Residue "c TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 63": "OD1" <-> "OD2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c GLU 192": "OE1" <-> "OE2" Residue "c ASP 234": "OD1" <-> "OD2" Residue "d ASP 63": "OD1" <-> "OD2" Residue "d TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 234": "OD1" <-> "OD2" Residue "e TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 95": "OE1" <-> "OE2" Residue "e GLU 192": "OE1" <-> "OE2" Residue "e PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 234": "OD1" <-> "OD2" Residue "f ASP 63": "OD1" <-> "OD2" Residue "f TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 95": "OE1" <-> "OE2" Residue "f PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 234": "OD1" <-> "OD2" Residue "g ASP 63": "OD1" <-> "OD2" Residue "g GLU 171": "OE1" <-> "OE2" Residue "g GLU 192": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 61908 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "B" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "C" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "D" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "E" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "F" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "G" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "H" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "I" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "J" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "K" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "L" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "M" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "N" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "O" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "P" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "Q" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "R" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "S" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "T" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "U" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "V" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "W" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "X" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "Y" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "Z" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "a" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "b" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "c" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "d" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "e" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "f" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Chain: "g" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 12, 'TRANS': 226} Time building chain proxies: 24.50, per 1000 atoms: 0.40 Number of scatterers: 61908 At special positions: 0 Unit cell: (334.9, 334.9, 91.8, 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 165 16.00 O 11847 8.00 N 11187 7.00 C 38709 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: 19.26 Conformation dependent library (CDL) restraints added in 8.4 seconds 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14652 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 0 sheets defined 15.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 27 through 32 removed outlier: 4.239A pdb=" N THR A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 137 removed outlier: 3.545A pdb=" N ARG A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.805A pdb=" N THR B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 27 through 32 removed outlier: 4.267A pdb=" N THR C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 137 removed outlier: 3.670A pdb=" N ARG C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 154 Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 27 through 34 removed outlier: 4.266A pdb=" N THR D 32 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY D 33 " --> pdb=" O GLN D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 27 through 34 removed outlier: 4.293A pdb=" N THR E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 147 through 154 Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 27 through 32 removed outlier: 3.817A pdb=" N THR F 32 " --> pdb=" O LEU F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 27 through 32 removed outlier: 4.176A pdb=" N THR G 32 " --> pdb=" O LEU G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 136 Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 27 through 34 removed outlier: 4.287A pdb=" N THR H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY H 33 " --> pdb=" O GLN H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 147 through 154 Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 126 through 137 removed outlier: 3.522A pdb=" N ARG I 137 " --> pdb=" O LEU I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 154 Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 126 through 137 removed outlier: 3.515A pdb=" N ARG J 137 " --> pdb=" O LEU J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 154 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 29 through 34 removed outlier: 3.597A pdb=" N GLY K 33 " --> pdb=" O GLN K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 147 through 154 Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 147 through 154 Processing helix chain 'M' and resid 5 through 15 Processing helix chain 'M' and resid 27 through 32 removed outlier: 4.427A pdb=" N THR M 32 " --> pdb=" O LEU M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 137 removed outlier: 3.745A pdb=" N ARG M 137 " --> pdb=" O LEU M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 154 Processing helix chain 'N' and resid 5 through 15 Processing helix chain 'N' and resid 27 through 34 removed outlier: 4.046A pdb=" N THR N 32 " --> pdb=" O LEU N 28 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY N 33 " --> pdb=" O GLN N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 147 through 154 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 27 through 34 removed outlier: 4.344A pdb=" N THR O 32 " --> pdb=" O LEU O 28 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY O 33 " --> pdb=" O GLN O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 147 through 154 Processing helix chain 'P' and resid 5 through 15 Processing helix chain 'P' and resid 126 through 137 removed outlier: 3.567A pdb=" N ARG P 137 " --> pdb=" O LEU P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 154 Processing helix chain 'Q' and resid 5 through 15 Processing helix chain 'Q' and resid 29 through 34 removed outlier: 3.990A pdb=" N GLY Q 33 " --> pdb=" O GLN Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 137 removed outlier: 3.781A pdb=" N ARG Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 154 Processing helix chain 'R' and resid 5 through 15 Processing helix chain 'R' and resid 27 through 34 removed outlier: 4.342A pdb=" N THR R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY R 33 " --> pdb=" O GLN R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 137 removed outlier: 3.701A pdb=" N ARG R 137 " --> pdb=" O LEU R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 154 Processing helix chain 'S' and resid 5 through 15 Processing helix chain 'S' and resid 29 through 34 removed outlier: 4.014A pdb=" N GLY S 33 " --> pdb=" O GLN S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 137 removed outlier: 3.882A pdb=" N ARG S 137 " --> pdb=" O LEU S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 154 Processing helix chain 'T' and resid 5 through 15 Processing helix chain 'T' and resid 27 through 31 removed outlier: 3.596A pdb=" N SER T 31 " --> pdb=" O LEU T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 147 through 154 Processing helix chain 'U' and resid 5 through 15 Processing helix chain 'U' and resid 29 through 34 removed outlier: 4.122A pdb=" N GLY U 33 " --> pdb=" O GLN U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 137 removed outlier: 3.617A pdb=" N ARG U 137 " --> pdb=" O LEU U 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 147 through 154 Processing helix chain 'V' and resid 5 through 15 Processing helix chain 'V' and resid 27 through 34 removed outlier: 3.951A pdb=" N THR V 32 " --> pdb=" O LEU V 28 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY V 33 " --> pdb=" O GLN V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 147 through 154 Processing helix chain 'W' and resid 5 through 15 Processing helix chain 'W' and resid 126 through 137 removed outlier: 3.864A pdb=" N ARG W 137 " --> pdb=" O LEU W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 154 Processing helix chain 'X' and resid 5 through 15 Processing helix chain 'X' and resid 27 through 32 removed outlier: 4.175A pdb=" N THR X 32 " --> pdb=" O LEU X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 126 through 136 Processing helix chain 'X' and resid 147 through 154 Processing helix chain 'Y' and resid 5 through 15 Processing helix chain 'Y' and resid 126 through 136 Processing helix chain 'Y' and resid 147 through 154 Processing helix chain 'Z' and resid 5 through 15 Processing helix chain 'Z' and resid 27 through 32 removed outlier: 4.210A pdb=" N THR Z 32 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 126 through 137 removed outlier: 3.531A pdb=" N ARG Z 137 " --> pdb=" O LEU Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 154 Processing helix chain 'a' and resid 5 through 15 Processing helix chain 'a' and resid 28 through 32 removed outlier: 3.625A pdb=" N SER a 31 " --> pdb=" O LEU a 28 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR a 32 " --> pdb=" O GLN a 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 28 through 32' Processing helix chain 'a' and resid 126 through 137 Processing helix chain 'a' and resid 147 through 154 Processing helix chain 'b' and resid 5 through 15 Processing helix chain 'b' and resid 27 through 32 removed outlier: 4.090A pdb=" N THR b 32 " --> pdb=" O LEU b 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 137 removed outlier: 3.657A pdb=" N ARG b 137 " --> pdb=" O LEU b 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 154 Processing helix chain 'c' and resid 5 through 15 Processing helix chain 'c' and resid 27 through 31 Processing helix chain 'c' and resid 126 through 137 Processing helix chain 'c' and resid 147 through 154 Processing helix chain 'd' and resid 5 through 15 Processing helix chain 'd' and resid 27 through 32 removed outlier: 3.915A pdb=" N THR d 32 " --> pdb=" O LEU d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 137 Processing helix chain 'd' and resid 147 through 154 Processing helix chain 'e' and resid 5 through 15 Processing helix chain 'e' and resid 27 through 34 removed outlier: 4.286A pdb=" N THR e 32 " --> pdb=" O LEU e 28 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY e 33 " --> pdb=" O GLN e 29 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 137 Processing helix chain 'e' and resid 147 through 154 Processing helix chain 'f' and resid 5 through 15 Processing helix chain 'f' and resid 27 through 34 removed outlier: 4.295A pdb=" N THR f 32 " --> pdb=" O LEU f 28 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY f 33 " --> pdb=" O GLN f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 137 removed outlier: 3.595A pdb=" N ARG f 137 " --> pdb=" O LEU f 133 " (cutoff:3.500A) Processing helix chain 'f' and resid 147 through 154 Processing helix chain 'g' and resid 5 through 15 Processing helix chain 'g' and resid 27 through 34 removed outlier: 4.302A pdb=" N THR g 32 " --> pdb=" O LEU g 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY g 33 " --> pdb=" O GLN g 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 126 through 137 removed outlier: 3.637A pdb=" N ARG g 137 " --> pdb=" O LEU g 133 " (cutoff:3.500A) Processing helix chain 'g' and resid 147 through 154 646 hydrogen bonds defined for protein. 1929 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.20 Time building geometry restraints manager: 21.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 20980 1.34 - 1.46: 12423 1.46 - 1.58: 29549 1.58 - 1.69: 12 1.69 - 1.81: 231 Bond restraints: 63195 Sorted by residual: bond pdb=" CA GLN N 167 " pdb=" CB GLN N 167 " ideal model delta sigma weight residual 1.527 1.602 -0.075 2.48e-02 1.63e+03 9.10e+00 bond pdb=" C GLN W 141 " pdb=" N PRO W 142 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.58e+00 bond pdb=" C ALA d 98 " pdb=" N PRO d 99 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.12e+00 bond pdb=" CA GLN Z 167 " pdb=" CB GLN Z 167 " ideal model delta sigma weight residual 1.531 1.599 -0.069 3.12e-02 1.03e+03 4.84e+00 bond pdb=" C ALA S 98 " pdb=" N PRO S 99 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.72e+00 ... (remaining 63190 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.89: 2112 106.89 - 113.92: 35273 113.92 - 120.94: 26295 120.94 - 127.96: 21267 127.96 - 134.99: 622 Bond angle restraints: 85569 Sorted by residual: angle pdb=" C GLN L 167 " pdb=" N LYS L 168 " pdb=" CA LYS L 168 " ideal model delta sigma weight residual 122.09 134.39 -12.30 1.86e+00 2.89e-01 4.38e+01 angle pdb=" C GLN K 167 " pdb=" N LYS K 168 " pdb=" CA LYS K 168 " ideal model delta sigma weight residual 121.54 132.62 -11.08 1.91e+00 2.74e-01 3.36e+01 angle pdb=" C GLN B 167 " pdb=" N LYS B 168 " pdb=" CA LYS B 168 " ideal model delta sigma weight residual 121.63 132.74 -11.11 1.92e+00 2.71e-01 3.35e+01 angle pdb=" C GLN V 167 " pdb=" N LYS V 168 " pdb=" CA LYS V 168 " ideal model delta sigma weight residual 122.19 134.99 -12.80 2.30e+00 1.89e-01 3.10e+01 angle pdb=" C GLN W 167 " pdb=" N LYS W 168 " pdb=" CA LYS W 168 " ideal model delta sigma weight residual 122.41 133.83 -11.42 2.09e+00 2.29e-01 2.99e+01 ... (remaining 85564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.26: 34411 18.26 - 36.53: 3105 36.53 - 54.79: 437 54.79 - 73.06: 198 73.06 - 91.32: 96 Dihedral angle restraints: 38247 sinusoidal: 15576 harmonic: 22671 Sorted by residual: dihedral pdb=" CA LEU C 65 " pdb=" C LEU C 65 " pdb=" N GLU C 66 " pdb=" CA GLU C 66 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ARG C 137 " pdb=" C ARG C 137 " pdb=" N HIS C 138 " pdb=" CA HIS C 138 " ideal model delta harmonic sigma weight residual -180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA VAL K 120 " pdb=" C VAL K 120 " pdb=" N TYR K 121 " pdb=" CA TYR K 121 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 38244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 8010 0.064 - 0.128: 1387 0.128 - 0.191: 62 0.191 - 0.255: 11 0.255 - 0.319: 1 Chirality restraints: 9471 Sorted by residual: chirality pdb=" CB ILE G 223 " pdb=" CA ILE G 223 " pdb=" CG1 ILE G 223 " pdb=" CG2 ILE G 223 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA HIS a 135 " pdb=" N HIS a 135 " pdb=" C HIS a 135 " pdb=" CB HIS a 135 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB THR N 173 " pdb=" CA THR N 173 " pdb=" OG1 THR N 173 " pdb=" CG2 THR N 173 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 9468 not shown) Planarity restraints: 11253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP f 126 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO f 127 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO f 127 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO f 127 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 232 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.29e+00 pdb=" C PHE R 232 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE R 232 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO R 233 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 121 " 0.021 2.00e-02 2.50e+03 1.77e-02 6.28e+00 pdb=" CG TYR N 121 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR N 121 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR N 121 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR N 121 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR N 121 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR N 121 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 121 " 0.002 2.00e-02 2.50e+03 ... (remaining 11250 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1764 2.68 - 3.23: 60459 3.23 - 3.79: 95411 3.79 - 4.34: 123148 4.34 - 4.90: 200384 Nonbonded interactions: 481166 Sorted by model distance: nonbonded pdb=" O HIS V 144 " pdb=" N GLN V 148 " model vdw 2.120 2.520 nonbonded pdb=" O HIS D 144 " pdb=" N GLN D 148 " model vdw 2.150 2.520 nonbonded pdb=" O SER Z 210 " pdb=" NH2 ARG a 78 " model vdw 2.154 2.520 nonbonded pdb=" O HIS Z 144 " pdb=" N GLN Z 148 " model vdw 2.163 2.520 nonbonded pdb=" O HIS d 144 " pdb=" N GLN d 148 " model vdw 2.171 2.520 ... (remaining 481161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 5.740 Check model and map are aligned: 0.700 Set scattering table: 0.440 Process input model: 114.250 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.560 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 63195 Z= 0.232 Angle : 0.752 13.001 85569 Z= 0.400 Chirality : 0.046 0.319 9471 Planarity : 0.005 0.086 11253 Dihedral : 15.066 91.319 23595 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.03 % Allowed : 0.52 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.09), residues: 7821 helix: 1.37 (0.17), residues: 891 sheet: -1.97 (0.09), residues: 3135 loop : -2.89 (0.09), residues: 3795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP P 48 HIS 0.013 0.001 HIS Y 135 PHE 0.041 0.001 PHE N 232 TYR 0.044 0.002 TYR N 121 ARG 0.009 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 956 time to evaluate : 5.528 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: A 95 GLU cc_start: 0.6111 (pp20) cc_final: 0.4536 (pp20) REVERT: A 169 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7138 (mm-30) REVERT: A 177 LYS cc_start: 0.8617 (mppt) cc_final: 0.8289 (mmtm) REVERT: B 162 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6547 (tp30) REVERT: B 234 ASP cc_start: 0.8329 (p0) cc_final: 0.7849 (p0) REVERT: C 83 TYR cc_start: 0.7687 (t80) cc_final: 0.7320 (t80) REVERT: C 118 MET cc_start: 0.7602 (tmm) cc_final: 0.7220 (tmm) REVERT: C 232 PHE cc_start: 0.6984 (p90) cc_final: 0.6668 (p90) REVERT: D 55 LYS cc_start: 0.8290 (mttm) cc_final: 0.8030 (mmtm) REVERT: F 155 ASP cc_start: 0.8467 (m-30) cc_final: 0.8112 (m-30) REVERT: F 223 ILE cc_start: 0.8284 (mt) cc_final: 0.8025 (mm) REVERT: G 83 TYR cc_start: 0.7775 (t80) cc_final: 0.7214 (t80) REVERT: H 28 LEU cc_start: 0.8047 (mm) cc_final: 0.7682 (mt) REVERT: H 29 GLN cc_start: 0.8045 (pp30) cc_final: 0.7134 (pp30) REVERT: H 48 TRP cc_start: 0.4939 (m-90) cc_final: 0.4375 (m-90) REVERT: H 51 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8270 (tptt) REVERT: I 83 TYR cc_start: 0.6865 (t80) cc_final: 0.6541 (t80) REVERT: J 232 PHE cc_start: 0.7902 (p90) cc_final: 0.7594 (p90) REVERT: K 28 LEU cc_start: 0.8186 (mm) cc_final: 0.7897 (mt) REVERT: K 177 LYS cc_start: 0.7946 (mppt) cc_final: 0.7575 (mmtm) REVERT: K 234 ASP cc_start: 0.7432 (p0) cc_final: 0.7078 (p0) REVERT: L 177 LYS cc_start: 0.8160 (mppt) cc_final: 0.7694 (mmtm) REVERT: M 28 LEU cc_start: 0.7782 (mm) cc_final: 0.7083 (mt) REVERT: M 63 ASP cc_start: 0.8031 (p0) cc_final: 0.7698 (p0) REVERT: M 177 LYS cc_start: 0.8097 (mppt) cc_final: 0.7818 (mmtm) REVERT: N 121 TYR cc_start: 0.7209 (m-80) cc_final: 0.6571 (m-10) REVERT: N 155 ASP cc_start: 0.8501 (m-30) cc_final: 0.8273 (m-30) REVERT: O 55 LYS cc_start: 0.7879 (mptt) cc_final: 0.7616 (mptt) REVERT: O 63 ASP cc_start: 0.8201 (p0) cc_final: 0.7939 (p0) REVERT: O 171 GLU cc_start: 0.7903 (pm20) cc_final: 0.7531 (pp20) REVERT: P 28 LEU cc_start: 0.7990 (tp) cc_final: 0.7606 (tp) REVERT: P 29 GLN cc_start: 0.8529 (pp30) cc_final: 0.7974 (pp30) REVERT: P 162 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7593 (mm-30) REVERT: Q 130 TRP cc_start: 0.8198 (m100) cc_final: 0.7585 (m100) REVERT: Q 171 GLU cc_start: 0.8344 (pm20) cc_final: 0.7355 (pm20) REVERT: R 15 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7983 (tp30) REVERT: R 135 HIS cc_start: 0.6490 (m90) cc_final: 0.6088 (m90) REVERT: R 234 ASP cc_start: 0.7734 (p0) cc_final: 0.7503 (p0) REVERT: S 55 LYS cc_start: 0.8189 (mptt) cc_final: 0.7735 (mmtt) REVERT: S 168 LYS cc_start: 0.8127 (mmmm) cc_final: 0.7818 (mmtm) REVERT: S 234 ASP cc_start: 0.7090 (p0) cc_final: 0.6774 (p0) REVERT: T 168 LYS cc_start: 0.7361 (mtmt) cc_final: 0.7155 (mtmm) REVERT: U 171 GLU cc_start: 0.7801 (pp20) cc_final: 0.7579 (pp20) REVERT: V 28 LEU cc_start: 0.7954 (mp) cc_final: 0.7715 (pp) REVERT: V 128 ASN cc_start: 0.8255 (m-40) cc_final: 0.8013 (m-40) REVERT: V 234 ASP cc_start: 0.7733 (p0) cc_final: 0.7385 (p0) REVERT: W 135 HIS cc_start: 0.6745 (m90) cc_final: 0.6481 (m90) REVERT: W 223 ILE cc_start: 0.7187 (mt) cc_final: 0.6971 (mt) REVERT: X 131 GLN cc_start: 0.8096 (pp30) cc_final: 0.7347 (pt0) REVERT: Y 37 TYR cc_start: 0.7463 (m-80) cc_final: 0.7137 (m-80) REVERT: Y 121 TYR cc_start: 0.6564 (m-10) cc_final: 0.6343 (m-80) REVERT: Y 234 ASP cc_start: 0.7877 (p0) cc_final: 0.7601 (p0) REVERT: Z 177 LYS cc_start: 0.7722 (mppt) cc_final: 0.7355 (mmtm) REVERT: a 79 SER cc_start: 0.7414 (m) cc_final: 0.7132 (t) REVERT: a 118 MET cc_start: 0.8320 (ptm) cc_final: 0.7628 (ttp) REVERT: a 131 GLN cc_start: 0.7874 (pp30) cc_final: 0.7117 (pt0) REVERT: a 135 HIS cc_start: 0.5781 (m90) cc_final: 0.5539 (m90) REVERT: a 171 GLU cc_start: 0.7057 (mp0) cc_final: 0.6729 (mp0) REVERT: a 177 LYS cc_start: 0.7997 (mppt) cc_final: 0.7487 (mmtm) REVERT: b 130 TRP cc_start: 0.8192 (m100) cc_final: 0.7916 (m100) REVERT: d 28 LEU cc_start: 0.6941 (mp) cc_final: 0.6526 (mp) REVERT: d 171 GLU cc_start: 0.7404 (mp0) cc_final: 0.6799 (mp0) REVERT: d 177 LYS cc_start: 0.8342 (mppt) cc_final: 0.8056 (mmtm) REVERT: e 138 HIS cc_start: 0.6893 (p90) cc_final: 0.6531 (p90) REVERT: f 162 GLU cc_start: 0.6612 (mp0) cc_final: 0.6337 (mp0) REVERT: g 192 GLU cc_start: 0.5102 (tt0) cc_final: 0.4616 (tm-30) outliers start: 2 outliers final: 1 residues processed: 958 average time/residue: 0.5835 time to fit residues: 924.4408 Evaluate side-chains 703 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 702 time to evaluate : 5.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 193 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 640 optimal weight: 3.9990 chunk 575 optimal weight: 3.9990 chunk 319 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 388 optimal weight: 1.9990 chunk 307 optimal weight: 7.9990 chunk 594 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 442 optimal weight: 4.9990 chunk 689 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN C 138 HIS D 91 GLN E 128 ASN G 81 HIS G 193 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 GLN I 135 HIS I 138 HIS ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 241 GLN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 241 GLN ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 HIS S 197 GLN S 237 GLN T 165 GLN U 119 ASN ** U 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 176 HIS ** V 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 HIS X 193 GLN a 138 HIS b 176 HIS ** b 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 165 GLN e 165 GLN e 241 GLN f 29 GLN f 35 GLN f 165 GLN f 241 GLN g 193 GLN g 241 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 63195 Z= 0.285 Angle : 0.674 10.386 85569 Z= 0.341 Chirality : 0.046 0.194 9471 Planarity : 0.004 0.069 11253 Dihedral : 5.473 32.837 8550 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 1.38 % Allowed : 9.69 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.09), residues: 7821 helix: 0.41 (0.17), residues: 990 sheet: -2.29 (0.09), residues: 3135 loop : -2.93 (0.09), residues: 3696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP f 130 HIS 0.020 0.001 HIS Y 135 PHE 0.032 0.002 PHE R 232 TYR 0.033 0.003 TYR M 121 ARG 0.006 0.001 ARG a 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 764 time to evaluate : 6.940 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: A 29 GLN cc_start: 0.8452 (pp30) cc_final: 0.7872 (pp30) REVERT: A 95 GLU cc_start: 0.6069 (pp20) cc_final: 0.5676 (pp20) REVERT: A 169 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7473 (mm-30) REVERT: A 234 ASP cc_start: 0.8160 (p0) cc_final: 0.7690 (p0) REVERT: B 234 ASP cc_start: 0.8445 (p0) cc_final: 0.7967 (p0) REVERT: D 29 GLN cc_start: 0.7098 (pp30) cc_final: 0.6542 (pp30) REVERT: F 28 LEU cc_start: 0.7854 (mt) cc_final: 0.7652 (mt) REVERT: F 223 ILE cc_start: 0.8345 (mt) cc_final: 0.8094 (mm) REVERT: H 28 LEU cc_start: 0.7876 (mm) cc_final: 0.7635 (mt) REVERT: H 29 GLN cc_start: 0.8085 (pp30) cc_final: 0.7134 (pp30) REVERT: H 83 TYR cc_start: 0.7883 (t80) cc_final: 0.7568 (t80) REVERT: I 28 LEU cc_start: 0.7922 (mm) cc_final: 0.7277 (mt) REVERT: I 83 TYR cc_start: 0.7304 (t80) cc_final: 0.6785 (t80) REVERT: I 223 ILE cc_start: 0.8125 (mm) cc_final: 0.7895 (mm) REVERT: K 28 LEU cc_start: 0.8395 (mm) cc_final: 0.8019 (mp) REVERT: K 177 LYS cc_start: 0.8005 (mppt) cc_final: 0.7576 (mmtm) REVERT: K 232 PHE cc_start: 0.7744 (p90) cc_final: 0.7494 (p90) REVERT: K 234 ASP cc_start: 0.7843 (p0) cc_final: 0.7419 (p0) REVERT: L 86 MET cc_start: 0.7751 (tmm) cc_final: 0.7352 (ttt) REVERT: L 171 GLU cc_start: 0.8128 (pm20) cc_final: 0.7839 (pp20) REVERT: M 28 LEU cc_start: 0.7914 (mm) cc_final: 0.7659 (mm) REVERT: M 177 LYS cc_start: 0.8205 (mppt) cc_final: 0.7641 (mmtm) REVERT: N 121 TYR cc_start: 0.7243 (m-80) cc_final: 0.6611 (m-80) REVERT: N 135 HIS cc_start: 0.7107 (m-70) cc_final: 0.6864 (m90) REVERT: N 155 ASP cc_start: 0.8286 (m-30) cc_final: 0.8052 (m-30) REVERT: O 95 GLU cc_start: 0.6333 (pt0) cc_final: 0.5833 (pm20) REVERT: O 145 LYS cc_start: 0.6533 (mppt) cc_final: 0.5713 (tttm) REVERT: P 29 GLN cc_start: 0.8680 (pp30) cc_final: 0.7968 (pp30) REVERT: Q 28 LEU cc_start: 0.8189 (mm) cc_final: 0.7981 (mm) REVERT: Q 128 ASN cc_start: 0.8668 (t0) cc_final: 0.8367 (t0) REVERT: Q 171 GLU cc_start: 0.8249 (pm20) cc_final: 0.7341 (pm20) REVERT: R 15 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8009 (tp30) REVERT: R 135 HIS cc_start: 0.6259 (m90) cc_final: 0.5834 (m90) REVERT: R 234 ASP cc_start: 0.8068 (p0) cc_final: 0.7818 (p0) REVERT: S 55 LYS cc_start: 0.8395 (mptt) cc_final: 0.7766 (mmtt) REVERT: S 135 HIS cc_start: 0.7222 (m90) cc_final: 0.6706 (m90) REVERT: S 234 ASP cc_start: 0.7308 (p0) cc_final: 0.6876 (p0) REVERT: T 29 GLN cc_start: 0.8514 (pp30) cc_final: 0.7805 (pp30) REVERT: T 162 GLU cc_start: 0.8015 (pp20) cc_final: 0.7805 (tm-30) REVERT: T 177 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8558 (ttpp) REVERT: U 64 ILE cc_start: 0.9356 (mm) cc_final: 0.9136 (mm) REVERT: U 171 GLU cc_start: 0.7962 (pp20) cc_final: 0.7592 (pp20) REVERT: V 136 GLU cc_start: 0.7812 (pt0) cc_final: 0.7588 (pt0) REVERT: V 234 ASP cc_start: 0.7202 (p0) cc_final: 0.6669 (p0) REVERT: W 177 LYS cc_start: 0.8596 (mppt) cc_final: 0.8309 (mppt) REVERT: W 223 ILE cc_start: 0.7326 (mt) cc_final: 0.7079 (mt) REVERT: X 131 GLN cc_start: 0.8237 (pp30) cc_final: 0.7329 (pt0) REVERT: Y 37 TYR cc_start: 0.7725 (m-80) cc_final: 0.7301 (m-80) REVERT: Y 234 ASP cc_start: 0.7763 (p0) cc_final: 0.7323 (p0) REVERT: Z 169 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7740 (mm-30) REVERT: Z 177 LYS cc_start: 0.8307 (mppt) cc_final: 0.7950 (mmtm) REVERT: a 118 MET cc_start: 0.8274 (ptm) cc_final: 0.8022 (ptp) REVERT: a 177 LYS cc_start: 0.8034 (mppt) cc_final: 0.7656 (mmtm) REVERT: b 28 LEU cc_start: 0.7317 (tt) cc_final: 0.6777 (mm) REVERT: c 167 GLN cc_start: 0.7998 (pm20) cc_final: 0.7578 (pm20) REVERT: d 171 GLU cc_start: 0.7396 (mp0) cc_final: 0.6960 (mp0) REVERT: d 177 LYS cc_start: 0.8563 (mppt) cc_final: 0.8214 (mmtm) REVERT: d 232 PHE cc_start: 0.7263 (p90) cc_final: 0.6978 (p90) REVERT: e 28 LEU cc_start: 0.8413 (tp) cc_final: 0.8088 (mm) REVERT: e 87 ASP cc_start: 0.8123 (p0) cc_final: 0.7654 (p0) REVERT: e 138 HIS cc_start: 0.7114 (p90) cc_final: 0.6723 (p90) REVERT: e 162 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7503 (mm-30) outliers start: 95 outliers final: 77 residues processed: 816 average time/residue: 0.5848 time to fit residues: 794.0362 Evaluate side-chains 752 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 675 time to evaluate : 5.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 48 TRP Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 121 TYR Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain Q residue 135 HIS Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 124 SER Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 232 PHE Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 162 GLU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 118 MET Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 132 THR Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 383 optimal weight: 0.0050 chunk 213 optimal weight: 6.9990 chunk 573 optimal weight: 5.9990 chunk 469 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 chunk 690 optimal weight: 6.9990 chunk 745 optimal weight: 20.0000 chunk 614 optimal weight: 4.9990 chunk 684 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 553 optimal weight: 4.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 176 HIS G 91 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 GLN J 176 HIS ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 HIS ** L 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 HIS ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 237 GLN ** Q 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 176 HIS ** R 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 GLN X 91 GLN X 241 GLN Y 237 GLN ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 237 GLN b 193 GLN c 165 GLN c 241 GLN d 237 GLN d 241 GLN ** e 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 241 GLN g 81 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 63195 Z= 0.348 Angle : 0.700 9.089 85569 Z= 0.360 Chirality : 0.046 0.225 9471 Planarity : 0.005 0.082 11253 Dihedral : 5.800 25.562 8547 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 2.77 % Allowed : 12.79 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.09), residues: 7821 helix: 0.29 (0.17), residues: 990 sheet: -2.61 (0.09), residues: 2871 loop : -2.71 (0.09), residues: 3960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP f 130 HIS 0.022 0.001 HIS Y 135 PHE 0.028 0.002 PHE d 5 TYR 0.030 0.002 TYR O 121 ARG 0.006 0.001 ARG N 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 723 time to evaluate : 5.743 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: A 22 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: A 29 GLN cc_start: 0.8466 (pp30) cc_final: 0.8058 (pp30) REVERT: A 51 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7290 (tptt) REVERT: A 95 GLU cc_start: 0.6244 (pp20) cc_final: 0.5966 (pp20) REVERT: A 169 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 234 ASP cc_start: 0.8324 (p0) cc_final: 0.7923 (p0) REVERT: A 235 LYS cc_start: 0.8062 (tptt) cc_final: 0.7808 (tptt) REVERT: B 29 GLN cc_start: 0.8452 (pp30) cc_final: 0.8140 (pp30) REVERT: B 234 ASP cc_start: 0.8530 (p0) cc_final: 0.8083 (p0) REVERT: D 86 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7443 (tmm) REVERT: H 28 LEU cc_start: 0.7969 (mm) cc_final: 0.7741 (mt) REVERT: H 171 GLU cc_start: 0.8162 (pm20) cc_final: 0.7880 (pp20) REVERT: I 28 LEU cc_start: 0.7944 (mm) cc_final: 0.7353 (mt) REVERT: I 83 TYR cc_start: 0.7733 (t80) cc_final: 0.6759 (t80) REVERT: I 223 ILE cc_start: 0.8228 (mm) cc_final: 0.8001 (mm) REVERT: J 192 GLU cc_start: 0.7731 (tp30) cc_final: 0.6376 (tm-30) REVERT: K 177 LYS cc_start: 0.7983 (mppt) cc_final: 0.7467 (mmtm) REVERT: K 232 PHE cc_start: 0.7887 (p90) cc_final: 0.7468 (p90) REVERT: K 234 ASP cc_start: 0.7916 (p0) cc_final: 0.7442 (p0) REVERT: L 86 MET cc_start: 0.7835 (tmm) cc_final: 0.7617 (ttt) REVERT: N 29 GLN cc_start: 0.8225 (pp30) cc_final: 0.7960 (pp30) REVERT: O 83 TYR cc_start: 0.7914 (t80) cc_final: 0.7701 (t80) REVERT: O 145 LYS cc_start: 0.6863 (mppt) cc_final: 0.6023 (tttm) REVERT: O 171 GLU cc_start: 0.8011 (pm20) cc_final: 0.7295 (pp20) REVERT: P 29 GLN cc_start: 0.8460 (pp30) cc_final: 0.7595 (pp30) REVERT: Q 28 LEU cc_start: 0.8360 (mm) cc_final: 0.7998 (mm) REVERT: Q 137 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7737 (mtm-85) REVERT: R 29 GLN cc_start: 0.8199 (pp30) cc_final: 0.7880 (pp30) REVERT: R 135 HIS cc_start: 0.6330 (m90) cc_final: 0.5735 (m90) REVERT: R 234 ASP cc_start: 0.8206 (p0) cc_final: 0.7948 (p0) REVERT: S 135 HIS cc_start: 0.7288 (m90) cc_final: 0.6795 (m90) REVERT: S 186 LEU cc_start: 0.1396 (OUTLIER) cc_final: 0.1009 (pp) REVERT: S 234 ASP cc_start: 0.7619 (p0) cc_final: 0.7162 (p0) REVERT: U 55 LYS cc_start: 0.8514 (mptt) cc_final: 0.8235 (mmtt) REVERT: U 64 ILE cc_start: 0.9349 (mm) cc_final: 0.9145 (mm) REVERT: U 130 TRP cc_start: 0.7830 (m100) cc_final: 0.7578 (m100) REVERT: V 135 HIS cc_start: 0.7415 (m90) cc_final: 0.7208 (m90) REVERT: V 169 GLU cc_start: 0.7603 (tp30) cc_final: 0.7401 (mm-30) REVERT: V 234 ASP cc_start: 0.7437 (p0) cc_final: 0.6884 (p0) REVERT: W 223 ILE cc_start: 0.7523 (mt) cc_final: 0.7299 (mt) REVERT: X 5 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7834 (m-10) REVERT: X 131 GLN cc_start: 0.8333 (pp30) cc_final: 0.7036 (pt0) REVERT: Y 37 TYR cc_start: 0.7933 (m-80) cc_final: 0.7623 (m-80) REVERT: Y 234 ASP cc_start: 0.7894 (p0) cc_final: 0.7372 (p0) REVERT: a 177 LYS cc_start: 0.8135 (mppt) cc_final: 0.7744 (mmtm) REVERT: b 55 LYS cc_start: 0.8501 (mtmm) cc_final: 0.8246 (mptt) REVERT: d 169 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7403 (mm-30) REVERT: d 232 PHE cc_start: 0.7590 (p90) cc_final: 0.7096 (p90) REVERT: e 28 LEU cc_start: 0.8546 (tp) cc_final: 0.8190 (mm) REVERT: e 65 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8034 (pp) REVERT: e 138 HIS cc_start: 0.7359 (p90) cc_final: 0.6931 (p90) REVERT: f 236 LYS cc_start: 0.8416 (mmpt) cc_final: 0.8191 (mmtt) outliers start: 191 outliers final: 150 residues processed: 859 average time/residue: 0.5795 time to fit residues: 831.0638 Evaluate side-chains 813 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 657 time to evaluate : 5.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 135 HIS Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain K residue 48 TRP Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 118 MET Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 LYS Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 5 PHE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 161 THR Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 124 SER Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 162 GLU Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 86 MET Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 168 LYS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 132 THR Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 84 ASP Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 682 optimal weight: 0.0870 chunk 519 optimal weight: 8.9990 chunk 358 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 463 optimal weight: 0.9980 chunk 692 optimal weight: 1.9990 chunk 733 optimal weight: 5.9990 chunk 362 optimal weight: 4.9990 chunk 656 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS C 128 ASN F 167 GLN G 91 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 GLN ** Q 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 237 GLN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 GLN W 165 GLN Z 128 ASN ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 ASN c 241 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 63195 Z= 0.250 Angle : 0.646 9.356 85569 Z= 0.329 Chirality : 0.045 0.185 9471 Planarity : 0.004 0.082 11253 Dihedral : 5.498 24.515 8547 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 3.23 % Allowed : 15.33 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.09), residues: 7821 helix: 0.47 (0.17), residues: 990 sheet: -2.67 (0.09), residues: 2871 loop : -2.63 (0.09), residues: 3960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP f 130 HIS 0.022 0.001 HIS Y 135 PHE 0.026 0.001 PHE R 232 TYR 0.028 0.002 TYR a 121 ARG 0.010 0.000 ARG K 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 724 time to evaluate : 6.922 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: A 28 LEU cc_start: 0.7352 (tp) cc_final: 0.6666 (mm) REVERT: A 29 GLN cc_start: 0.8346 (pp30) cc_final: 0.8038 (pp30) REVERT: A 51 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7793 (tptt) REVERT: A 95 GLU cc_start: 0.6239 (pp20) cc_final: 0.5983 (pp20) REVERT: A 169 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7817 (mm-30) REVERT: A 234 ASP cc_start: 0.8321 (p0) cc_final: 0.7903 (p0) REVERT: A 235 LYS cc_start: 0.8021 (tptt) cc_final: 0.7708 (tptt) REVERT: B 29 GLN cc_start: 0.8195 (pp30) cc_final: 0.7907 (pp30) REVERT: B 130 TRP cc_start: 0.7698 (m100) cc_final: 0.7443 (m100) REVERT: B 234 ASP cc_start: 0.8294 (p0) cc_final: 0.7827 (p0) REVERT: D 86 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7483 (tmm) REVERT: E 163 VAL cc_start: 0.9319 (t) cc_final: 0.9048 (p) REVERT: F 169 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7890 (mm-30) REVERT: H 155 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: I 28 LEU cc_start: 0.7908 (mm) cc_final: 0.7299 (mt) REVERT: I 95 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6836 (tm-30) REVERT: J 192 GLU cc_start: 0.7697 (tp30) cc_final: 0.6393 (tm-30) REVERT: K 177 LYS cc_start: 0.8104 (mppt) cc_final: 0.7667 (mmtm) REVERT: K 232 PHE cc_start: 0.7734 (p90) cc_final: 0.7268 (p90) REVERT: K 234 ASP cc_start: 0.8120 (p0) cc_final: 0.7624 (p0) REVERT: L 39 LEU cc_start: 0.9216 (mp) cc_final: 0.8964 (mm) REVERT: L 95 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6840 (tm-30) REVERT: M 28 LEU cc_start: 0.7824 (mm) cc_final: 0.7505 (mm) REVERT: P 29 GLN cc_start: 0.8205 (pp30) cc_final: 0.7467 (pp30) REVERT: P 232 PHE cc_start: 0.8067 (p90) cc_final: 0.7841 (p90) REVERT: Q 28 LEU cc_start: 0.8201 (mm) cc_final: 0.7953 (mm) REVERT: Q 137 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7502 (mtm-85) REVERT: R 29 GLN cc_start: 0.8355 (pp30) cc_final: 0.8012 (pp30) REVERT: R 135 HIS cc_start: 0.6216 (m90) cc_final: 0.5866 (m90) REVERT: R 234 ASP cc_start: 0.8204 (p0) cc_final: 0.7955 (p0) REVERT: S 55 LYS cc_start: 0.8522 (mptt) cc_final: 0.8312 (mptt) REVERT: S 135 HIS cc_start: 0.7318 (m90) cc_final: 0.6806 (m90) REVERT: S 171 GLU cc_start: 0.8441 (pm20) cc_final: 0.7928 (pp20) REVERT: S 186 LEU cc_start: 0.1291 (OUTLIER) cc_final: 0.0904 (pp) REVERT: S 234 ASP cc_start: 0.7569 (p0) cc_final: 0.7185 (p0) REVERT: T 55 LYS cc_start: 0.8295 (mmtm) cc_final: 0.7875 (mmtt) REVERT: T 165 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: U 28 LEU cc_start: 0.8346 (mm) cc_final: 0.8042 (mm) REVERT: U 54 TYR cc_start: 0.8126 (m-80) cc_final: 0.7724 (m-80) REVERT: U 55 LYS cc_start: 0.8512 (mptt) cc_final: 0.7917 (mptt) REVERT: U 64 ILE cc_start: 0.9363 (mm) cc_final: 0.9159 (mm) REVERT: U 130 TRP cc_start: 0.7824 (m100) cc_final: 0.7559 (m100) REVERT: U 169 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6915 (mm-30) REVERT: V 135 HIS cc_start: 0.7270 (m90) cc_final: 0.7002 (m90) REVERT: V 169 GLU cc_start: 0.7632 (tp30) cc_final: 0.7319 (mm-30) REVERT: V 234 ASP cc_start: 0.7408 (p0) cc_final: 0.6829 (p0) REVERT: W 135 HIS cc_start: 0.6133 (m-70) cc_final: 0.5275 (m-70) REVERT: W 223 ILE cc_start: 0.7494 (mt) cc_final: 0.7274 (mt) REVERT: X 5 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7750 (m-10) REVERT: X 131 GLN cc_start: 0.7698 (pp30) cc_final: 0.6581 (pt0) REVERT: Y 37 TYR cc_start: 0.7856 (m-80) cc_final: 0.7544 (m-80) REVERT: Y 234 ASP cc_start: 0.7915 (p0) cc_final: 0.7365 (p0) REVERT: Z 177 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8052 (tppt) REVERT: a 177 LYS cc_start: 0.8069 (mppt) cc_final: 0.7653 (mmtm) REVERT: b 55 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8191 (mptt) REVERT: c 208 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8633 (mm) REVERT: d 232 PHE cc_start: 0.7544 (p90) cc_final: 0.6901 (p90) REVERT: e 28 LEU cc_start: 0.8488 (tp) cc_final: 0.8101 (mm) REVERT: e 232 PHE cc_start: 0.7919 (p90) cc_final: 0.7690 (p90) REVERT: g 184 PHE cc_start: 0.7406 (m-10) cc_final: 0.7180 (m-10) outliers start: 223 outliers final: 161 residues processed: 895 average time/residue: 0.6090 time to fit residues: 916.1098 Evaluate side-chains 850 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 681 time to evaluate : 5.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 135 HIS Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 48 TRP Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 PHE Chi-restraints excluded: chain L residue 118 MET Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 LYS Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 168 LYS Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 165 GLN Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 161 THR Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 166 THR Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain W residue 236 LYS Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 124 SER Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 170 VAL Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 157 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 177 LYS Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 66 GLU Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 128 ASN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 171 GLU Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 132 THR Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 28 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 611 optimal weight: 0.7980 chunk 416 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 546 optimal weight: 4.9990 chunk 302 optimal weight: 5.9990 chunk 626 optimal weight: 4.9990 chunk 507 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 374 optimal weight: 0.4980 chunk 658 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 GLN G 91 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 GLN J 81 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 GLN ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 63195 Z= 0.222 Angle : 0.632 9.387 85569 Z= 0.320 Chirality : 0.044 0.214 9471 Planarity : 0.004 0.048 11253 Dihedral : 5.298 23.139 8547 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 3.19 % Allowed : 16.63 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.09), residues: 7821 helix: 0.59 (0.17), residues: 990 sheet: -2.64 (0.09), residues: 2871 loop : -2.57 (0.09), residues: 3960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 130 HIS 0.024 0.001 HIS Y 135 PHE 0.024 0.001 PHE H 5 TYR 0.032 0.002 TYR a 121 ARG 0.009 0.000 ARG K 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 738 time to evaluate : 5.660 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: A 28 LEU cc_start: 0.7301 (tp) cc_final: 0.6688 (mm) REVERT: A 29 GLN cc_start: 0.8249 (pp30) cc_final: 0.8015 (pp30) REVERT: A 169 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7804 (mm-30) REVERT: A 234 ASP cc_start: 0.8286 (p0) cc_final: 0.7872 (p0) REVERT: B 28 LEU cc_start: 0.8101 (mp) cc_final: 0.7667 (pp) REVERT: B 29 GLN cc_start: 0.8150 (pp30) cc_final: 0.7889 (pp30) REVERT: B 234 ASP cc_start: 0.8286 (p0) cc_final: 0.7821 (p0) REVERT: C 169 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7434 (mm-30) REVERT: C 192 GLU cc_start: 0.5340 (tm-30) cc_final: 0.4735 (tm-30) REVERT: D 86 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7395 (tmm) REVERT: E 163 VAL cc_start: 0.9288 (t) cc_final: 0.9041 (p) REVERT: F 37 TYR cc_start: 0.8473 (m-80) cc_final: 0.8190 (m-80) REVERT: F 169 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7718 (mm-30) REVERT: G 128 ASN cc_start: 0.8306 (m-40) cc_final: 0.8071 (m-40) REVERT: G 232 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7918 (p90) REVERT: H 155 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: H 171 GLU cc_start: 0.7981 (pm20) cc_final: 0.7715 (pp20) REVERT: I 28 LEU cc_start: 0.7831 (mm) cc_final: 0.7282 (mt) REVERT: I 95 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6857 (tm-30) REVERT: J 192 GLU cc_start: 0.7718 (tp30) cc_final: 0.6341 (tm-30) REVERT: K 5 PHE cc_start: 0.7316 (t80) cc_final: 0.7035 (t80) REVERT: K 155 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8362 (m-30) REVERT: K 177 LYS cc_start: 0.8054 (mppt) cc_final: 0.7637 (mmtm) REVERT: K 232 PHE cc_start: 0.7967 (p90) cc_final: 0.7552 (p90) REVERT: K 234 ASP cc_start: 0.8106 (p0) cc_final: 0.7601 (p0) REVERT: L 39 LEU cc_start: 0.9217 (mp) cc_final: 0.8965 (mm) REVERT: L 133 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9010 (mp) REVERT: M 28 LEU cc_start: 0.7818 (mm) cc_final: 0.7473 (mm) REVERT: N 203 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8765 (mtpp) REVERT: O 145 LYS cc_start: 0.7192 (mppt) cc_final: 0.6430 (tttm) REVERT: O 171 GLU cc_start: 0.8050 (pm20) cc_final: 0.7386 (pp20) REVERT: P 29 GLN cc_start: 0.8145 (pp30) cc_final: 0.7774 (pp30) REVERT: Q 9 VAL cc_start: 0.8503 (t) cc_final: 0.8291 (p) REVERT: Q 28 LEU cc_start: 0.8154 (mm) cc_final: 0.7903 (mm) REVERT: Q 137 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7499 (mtm-85) REVERT: Q 232 PHE cc_start: 0.7667 (p90) cc_final: 0.7425 (p90) REVERT: R 29 GLN cc_start: 0.8246 (pp30) cc_final: 0.7895 (pp30) REVERT: R 86 MET cc_start: 0.7267 (ttm) cc_final: 0.6912 (tmm) REVERT: R 135 HIS cc_start: 0.6256 (m90) cc_final: 0.5866 (m90) REVERT: R 234 ASP cc_start: 0.8177 (p0) cc_final: 0.7922 (p0) REVERT: S 55 LYS cc_start: 0.8574 (mptt) cc_final: 0.8338 (mptt) REVERT: S 135 HIS cc_start: 0.7310 (m90) cc_final: 0.6811 (m90) REVERT: S 171 GLU cc_start: 0.8467 (pm20) cc_final: 0.7912 (pp20) REVERT: S 234 ASP cc_start: 0.7553 (p0) cc_final: 0.7117 (p0) REVERT: T 165 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.8022 (pm20) REVERT: U 28 LEU cc_start: 0.8313 (mm) cc_final: 0.7850 (mt) REVERT: U 54 TYR cc_start: 0.8129 (m-80) cc_final: 0.7601 (m-80) REVERT: U 55 LYS cc_start: 0.8563 (mptt) cc_final: 0.8064 (mptt) REVERT: U 130 TRP cc_start: 0.7799 (m100) cc_final: 0.7535 (m100) REVERT: U 169 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6858 (mm-30) REVERT: V 135 HIS cc_start: 0.7579 (m90) cc_final: 0.7237 (m90) REVERT: V 234 ASP cc_start: 0.7411 (p0) cc_final: 0.6816 (p0) REVERT: W 135 HIS cc_start: 0.6129 (m-70) cc_final: 0.5152 (m-70) REVERT: W 162 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7378 (tm-30) REVERT: W 223 ILE cc_start: 0.7499 (mt) cc_final: 0.7276 (mt) REVERT: X 5 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7814 (m-10) REVERT: X 131 GLN cc_start: 0.7606 (pp30) cc_final: 0.6555 (pt0) REVERT: Y 37 TYR cc_start: 0.7835 (m-80) cc_final: 0.7530 (m-80) REVERT: Y 234 ASP cc_start: 0.7769 (p0) cc_final: 0.7212 (p0) REVERT: Z 135 HIS cc_start: 0.6921 (m90) cc_final: 0.6206 (m90) REVERT: a 177 LYS cc_start: 0.8049 (mppt) cc_final: 0.7644 (mmtm) REVERT: b 55 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8182 (mptt) REVERT: c 208 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8616 (mm) REVERT: d 28 LEU cc_start: 0.7525 (mt) cc_final: 0.7266 (mp) REVERT: d 29 GLN cc_start: 0.7638 (pp30) cc_final: 0.7001 (tm-30) REVERT: d 137 ARG cc_start: 0.8505 (mtm110) cc_final: 0.8303 (ttp80) REVERT: d 221 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7903 (pp) REVERT: d 232 PHE cc_start: 0.7715 (p90) cc_final: 0.6979 (p90) REVERT: e 28 LEU cc_start: 0.8475 (tp) cc_final: 0.8128 (mm) REVERT: g 83 TYR cc_start: 0.7880 (t80) cc_final: 0.7432 (t80) outliers start: 220 outliers final: 171 residues processed: 906 average time/residue: 0.5647 time to fit residues: 856.0073 Evaluate side-chains 857 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 675 time to evaluate : 5.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 48 TRP Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 PHE Chi-restraints excluded: chain L residue 118 MET Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 LYS Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 168 LYS Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 203 LYS Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 90 ILE Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 165 GLN Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 170 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 161 THR Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 166 THR Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 170 VAL Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 229 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 177 LYS Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 132 THR Chi-restraints excluded: chain d residue 133 LEU Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 221 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 28 LEU Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain g residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 246 optimal weight: 3.9990 chunk 660 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 430 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 734 optimal weight: 0.9980 chunk 609 optimal weight: 2.9990 chunk 340 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 242 optimal weight: 0.6980 chunk 385 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN G 144 HIS ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 HIS ** I 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 GLN ** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 135 HIS ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 ASN ** W 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 128 ASN a 165 GLN ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 ASN c 241 GLN ** f 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 63195 Z= 0.259 Angle : 0.649 9.567 85569 Z= 0.330 Chirality : 0.045 0.269 9471 Planarity : 0.004 0.052 11253 Dihedral : 5.369 23.629 8547 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 3.77 % Allowed : 17.95 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.09), residues: 7821 helix: 0.60 (0.17), residues: 990 sheet: -2.76 (0.09), residues: 2871 loop : -2.58 (0.09), residues: 3960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 48 HIS 0.024 0.001 HIS Y 135 PHE 0.023 0.001 PHE d 5 TYR 0.035 0.002 TYR a 121 ARG 0.007 0.000 ARG K 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 708 time to evaluate : 5.534 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: A 28 LEU cc_start: 0.7558 (tp) cc_final: 0.6942 (mm) REVERT: A 29 GLN cc_start: 0.8270 (pp30) cc_final: 0.8019 (pp30) REVERT: A 234 ASP cc_start: 0.8191 (p0) cc_final: 0.7916 (p0) REVERT: B 28 LEU cc_start: 0.8143 (mp) cc_final: 0.7691 (pp) REVERT: B 29 GLN cc_start: 0.8229 (pp30) cc_final: 0.7995 (pp30) REVERT: B 234 ASP cc_start: 0.8258 (p0) cc_final: 0.7734 (p0) REVERT: C 192 GLU cc_start: 0.5398 (tm-30) cc_final: 0.4770 (tm-30) REVERT: D 86 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7500 (tmm) REVERT: E 163 VAL cc_start: 0.9299 (t) cc_final: 0.9076 (p) REVERT: F 37 TYR cc_start: 0.8502 (m-80) cc_final: 0.8223 (m-80) REVERT: F 128 ASN cc_start: 0.8246 (t0) cc_final: 0.8015 (t0) REVERT: F 171 GLU cc_start: 0.7958 (pm20) cc_final: 0.7670 (pp20) REVERT: G 128 ASN cc_start: 0.8364 (m-40) cc_final: 0.8118 (m-40) REVERT: G 171 GLU cc_start: 0.8584 (pp20) cc_final: 0.7851 (pp20) REVERT: G 232 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7980 (p90) REVERT: H 28 LEU cc_start: 0.7514 (mp) cc_final: 0.7253 (pp) REVERT: H 130 TRP cc_start: 0.8301 (m100) cc_final: 0.8062 (m100) REVERT: H 155 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7945 (m-30) REVERT: H 171 GLU cc_start: 0.8039 (pm20) cc_final: 0.7703 (pp20) REVERT: I 28 LEU cc_start: 0.7878 (mm) cc_final: 0.7287 (mt) REVERT: I 95 GLU cc_start: 0.7528 (tm-30) cc_final: 0.6844 (tm-30) REVERT: J 192 GLU cc_start: 0.7722 (tp30) cc_final: 0.6437 (tm-30) REVERT: K 65 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8564 (pp) REVERT: K 155 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: K 177 LYS cc_start: 0.8067 (mppt) cc_final: 0.7638 (mmtm) REVERT: K 232 PHE cc_start: 0.7330 (p90) cc_final: 0.6985 (p90) REVERT: K 234 ASP cc_start: 0.8159 (p0) cc_final: 0.7650 (p0) REVERT: L 39 LEU cc_start: 0.9205 (mp) cc_final: 0.8948 (mm) REVERT: M 28 LEU cc_start: 0.8057 (mm) cc_final: 0.7775 (mm) REVERT: M 87 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7336 (p0) REVERT: N 203 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8800 (mtpp) REVERT: O 145 LYS cc_start: 0.7317 (mppt) cc_final: 0.6400 (tttm) REVERT: O 171 GLU cc_start: 0.8075 (pm20) cc_final: 0.7017 (pp20) REVERT: O 221 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8310 (pp) REVERT: P 29 GLN cc_start: 0.8113 (pp30) cc_final: 0.7803 (pp30) REVERT: Q 9 VAL cc_start: 0.8613 (t) cc_final: 0.8387 (p) REVERT: Q 28 LEU cc_start: 0.8191 (mm) cc_final: 0.7953 (mm) REVERT: Q 128 ASN cc_start: 0.8403 (t0) cc_final: 0.7914 (t0) REVERT: Q 137 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7564 (mtm-85) REVERT: R 29 GLN cc_start: 0.8246 (pp30) cc_final: 0.7904 (pp30) REVERT: R 86 MET cc_start: 0.7574 (ttm) cc_final: 0.7308 (tmm) REVERT: R 135 HIS cc_start: 0.6226 (m90) cc_final: 0.5835 (m90) REVERT: R 234 ASP cc_start: 0.8237 (p0) cc_final: 0.7983 (p0) REVERT: S 55 LYS cc_start: 0.8616 (mptt) cc_final: 0.8348 (mptt) REVERT: S 135 HIS cc_start: 0.7337 (m90) cc_final: 0.6815 (m90) REVERT: S 168 LYS cc_start: 0.8242 (mmmm) cc_final: 0.7841 (ttpt) REVERT: S 234 ASP cc_start: 0.7536 (p0) cc_final: 0.7087 (p0) REVERT: T 165 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: T 168 LYS cc_start: 0.7545 (mtmt) cc_final: 0.7267 (mttp) REVERT: U 28 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7781 (mt) REVERT: U 54 TYR cc_start: 0.8190 (m-80) cc_final: 0.7790 (m-80) REVERT: U 55 LYS cc_start: 0.8616 (mptt) cc_final: 0.8102 (mptt) REVERT: V 135 HIS cc_start: 0.7509 (m90) cc_final: 0.7172 (m90) REVERT: V 234 ASP cc_start: 0.7465 (p0) cc_final: 0.6874 (p0) REVERT: X 5 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7757 (m-10) REVERT: X 131 GLN cc_start: 0.7639 (pp30) cc_final: 0.6505 (pt0) REVERT: Y 37 TYR cc_start: 0.7742 (m-80) cc_final: 0.7519 (m-80) REVERT: Y 234 ASP cc_start: 0.7811 (p0) cc_final: 0.7233 (p0) REVERT: Z 53 ARG cc_start: 0.6893 (mmt180) cc_final: 0.6687 (mmt180) REVERT: Z 135 HIS cc_start: 0.6881 (m90) cc_final: 0.6190 (m90) REVERT: a 177 LYS cc_start: 0.8115 (mppt) cc_final: 0.7698 (mmtm) REVERT: b 55 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8241 (mptt) REVERT: c 128 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7889 (m-40) REVERT: c 208 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8625 (mm) REVERT: d 29 GLN cc_start: 0.7895 (pp30) cc_final: 0.7295 (tm-30) REVERT: d 221 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7948 (pp) REVERT: d 232 PHE cc_start: 0.7821 (p90) cc_final: 0.7032 (p90) REVERT: e 28 LEU cc_start: 0.8604 (tp) cc_final: 0.8128 (mm) REVERT: g 83 TYR cc_start: 0.7629 (t80) cc_final: 0.7316 (t80) outliers start: 260 outliers final: 211 residues processed: 915 average time/residue: 0.5570 time to fit residues: 859.8680 Evaluate side-chains 896 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 670 time to evaluate : 5.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 48 TRP Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 PHE Chi-restraints excluded: chain L residue 118 MET Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 LYS Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 168 LYS Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 203 LYS Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 131 GLN Chi-restraints excluded: chain O residue 135 HIS Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain O residue 221 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 90 ILE Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 165 GLN Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 170 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 166 THR Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain W residue 236 LYS Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 124 SER Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 170 VAL Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 229 VAL Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 157 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 162 GLU Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 177 LYS Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 128 ASN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 132 THR Chi-restraints excluded: chain d residue 133 LEU Chi-restraints excluded: chain d residue 145 LYS Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 221 LEU Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 157 VAL Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 170 VAL Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 84 ASP Chi-restraints excluded: chain g residue 90 ILE Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 186 LEU Chi-restraints excluded: chain g residue 221 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 708 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 418 optimal weight: 4.9990 chunk 536 optimal weight: 4.9990 chunk 415 optimal weight: 6.9990 chunk 618 optimal weight: 2.9990 chunk 410 optimal weight: 2.9990 chunk 731 optimal weight: 2.9990 chunk 457 optimal weight: 0.9990 chunk 446 optimal weight: 1.9990 chunk 337 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN M 89 GLN ** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 135 HIS ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 GLN ** f 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 63195 Z= 0.235 Angle : 0.643 9.548 85569 Z= 0.326 Chirality : 0.045 0.227 9471 Planarity : 0.004 0.051 11253 Dihedral : 5.279 23.681 8547 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 3.58 % Allowed : 18.89 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.09), residues: 7821 helix: 0.67 (0.17), residues: 990 sheet: -2.70 (0.08), residues: 3234 loop : -2.93 (0.09), residues: 3597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 48 HIS 0.027 0.001 HIS Y 135 PHE 0.023 0.001 PHE Y 5 TYR 0.040 0.002 TYR a 121 ARG 0.009 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 722 time to evaluate : 5.637 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: A 28 LEU cc_start: 0.7666 (tp) cc_final: 0.7079 (mm) REVERT: A 29 GLN cc_start: 0.8237 (pp30) cc_final: 0.7993 (pp30) REVERT: A 87 ASP cc_start: 0.8208 (p0) cc_final: 0.7943 (p0) REVERT: A 234 ASP cc_start: 0.7887 (p0) cc_final: 0.7544 (p0) REVERT: B 28 LEU cc_start: 0.8129 (mp) cc_final: 0.7697 (pp) REVERT: B 29 GLN cc_start: 0.8236 (pp30) cc_final: 0.8014 (pp30) REVERT: B 234 ASP cc_start: 0.8256 (p0) cc_final: 0.7730 (p0) REVERT: C 169 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7760 (mm-30) REVERT: C 192 GLU cc_start: 0.5407 (tm-30) cc_final: 0.4977 (tm-30) REVERT: D 86 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7501 (tmm) REVERT: E 137 ARG cc_start: 0.7256 (ptm160) cc_final: 0.7054 (ptt180) REVERT: E 163 VAL cc_start: 0.9166 (t) cc_final: 0.8883 (p) REVERT: F 37 TYR cc_start: 0.8474 (m-80) cc_final: 0.8247 (m-80) REVERT: F 95 GLU cc_start: 0.6528 (tm-30) cc_final: 0.5801 (tm-30) REVERT: F 171 GLU cc_start: 0.8068 (pm20) cc_final: 0.7728 (pp20) REVERT: G 128 ASN cc_start: 0.8352 (m-40) cc_final: 0.8088 (m-40) REVERT: G 135 HIS cc_start: 0.7616 (m-70) cc_final: 0.7229 (m170) REVERT: G 232 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7977 (p90) REVERT: H 155 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: I 28 LEU cc_start: 0.7861 (mm) cc_final: 0.7236 (mt) REVERT: I 95 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6859 (tm-30) REVERT: I 121 TYR cc_start: 0.7251 (m-10) cc_final: 0.7017 (m-10) REVERT: J 192 GLU cc_start: 0.7701 (tp30) cc_final: 0.6433 (tm-30) REVERT: K 86 MET cc_start: 0.8356 (ttm) cc_final: 0.7972 (ttt) REVERT: K 155 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7488 (m-30) REVERT: K 177 LYS cc_start: 0.8031 (mppt) cc_final: 0.7620 (mmtm) REVERT: K 232 PHE cc_start: 0.8108 (p90) cc_final: 0.7673 (p90) REVERT: K 234 ASP cc_start: 0.8153 (p0) cc_final: 0.7598 (p0) REVERT: L 39 LEU cc_start: 0.9194 (mp) cc_final: 0.8948 (mm) REVERT: M 28 LEU cc_start: 0.8007 (mm) cc_final: 0.7725 (mm) REVERT: M 84 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8179 (p0) REVERT: N 203 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8705 (mtpp) REVERT: O 221 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8172 (pp) REVERT: P 29 GLN cc_start: 0.8156 (pp30) cc_final: 0.7861 (pp30) REVERT: Q 9 VAL cc_start: 0.8617 (t) cc_final: 0.8387 (p) REVERT: Q 28 LEU cc_start: 0.8156 (mm) cc_final: 0.7900 (mm) REVERT: Q 199 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7563 (p90) REVERT: R 29 GLN cc_start: 0.8204 (pp30) cc_final: 0.7876 (pp30) REVERT: R 86 MET cc_start: 0.7539 (ttm) cc_final: 0.7294 (tmm) REVERT: R 135 HIS cc_start: 0.6205 (m90) cc_final: 0.5843 (m90) REVERT: R 234 ASP cc_start: 0.8228 (p0) cc_final: 0.7981 (p0) REVERT: S 55 LYS cc_start: 0.8607 (mptt) cc_final: 0.8321 (mptt) REVERT: S 135 HIS cc_start: 0.7411 (m90) cc_final: 0.6925 (m90) REVERT: S 168 LYS cc_start: 0.8252 (mmmm) cc_final: 0.7812 (ttpt) REVERT: T 128 ASN cc_start: 0.7387 (m-40) cc_final: 0.7179 (m110) REVERT: T 168 LYS cc_start: 0.7507 (mtmt) cc_final: 0.7184 (mtmm) REVERT: U 28 LEU cc_start: 0.8207 (mm) cc_final: 0.7775 (mt) REVERT: U 54 TYR cc_start: 0.8185 (m-80) cc_final: 0.7724 (m-80) REVERT: U 55 LYS cc_start: 0.8714 (mptt) cc_final: 0.8111 (mptt) REVERT: U 130 TRP cc_start: 0.7915 (m100) cc_final: 0.7682 (m100) REVERT: U 169 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7122 (mm-30) REVERT: V 135 HIS cc_start: 0.7630 (m90) cc_final: 0.7316 (m90) REVERT: V 234 ASP cc_start: 0.7481 (p0) cc_final: 0.6884 (p0) REVERT: W 171 GLU cc_start: 0.8299 (pp20) cc_final: 0.8080 (pp20) REVERT: X 5 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7728 (m-10) REVERT: Y 37 TYR cc_start: 0.7775 (m-80) cc_final: 0.7514 (m-80) REVERT: Y 234 ASP cc_start: 0.7801 (p0) cc_final: 0.7220 (p0) REVERT: Z 135 HIS cc_start: 0.6816 (m90) cc_final: 0.6102 (m90) REVERT: a 177 LYS cc_start: 0.8395 (mppt) cc_final: 0.7845 (mmtm) REVERT: b 55 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8229 (mptt) REVERT: c 208 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8556 (mm) REVERT: d 28 LEU cc_start: 0.8475 (mp) cc_final: 0.8017 (pp) REVERT: d 29 GLN cc_start: 0.7981 (pp30) cc_final: 0.7501 (tm-30) REVERT: d 232 PHE cc_start: 0.7888 (p90) cc_final: 0.7125 (p90) REVERT: e 28 LEU cc_start: 0.8630 (tp) cc_final: 0.8233 (mm) REVERT: g 83 TYR cc_start: 0.7518 (t80) cc_final: 0.7215 (t80) outliers start: 247 outliers final: 206 residues processed: 913 average time/residue: 0.5871 time to fit residues: 908.5520 Evaluate side-chains 895 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 679 time to evaluate : 5.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 PHE Chi-restraints excluded: chain L residue 118 MET Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 208 ILE Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 84 ASP Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 LYS Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 168 LYS Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 203 LYS Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 131 GLN Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain O residue 221 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 90 ILE Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 199 HIS Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 170 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 145 LYS Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 121 TYR Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 166 THR Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain W residue 236 LYS Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 90 ILE Chi-restraints excluded: chain X residue 124 SER Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 170 VAL Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 157 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 177 LYS Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 166 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 132 THR Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 221 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 28 LEU Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 170 VAL Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 452 optimal weight: 0.9990 chunk 292 optimal weight: 1.9990 chunk 436 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 465 optimal weight: 0.9980 chunk 498 optimal weight: 2.9990 chunk 361 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 575 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 ASN c 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 63195 Z= 0.236 Angle : 0.648 10.664 85569 Z= 0.328 Chirality : 0.045 0.283 9471 Planarity : 0.004 0.050 11253 Dihedral : 5.247 23.377 8547 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 3.80 % Allowed : 19.33 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.09), residues: 7821 helix: 0.72 (0.17), residues: 990 sheet: -2.72 (0.09), residues: 3234 loop : -2.91 (0.09), residues: 3597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 48 HIS 0.027 0.001 HIS Y 135 PHE 0.023 0.001 PHE Y 5 TYR 0.042 0.002 TYR L 121 ARG 0.009 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 698 time to evaluate : 5.617 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: A 28 LEU cc_start: 0.7693 (tp) cc_final: 0.7104 (mm) REVERT: A 29 GLN cc_start: 0.8226 (pp30) cc_final: 0.8010 (pp30) REVERT: A 234 ASP cc_start: 0.7931 (p0) cc_final: 0.7582 (p0) REVERT: B 28 LEU cc_start: 0.8119 (mp) cc_final: 0.7703 (pp) REVERT: B 29 GLN cc_start: 0.8276 (pp30) cc_final: 0.8022 (pp30) REVERT: B 234 ASP cc_start: 0.7904 (p0) cc_final: 0.7369 (p0) REVERT: C 171 GLU cc_start: 0.8340 (pp20) cc_final: 0.8046 (pm20) REVERT: C 192 GLU cc_start: 0.5415 (tm-30) cc_final: 0.4919 (tm-30) REVERT: C 193 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: D 86 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7499 (tmm) REVERT: E 162 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7344 (tm-30) REVERT: E 163 VAL cc_start: 0.9075 (t) cc_final: 0.8783 (p) REVERT: F 37 TYR cc_start: 0.8482 (m-80) cc_final: 0.8173 (m-80) REVERT: F 171 GLU cc_start: 0.8083 (pm20) cc_final: 0.7764 (pp20) REVERT: G 128 ASN cc_start: 0.8344 (m-40) cc_final: 0.8053 (m-40) REVERT: H 28 LEU cc_start: 0.6212 (pp) cc_final: 0.5884 (mp) REVERT: I 28 LEU cc_start: 0.7877 (mm) cc_final: 0.7259 (mt) REVERT: J 192 GLU cc_start: 0.7734 (tp30) cc_final: 0.6464 (tm-30) REVERT: K 86 MET cc_start: 0.8414 (ttm) cc_final: 0.8041 (ttt) REVERT: K 155 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: K 177 LYS cc_start: 0.8030 (mppt) cc_final: 0.7603 (mmtm) REVERT: K 232 PHE cc_start: 0.7470 (p90) cc_final: 0.7175 (p90) REVERT: K 234 ASP cc_start: 0.8132 (p0) cc_final: 0.7607 (p0) REVERT: L 39 LEU cc_start: 0.9197 (mp) cc_final: 0.8959 (mm) REVERT: M 28 LEU cc_start: 0.8018 (mm) cc_final: 0.7725 (mm) REVERT: M 83 TYR cc_start: 0.8292 (t80) cc_final: 0.7575 (t80) REVERT: M 84 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8226 (p0) REVERT: M 87 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7392 (p0) REVERT: N 203 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8726 (mtpp) REVERT: O 171 GLU cc_start: 0.8076 (pm20) cc_final: 0.7452 (pp20) REVERT: P 29 GLN cc_start: 0.8174 (pp30) cc_final: 0.7907 (pp30) REVERT: P 171 GLU cc_start: 0.8074 (pp20) cc_final: 0.7606 (pp20) REVERT: Q 9 VAL cc_start: 0.8632 (t) cc_final: 0.8395 (p) REVERT: Q 28 LEU cc_start: 0.8482 (mm) cc_final: 0.8144 (mm) REVERT: Q 199 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7648 (p90) REVERT: R 29 GLN cc_start: 0.8166 (pp30) cc_final: 0.7859 (pp30) REVERT: R 135 HIS cc_start: 0.6200 (m90) cc_final: 0.5829 (m90) REVERT: R 234 ASP cc_start: 0.8241 (p0) cc_final: 0.7994 (p0) REVERT: S 55 LYS cc_start: 0.8625 (mptt) cc_final: 0.8317 (mptt) REVERT: S 135 HIS cc_start: 0.7413 (m90) cc_final: 0.6932 (m90) REVERT: S 168 LYS cc_start: 0.8400 (mmmm) cc_final: 0.7905 (ttpt) REVERT: T 168 LYS cc_start: 0.7435 (mtmt) cc_final: 0.7123 (mttp) REVERT: U 28 LEU cc_start: 0.8127 (mm) cc_final: 0.7712 (mt) REVERT: U 54 TYR cc_start: 0.8206 (m-80) cc_final: 0.7964 (m-80) REVERT: U 55 LYS cc_start: 0.8733 (mptt) cc_final: 0.8122 (mptt) REVERT: U 130 TRP cc_start: 0.7899 (m100) cc_final: 0.7665 (m100) REVERT: V 5 PHE cc_start: 0.7627 (t80) cc_final: 0.7317 (t80) REVERT: V 28 LEU cc_start: 0.8492 (mp) cc_final: 0.7884 (pp) REVERT: V 29 GLN cc_start: 0.8002 (pp30) cc_final: 0.7723 (pp30) REVERT: V 135 HIS cc_start: 0.7620 (m90) cc_final: 0.7325 (m90) REVERT: V 234 ASP cc_start: 0.7505 (p0) cc_final: 0.6902 (p0) REVERT: Y 37 TYR cc_start: 0.7796 (m-80) cc_final: 0.7553 (m-80) REVERT: Y 234 ASP cc_start: 0.7769 (p0) cc_final: 0.7190 (p0) REVERT: Z 135 HIS cc_start: 0.6991 (m90) cc_final: 0.6269 (m90) REVERT: a 177 LYS cc_start: 0.8390 (mppt) cc_final: 0.7847 (mmtm) REVERT: b 28 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6789 (mm) REVERT: b 55 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8242 (mptt) REVERT: c 28 LEU cc_start: 0.8052 (mm) cc_final: 0.7800 (mt) REVERT: c 208 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8523 (mm) REVERT: d 28 LEU cc_start: 0.8548 (mp) cc_final: 0.8082 (pp) REVERT: d 29 GLN cc_start: 0.7998 (pp30) cc_final: 0.7425 (tm-30) REVERT: d 171 GLU cc_start: 0.7984 (mp0) cc_final: 0.7526 (mp0) REVERT: d 232 PHE cc_start: 0.7739 (p90) cc_final: 0.6950 (p90) REVERT: e 28 LEU cc_start: 0.8622 (tp) cc_final: 0.8227 (mm) REVERT: g 83 TYR cc_start: 0.7556 (t80) cc_final: 0.7229 (t80) outliers start: 262 outliers final: 219 residues processed: 907 average time/residue: 0.5521 time to fit residues: 849.3265 Evaluate side-chains 898 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 670 time to evaluate : 5.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 118 MET Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 208 ILE Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 84 ASP Chi-restraints excluded: chain M residue 87 ASP Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 LYS Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 168 LYS Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 203 LYS Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 90 ILE Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 199 HIS Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 218 VAL Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 170 VAL Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 145 LYS Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 161 THR Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 166 THR Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain W residue 236 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 90 ILE Chi-restraints excluded: chain X residue 124 SER Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 170 VAL Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 157 VAL Chi-restraints excluded: chain Z residue 163 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain b residue 177 LYS Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 166 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain d residue 132 THR Chi-restraints excluded: chain d residue 145 LYS Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 221 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 170 VAL Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 84 ASP Chi-restraints excluded: chain g residue 90 ILE Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 221 LEU Chi-restraints excluded: chain g residue 229 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 665 optimal weight: 3.9990 chunk 700 optimal weight: 20.0000 chunk 639 optimal weight: 4.9990 chunk 681 optimal weight: 0.9980 chunk 410 optimal weight: 5.9990 chunk 296 optimal weight: 5.9990 chunk 535 optimal weight: 0.9990 chunk 209 optimal weight: 0.9990 chunk 616 optimal weight: 0.9990 chunk 644 optimal weight: 1.9990 chunk 679 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 241 GLN O 89 GLN ** O 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 GLN ** Q 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 ASN ** X 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 63195 Z= 0.195 Angle : 0.636 9.519 85569 Z= 0.319 Chirality : 0.045 0.278 9471 Planarity : 0.004 0.049 11253 Dihedral : 5.031 24.335 8547 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 2.91 % Allowed : 20.46 % Favored : 76.63 % 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: -3.46 (0.09), residues: 7821 helix: 0.80 (0.17), residues: 990 sheet: -2.60 (0.08), residues: 3267 loop : -2.83 (0.09), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 48 HIS 0.026 0.001 HIS Y 135 PHE 0.040 0.001 PHE K 5 TYR 0.042 0.001 TYR a 121 ARG 0.008 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 714 time to evaluate : 5.599 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: A 28 LEU cc_start: 0.7846 (tp) cc_final: 0.7400 (mm) REVERT: B 28 LEU cc_start: 0.8068 (mp) cc_final: 0.7646 (pp) REVERT: B 234 ASP cc_start: 0.7975 (p0) cc_final: 0.7481 (p0) REVERT: C 138 HIS cc_start: 0.6853 (t-90) cc_final: 0.6633 (t-90) REVERT: C 169 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7787 (mm-30) REVERT: C 192 GLU cc_start: 0.5433 (tm-30) cc_final: 0.4772 (tm-30) REVERT: C 193 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: C 232 PHE cc_start: 0.7806 (p90) cc_final: 0.7528 (p90) REVERT: D 86 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7322 (tmm) REVERT: E 162 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7334 (tm-30) REVERT: E 163 VAL cc_start: 0.9030 (t) cc_final: 0.8741 (p) REVERT: E 171 GLU cc_start: 0.7687 (pp20) cc_final: 0.7121 (pp20) REVERT: F 37 TYR cc_start: 0.8399 (m-80) cc_final: 0.8158 (m-80) REVERT: F 95 GLU cc_start: 0.6517 (tm-30) cc_final: 0.5835 (tm-30) REVERT: F 171 GLU cc_start: 0.8090 (pm20) cc_final: 0.7745 (pp20) REVERT: G 128 ASN cc_start: 0.8295 (m-40) cc_final: 0.8017 (m-40) REVERT: G 135 HIS cc_start: 0.7622 (m-70) cc_final: 0.7421 (m170) REVERT: G 163 VAL cc_start: 0.9460 (t) cc_final: 0.9125 (p) REVERT: G 232 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7669 (p90) REVERT: H 28 LEU cc_start: 0.7388 (pp) cc_final: 0.6921 (mp) REVERT: H 83 TYR cc_start: 0.7772 (t80) cc_final: 0.7400 (t80) REVERT: I 28 LEU cc_start: 0.7806 (mm) cc_final: 0.7202 (mt) REVERT: J 192 GLU cc_start: 0.7683 (tp30) cc_final: 0.6448 (tm-30) REVERT: K 86 MET cc_start: 0.8234 (ttm) cc_final: 0.7913 (ttt) REVERT: K 155 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: K 177 LYS cc_start: 0.7980 (mppt) cc_final: 0.7581 (mmmm) REVERT: K 232 PHE cc_start: 0.7973 (p90) cc_final: 0.7633 (p90) REVERT: K 234 ASP cc_start: 0.8129 (p0) cc_final: 0.7626 (p0) REVERT: L 39 LEU cc_start: 0.9205 (mp) cc_final: 0.8979 (mm) REVERT: L 55 LYS cc_start: 0.8538 (mptt) cc_final: 0.8137 (mmtt) REVERT: L 128 ASN cc_start: 0.8523 (m-40) cc_final: 0.8296 (m110) REVERT: L 157 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9052 (p) REVERT: M 28 LEU cc_start: 0.8039 (mm) cc_final: 0.7743 (mm) REVERT: N 203 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8623 (mtpp) REVERT: O 137 ARG cc_start: 0.8182 (mtm110) cc_final: 0.7789 (mtm180) REVERT: O 169 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7796 (mm-30) REVERT: O 171 GLU cc_start: 0.8241 (pm20) cc_final: 0.7532 (pp20) REVERT: O 234 ASP cc_start: 0.8834 (p0) cc_final: 0.8245 (p0) REVERT: P 29 GLN cc_start: 0.8119 (pp30) cc_final: 0.7875 (pp30) REVERT: P 171 GLU cc_start: 0.7768 (pp20) cc_final: 0.7332 (pp20) REVERT: Q 9 VAL cc_start: 0.8612 (t) cc_final: 0.8347 (p) REVERT: Q 28 LEU cc_start: 0.8403 (mm) cc_final: 0.8074 (mm) REVERT: Q 199 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.7530 (p90) REVERT: R 29 GLN cc_start: 0.8120 (pp30) cc_final: 0.7819 (pp30) REVERT: R 135 HIS cc_start: 0.6178 (m90) cc_final: 0.5810 (m90) REVERT: R 234 ASP cc_start: 0.8193 (p0) cc_final: 0.7947 (p0) REVERT: S 55 LYS cc_start: 0.8574 (mptt) cc_final: 0.8288 (mptt) REVERT: S 135 HIS cc_start: 0.7354 (m90) cc_final: 0.6852 (m90) REVERT: S 234 ASP cc_start: 0.7414 (p0) cc_final: 0.6759 (p0) REVERT: T 63 ASP cc_start: 0.7744 (p0) cc_final: 0.7528 (p0) REVERT: T 168 LYS cc_start: 0.7423 (mtmt) cc_final: 0.6777 (mtmm) REVERT: U 28 LEU cc_start: 0.8036 (mm) cc_final: 0.7586 (mt) REVERT: U 54 TYR cc_start: 0.8184 (m-80) cc_final: 0.7954 (m-80) REVERT: U 55 LYS cc_start: 0.8720 (mptt) cc_final: 0.8075 (mptt) REVERT: U 130 TRP cc_start: 0.7844 (m100) cc_final: 0.7598 (m100) REVERT: U 162 GLU cc_start: 0.6893 (mp0) cc_final: 0.6661 (mp0) REVERT: V 5 PHE cc_start: 0.7579 (t80) cc_final: 0.7266 (t80) REVERT: V 28 LEU cc_start: 0.8454 (mp) cc_final: 0.7904 (pp) REVERT: V 169 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7058 (tp30) REVERT: V 234 ASP cc_start: 0.7478 (p0) cc_final: 0.6878 (p0) REVERT: W 13 VAL cc_start: 0.7533 (t) cc_final: 0.7126 (p) REVERT: W 135 HIS cc_start: 0.7023 (m-70) cc_final: 0.6719 (m-70) REVERT: Y 37 TYR cc_start: 0.7751 (m-80) cc_final: 0.7472 (m-80) REVERT: Y 234 ASP cc_start: 0.7726 (p0) cc_final: 0.7164 (p0) REVERT: Z 5 PHE cc_start: 0.7260 (t80) cc_final: 0.6778 (t80) REVERT: Z 135 HIS cc_start: 0.6647 (m90) cc_final: 0.6050 (m90) REVERT: a 177 LYS cc_start: 0.8350 (mppt) cc_final: 0.7790 (mmtm) REVERT: b 28 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6584 (mm) REVERT: b 55 LYS cc_start: 0.8470 (mtmm) cc_final: 0.8173 (mptt) REVERT: c 28 LEU cc_start: 0.7964 (mm) cc_final: 0.7727 (mt) REVERT: c 208 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8770 (mm) REVERT: d 29 GLN cc_start: 0.7939 (pp30) cc_final: 0.7234 (tm-30) REVERT: d 232 PHE cc_start: 0.8324 (p90) cc_final: 0.7289 (p90) REVERT: g 83 TYR cc_start: 0.7435 (t80) cc_final: 0.7024 (t80) outliers start: 201 outliers final: 176 residues processed: 873 average time/residue: 0.5548 time to fit residues: 818.6746 Evaluate side-chains 873 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 688 time to evaluate : 5.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 118 MET Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 208 ILE Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 LYS Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 168 LYS Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 203 LYS Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 90 ILE Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 199 HIS Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 170 VAL Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 145 LYS Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 161 THR Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain W residue 236 LYS Chi-restraints excluded: chain X residue 124 SER Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 155 ASP Chi-restraints excluded: chain X residue 170 VAL Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 90 ILE Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 157 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain b residue 177 LYS Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 132 THR Chi-restraints excluded: chain d residue 145 LYS Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 221 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 90 ILE Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 221 LEU Chi-restraints excluded: chain g residue 229 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 447 optimal weight: 8.9990 chunk 720 optimal weight: 0.9980 chunk 439 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 chunk 501 optimal weight: 5.9990 chunk 756 optimal weight: 2.9990 chunk 695 optimal weight: 7.9990 chunk 602 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 465 optimal weight: 5.9990 chunk 369 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN N 241 GLN ** O 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 ASN ** U 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 167 GLN ** X 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 63195 Z= 0.253 Angle : 0.666 10.714 85569 Z= 0.338 Chirality : 0.045 0.264 9471 Planarity : 0.004 0.050 11253 Dihedral : 5.211 24.404 8547 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 3.10 % Allowed : 20.37 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.09), residues: 7821 helix: 0.79 (0.17), residues: 990 sheet: -2.72 (0.08), residues: 3267 loop : -2.85 (0.09), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 48 HIS 0.028 0.001 HIS Y 135 PHE 0.039 0.001 PHE K 5 TYR 0.039 0.002 TYR a 121 ARG 0.008 0.000 ARG C 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15642 Ramachandran restraints generated. 7821 Oldfield, 0 Emsley, 7821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 700 time to evaluate : 5.800 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: A 28 LEU cc_start: 0.7984 (tp) cc_final: 0.7509 (mm) REVERT: B 28 LEU cc_start: 0.8200 (mp) cc_final: 0.7833 (pp) REVERT: B 234 ASP cc_start: 0.8029 (p0) cc_final: 0.7530 (p0) REVERT: C 55 LYS cc_start: 0.8677 (mttp) cc_final: 0.8360 (mptt) REVERT: C 192 GLU cc_start: 0.5639 (tm-30) cc_final: 0.5148 (tm-30) REVERT: C 193 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: D 86 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7464 (tmm) REVERT: E 171 GLU cc_start: 0.7786 (pp20) cc_final: 0.7188 (pp20) REVERT: F 37 TYR cc_start: 0.8511 (m-80) cc_final: 0.8201 (m-80) REVERT: G 128 ASN cc_start: 0.8322 (m-40) cc_final: 0.8035 (m-40) REVERT: G 135 HIS cc_start: 0.7677 (m-70) cc_final: 0.7452 (m170) REVERT: H 28 LEU cc_start: 0.6228 (pp) cc_final: 0.5952 (mp) REVERT: H 128 ASN cc_start: 0.8628 (t0) cc_final: 0.8338 (m-40) REVERT: I 28 LEU cc_start: 0.7908 (mm) cc_final: 0.7297 (mt) REVERT: J 192 GLU cc_start: 0.7734 (tp30) cc_final: 0.6463 (tm-30) REVERT: K 86 MET cc_start: 0.8434 (ttm) cc_final: 0.8142 (ttt) REVERT: K 155 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: K 177 LYS cc_start: 0.8043 (mppt) cc_final: 0.7612 (mmmm) REVERT: K 232 PHE cc_start: 0.7355 (p90) cc_final: 0.7143 (p90) REVERT: K 234 ASP cc_start: 0.8135 (p0) cc_final: 0.7611 (p0) REVERT: L 39 LEU cc_start: 0.9358 (mp) cc_final: 0.9113 (mm) REVERT: L 157 VAL cc_start: 0.9339 (OUTLIER) cc_final: 0.9054 (p) REVERT: M 28 LEU cc_start: 0.8154 (mm) cc_final: 0.7894 (mm) REVERT: N 203 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8775 (mtpp) REVERT: O 145 LYS cc_start: 0.7136 (mppt) cc_final: 0.6570 (tttm) REVERT: O 171 GLU cc_start: 0.8156 (pm20) cc_final: 0.7425 (pp20) REVERT: P 29 GLN cc_start: 0.8246 (pp30) cc_final: 0.7945 (pp30) REVERT: P 232 PHE cc_start: 0.7926 (p90) cc_final: 0.7444 (p90) REVERT: Q 9 VAL cc_start: 0.8630 (t) cc_final: 0.8367 (p) REVERT: Q 28 LEU cc_start: 0.8486 (mm) cc_final: 0.8150 (mm) REVERT: Q 128 ASN cc_start: 0.8570 (t0) cc_final: 0.7996 (t0) REVERT: Q 199 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7696 (p90) REVERT: R 29 GLN cc_start: 0.8160 (pp30) cc_final: 0.7892 (pp30) REVERT: R 135 HIS cc_start: 0.6254 (m90) cc_final: 0.5817 (m90) REVERT: R 234 ASP cc_start: 0.8237 (p0) cc_final: 0.8026 (p0) REVERT: S 55 LYS cc_start: 0.8644 (mptt) cc_final: 0.8334 (mptt) REVERT: S 135 HIS cc_start: 0.7252 (m90) cc_final: 0.6731 (m90) REVERT: S 168 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7565 (ttpt) REVERT: T 55 LYS cc_start: 0.8479 (mmtm) cc_final: 0.8269 (mmtt) REVERT: T 168 LYS cc_start: 0.7384 (mtmt) cc_final: 0.6887 (mtmm) REVERT: U 28 LEU cc_start: 0.8061 (mm) cc_final: 0.7672 (mt) REVERT: U 54 TYR cc_start: 0.8222 (m-80) cc_final: 0.7941 (m-80) REVERT: U 55 LYS cc_start: 0.8770 (mptt) cc_final: 0.8127 (mptt) REVERT: U 130 TRP cc_start: 0.7920 (m100) cc_final: 0.7692 (m100) REVERT: U 171 GLU cc_start: 0.7718 (pm20) cc_final: 0.7138 (pm20) REVERT: U 236 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8217 (tptt) REVERT: V 5 PHE cc_start: 0.7682 (t80) cc_final: 0.7354 (t80) REVERT: V 28 LEU cc_start: 0.8582 (mp) cc_final: 0.7933 (pp) REVERT: V 29 GLN cc_start: 0.8022 (pp30) cc_final: 0.7738 (pp30) REVERT: V 171 GLU cc_start: 0.8155 (pm20) cc_final: 0.7860 (pp20) REVERT: V 234 ASP cc_start: 0.7562 (p0) cc_final: 0.6926 (p0) REVERT: Y 37 TYR cc_start: 0.7848 (m-80) cc_final: 0.7565 (m-80) REVERT: Y 234 ASP cc_start: 0.7774 (p0) cc_final: 0.7198 (p0) REVERT: Z 5 PHE cc_start: 0.7312 (t80) cc_final: 0.6852 (t80) REVERT: Z 135 HIS cc_start: 0.6889 (m90) cc_final: 0.6269 (m90) REVERT: a 177 LYS cc_start: 0.8391 (mppt) cc_final: 0.7855 (mmtm) REVERT: b 28 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6679 (mm) REVERT: b 55 LYS cc_start: 0.8538 (mtmm) cc_final: 0.8250 (mptt) REVERT: b 135 HIS cc_start: 0.6944 (m90) cc_final: 0.6194 (m-70) REVERT: c 208 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8613 (mm) REVERT: d 29 GLN cc_start: 0.8048 (pp30) cc_final: 0.7152 (tm-30) REVERT: d 232 PHE cc_start: 0.8112 (p90) cc_final: 0.7198 (p90) REVERT: f 234 ASP cc_start: 0.6769 (p0) cc_final: 0.6500 (p0) REVERT: g 83 TYR cc_start: 0.7723 (t80) cc_final: 0.7459 (t80) outliers start: 214 outliers final: 192 residues processed: 876 average time/residue: 0.5672 time to fit residues: 842.9015 Evaluate side-chains 877 residues out of total 6897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 677 time to evaluate : 5.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 229 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 118 MET Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 LYS Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 5 PHE Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 168 LYS Chi-restraints excluded: chain N residue 170 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 203 LYS Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 90 ILE Chi-restraints excluded: chain P residue 118 MET Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 199 HIS Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 HIS Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 222 VAL Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain U residue 170 VAL Chi-restraints excluded: chain U residue 173 THR Chi-restraints excluded: chain U residue 186 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 145 LYS Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 161 THR Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 136 GLU Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain W residue 236 LYS Chi-restraints excluded: chain X residue 90 ILE Chi-restraints excluded: chain X residue 124 SER Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain X residue 170 VAL Chi-restraints excluded: chain X residue 186 LEU Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain Y residue 90 ILE Chi-restraints excluded: chain Y residue 155 ASP Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 90 ILE Chi-restraints excluded: chain Z residue 157 VAL Chi-restraints excluded: chain Z residue 163 VAL Chi-restraints excluded: chain Z residue 166 THR Chi-restraints excluded: chain Z residue 170 VAL Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain a residue 18 HIS Chi-restraints excluded: chain a residue 90 ILE Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 232 PHE Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain b residue 177 LYS Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 218 VAL Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 166 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 208 ILE Chi-restraints excluded: chain d residue 132 THR Chi-restraints excluded: chain d residue 133 LEU Chi-restraints excluded: chain d residue 145 LYS Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 221 LEU Chi-restraints excluded: chain e residue 18 HIS Chi-restraints excluded: chain e residue 139 LEU Chi-restraints excluded: chain e residue 166 THR Chi-restraints excluded: chain e residue 170 VAL Chi-restraints excluded: chain e residue 186 LEU Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 90 ILE Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 25 VAL Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 166 THR Chi-restraints excluded: chain g residue 170 VAL Chi-restraints excluded: chain g residue 221 LEU Chi-restraints excluded: chain g residue 229 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 759 random chunks: chunk 478 optimal weight: 0.5980 chunk 641 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 555 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 603 optimal weight: 8.9990 chunk 252 optimal weight: 0.7980 chunk 619 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN F 197 GLN G 91 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN L 128 ASN ** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 ASN ** U 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.125168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.102843 restraints weight = 151656.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.102931 restraints weight = 124063.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.103419 restraints weight = 98518.520| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 63195 Z= 0.224 Angle : 0.659 11.678 85569 Z= 0.332 Chirality : 0.045 0.263 9471 Planarity : 0.004 0.050 11253 Dihedral : 5.127 26.691 8547 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 3.09 % Allowed : 20.59 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.09), residues: 7821 helix: 0.80 (0.17), residues: 990 sheet: -2.70 (0.08), residues: 3267 loop : -2.83 (0.09), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 48 HIS 0.029 0.001 HIS Y 135 PHE 0.039 0.001 PHE K 5 TYR 0.040 0.002 TYR a 121 ARG 0.008 0.000 ARG C 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12979.97 seconds wall clock time: 228 minutes 59.81 seconds (13739.81 seconds total)