Starting phenix.real_space_refine on Wed Aug 27 02:16:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f66_28876/08_2025/8f66_28876_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f66_28876/08_2025/8f66_28876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f66_28876/08_2025/8f66_28876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f66_28876/08_2025/8f66_28876.map" model { file = "/net/cci-nas-00/data/ceres_data/8f66_28876/08_2025/8f66_28876_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f66_28876/08_2025/8f66_28876_neut.cif" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 29470 2.51 5 N 7868 2.21 5 O 8974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 183 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46508 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "B" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "C" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "D" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "E" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "F" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "G" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "H" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "I" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "J" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "K" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "L" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "M" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "N" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "O" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "P" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "Q" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "R" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "S" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "T" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "U" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "V" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "W" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "X" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "Y" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "Z" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "a" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "b" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Time building chain proxies: 10.64, per 1000 atoms: 0.23 Number of scatterers: 46508 At special positions: 0 Unit cell: (133.523, 132.89, 170.226, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 8974 8.00 N 7868 7.00 C 29470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.91 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11060 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 70 sheets defined 40.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'B' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA B 30 " --> pdb=" O TYR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 185 through 199 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.503A pdb=" N ALA C 30 " --> pdb=" O TYR C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 104 Processing helix chain 'C' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'D' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 185 through 199 Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 123 removed outlier: 3.972A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'E' and resid 185 through 199 Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'F' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA F 30 " --> pdb=" O TYR F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 Processing helix chain 'F' and resid 185 through 199 Processing helix chain 'F' and resid 225 through 231 Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 180 Processing helix chain 'G' and resid 185 through 199 Processing helix chain 'G' and resid 225 through 231 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 147 through 166 Processing helix chain 'H' and resid 188 through 200 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'I' and resid 188 through 200 Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 147 through 166 Processing helix chain 'J' and resid 188 through 200 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.836A pdb=" N VAL K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 Processing helix chain 'K' and resid 147 through 166 Processing helix chain 'K' and resid 188 through 200 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.836A pdb=" N VAL L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 Processing helix chain 'L' and resid 147 through 166 Processing helix chain 'L' and resid 188 through 200 Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 90 removed outlier: 3.836A pdb=" N VAL M 90 " --> pdb=" O MET M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 147 through 166 Processing helix chain 'M' and resid 188 through 200 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 142 Processing helix chain 'N' and resid 147 through 166 Processing helix chain 'N' and resid 188 through 200 Processing helix chain 'O' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA O 30 " --> pdb=" O TYR O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 104 Processing helix chain 'O' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 180 Processing helix chain 'O' and resid 185 through 199 Processing helix chain 'O' and resid 225 through 231 Processing helix chain 'P' and resid 21 through 32 removed outlier: 3.503A pdb=" N ALA P 30 " --> pdb=" O TYR P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 104 Processing helix chain 'P' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU P 112 " --> pdb=" O ASN P 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 180 Processing helix chain 'P' and resid 185 through 199 Processing helix chain 'P' and resid 225 through 231 Processing helix chain 'Q' and resid 21 through 32 removed outlier: 3.503A pdb=" N ALA Q 30 " --> pdb=" O TYR Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 104 Processing helix chain 'Q' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU Q 112 " --> pdb=" O ASN Q 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 180 Processing helix chain 'Q' and resid 185 through 199 Processing helix chain 'Q' and resid 225 through 231 Processing helix chain 'R' and resid 21 through 32 removed outlier: 3.503A pdb=" N ALA R 30 " --> pdb=" O TYR R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 104 Processing helix chain 'R' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU R 112 " --> pdb=" O ASN R 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 180 Processing helix chain 'R' and resid 185 through 199 Processing helix chain 'R' and resid 225 through 231 Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA S 30 " --> pdb=" O TYR S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 104 Processing helix chain 'S' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR S 123 " --> pdb=" O GLN S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 180 Processing helix chain 'S' and resid 185 through 199 Processing helix chain 'S' and resid 225 through 231 Processing helix chain 'T' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA T 30 " --> pdb=" O TYR T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 104 Processing helix chain 'T' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU T 112 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 180 Processing helix chain 'T' and resid 185 through 199 Processing helix chain 'T' and resid 225 through 231 Processing helix chain 'U' and resid 21 through 32 removed outlier: 3.504A pdb=" N ALA U 30 " --> pdb=" O TYR U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 123 removed outlier: 3.971A pdb=" N LEU U 112 " --> pdb=" O ASN U 108 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 180 Processing helix chain 'U' and resid 185 through 199 Processing helix chain 'U' and resid 225 through 231 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 Processing helix chain 'V' and resid 147 through 166 Processing helix chain 'V' and resid 188 through 200 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.836A pdb=" N VAL W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'W' and resid 188 through 200 Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL X 90 " --> pdb=" O MET X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 142 Processing helix chain 'X' and resid 147 through 166 Processing helix chain 'X' and resid 188 through 200 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 142 Processing helix chain 'Y' and resid 147 through 166 Processing helix chain 'Y' and resid 188 through 200 Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 142 Processing helix chain 'Z' and resid 147 through 166 Processing helix chain 'Z' and resid 188 through 200 Processing helix chain 'a' and resid 48 through 71 Processing helix chain 'a' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL a 90 " --> pdb=" O MET a 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 142 Processing helix chain 'a' and resid 147 through 166 Processing helix chain 'a' and resid 188 through 200 Processing helix chain 'b' and resid 48 through 71 Processing helix chain 'b' and resid 75 through 90 removed outlier: 3.835A pdb=" N VAL b 90 " --> pdb=" O MET b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 142 Processing helix chain 'b' and resid 147 through 166 Processing helix chain 'b' and resid 188 through 200 Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 165 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN A 158 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN B 158 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN C 158 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 162 through 165 Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN D 158 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 162 through 165 Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN E 158 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 162 through 165 Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.795A pdb=" N ASN F 158 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.793A pdb=" N ASN G 158 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 124 through 127 Processing sheet with id=AB7, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AB8, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL H 110 " --> pdb=" O ASP H 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 124 through 127 Processing sheet with id=AC1, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AC2, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.414A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL I 110 " --> pdb=" O ASP I 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 124 through 127 Processing sheet with id=AC4, first strand: chain 'J' and resid 20 through 21 Processing sheet with id=AC5, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL J 110 " --> pdb=" O ASP J 122 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 124 through 127 Processing sheet with id=AC7, first strand: chain 'K' and resid 20 through 21 Processing sheet with id=AC8, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL K 110 " --> pdb=" O ASP K 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 124 through 127 Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 21 Processing sheet with id=AD2, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL L 110 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 124 through 127 Processing sheet with id=AD4, first strand: chain 'M' and resid 20 through 21 Processing sheet with id=AD5, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL M 110 " --> pdb=" O ASP M 122 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 124 through 127 Processing sheet with id=AD7, first strand: chain 'N' and resid 20 through 21 Processing sheet with id=AD8, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.414A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL N 110 " --> pdb=" O ASP N 122 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 162 through 165 Processing sheet with id=AE1, first strand: chain 'O' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN O 158 " --> pdb=" O ASP O 150 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 162 through 165 Processing sheet with id=AE3, first strand: chain 'P' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN P 158 " --> pdb=" O ASP P 150 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 162 through 165 Processing sheet with id=AE5, first strand: chain 'Q' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN Q 158 " --> pdb=" O ASP Q 150 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 162 through 165 Processing sheet with id=AE7, first strand: chain 'R' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN R 158 " --> pdb=" O ASP R 150 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 162 through 165 Processing sheet with id=AE9, first strand: chain 'S' and resid 67 through 69 removed outlier: 3.795A pdb=" N ASN S 158 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 162 through 165 Processing sheet with id=AF2, first strand: chain 'T' and resid 67 through 69 removed outlier: 3.793A pdb=" N ASN T 158 " --> pdb=" O ASP T 150 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AF4, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.794A pdb=" N ASN U 158 " --> pdb=" O ASP U 150 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 124 through 127 Processing sheet with id=AF6, first strand: chain 'V' and resid 20 through 21 Processing sheet with id=AF7, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL V 110 " --> pdb=" O ASP V 122 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 124 through 127 Processing sheet with id=AF9, first strand: chain 'W' and resid 20 through 21 Processing sheet with id=AG1, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.414A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL W 110 " --> pdb=" O ASP W 122 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'X' and resid 124 through 127 Processing sheet with id=AG3, first strand: chain 'X' and resid 20 through 21 Processing sheet with id=AG4, first strand: chain 'X' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL X 110 " --> pdb=" O ASP X 122 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 124 through 127 Processing sheet with id=AG6, first strand: chain 'Y' and resid 20 through 21 Processing sheet with id=AG7, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL Y 110 " --> pdb=" O ASP Y 122 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 124 through 127 Processing sheet with id=AG9, first strand: chain 'Z' and resid 20 through 21 Processing sheet with id=AH1, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL Z 110 " --> pdb=" O ASP Z 122 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'a' and resid 124 through 127 Processing sheet with id=AH3, first strand: chain 'a' and resid 20 through 21 Processing sheet with id=AH4, first strand: chain 'a' and resid 34 through 38 removed outlier: 6.414A pdb=" N THR a 41 " --> pdb=" O ILE a 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL a 110 " --> pdb=" O ASP a 122 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 124 through 127 Processing sheet with id=AH6, first strand: chain 'b' and resid 20 through 21 Processing sheet with id=AH7, first strand: chain 'b' and resid 34 through 38 removed outlier: 6.415A pdb=" N THR b 41 " --> pdb=" O ILE b 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL b 110 " --> pdb=" O ASP b 122 " (cutoff:3.500A) 2772 hydrogen bonds defined for protein. 7896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.86 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8034 1.31 - 1.43: 10958 1.43 - 1.56: 27754 1.56 - 1.68: 0 1.68 - 1.81: 378 Bond restraints: 47124 Sorted by residual: bond pdb=" C THR O 13 " pdb=" N VAL O 14 " ideal model delta sigma weight residual 1.330 1.265 0.065 1.26e-02 6.30e+03 2.67e+01 bond pdb=" C THR F 13 " pdb=" N VAL F 14 " ideal model delta sigma weight residual 1.330 1.266 0.065 1.26e-02 6.30e+03 2.64e+01 bond pdb=" C THR C 13 " pdb=" N VAL C 14 " ideal model delta sigma weight residual 1.330 1.266 0.065 1.26e-02 6.30e+03 2.64e+01 bond pdb=" C THR D 13 " pdb=" N VAL D 14 " ideal model delta sigma weight residual 1.330 1.266 0.065 1.26e-02 6.30e+03 2.63e+01 bond pdb=" C THR P 13 " pdb=" N VAL P 14 " ideal model delta sigma weight residual 1.330 1.266 0.065 1.26e-02 6.30e+03 2.63e+01 ... (remaining 47119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 62579 2.48 - 4.96: 869 4.96 - 7.43: 112 7.43 - 9.91: 14 9.91 - 12.39: 28 Bond angle restraints: 63602 Sorted by residual: angle pdb=" CA ASP T 84 " pdb=" CB ASP T 84 " pdb=" CG ASP T 84 " ideal model delta sigma weight residual 112.60 119.20 -6.60 1.00e+00 1.00e+00 4.36e+01 angle pdb=" CA ASP E 84 " pdb=" CB ASP E 84 " pdb=" CG ASP E 84 " ideal model delta sigma weight residual 112.60 119.17 -6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" CA ASP P 84 " pdb=" CB ASP P 84 " pdb=" CG ASP P 84 " ideal model delta sigma weight residual 112.60 119.17 -6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" CA ASP R 84 " pdb=" CB ASP R 84 " pdb=" CG ASP R 84 " ideal model delta sigma weight residual 112.60 119.16 -6.56 1.00e+00 1.00e+00 4.31e+01 angle pdb=" CA ASP S 84 " pdb=" CB ASP S 84 " pdb=" CG ASP S 84 " ideal model delta sigma weight residual 112.60 119.15 -6.55 1.00e+00 1.00e+00 4.29e+01 ... (remaining 63597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 24639 17.64 - 35.29: 2801 35.29 - 52.93: 924 52.93 - 70.58: 252 70.58 - 88.22: 196 Dihedral angle restraints: 28812 sinusoidal: 11480 harmonic: 17332 Sorted by residual: dihedral pdb=" CA MET V 93 " pdb=" C MET V 93 " pdb=" N PRO V 94 " pdb=" CA PRO V 94 " ideal model delta harmonic sigma weight residual -180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA MET K 93 " pdb=" C MET K 93 " pdb=" N PRO K 94 " pdb=" CA PRO K 94 " ideal model delta harmonic sigma weight residual -180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA MET a 93 " pdb=" C MET a 93 " pdb=" N PRO a 94 " pdb=" CA PRO a 94 " ideal model delta harmonic sigma weight residual -180.00 -156.14 -23.86 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 28809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 5578 0.044 - 0.089: 1180 0.089 - 0.133: 564 0.133 - 0.178: 56 0.178 - 0.222: 28 Chirality restraints: 7406 Sorted by residual: chirality pdb=" CA PRO Q 17 " pdb=" N PRO Q 17 " pdb=" C PRO Q 17 " pdb=" CB PRO Q 17 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA PRO O 17 " pdb=" N PRO O 17 " pdb=" C PRO O 17 " pdb=" CB PRO O 17 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA PRO U 17 " pdb=" N PRO U 17 " pdb=" C PRO U 17 " pdb=" CB PRO U 17 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 7403 not shown) Planarity restraints: 8162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 13 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C THR B 13 " -0.071 2.00e-02 2.50e+03 pdb=" O THR B 13 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL B 14 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 13 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR G 13 " 0.071 2.00e-02 2.50e+03 pdb=" O THR G 13 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL G 14 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR U 13 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR U 13 " 0.071 2.00e-02 2.50e+03 pdb=" O THR U 13 " -0.026 2.00e-02 2.50e+03 pdb=" N VAL U 14 " -0.025 2.00e-02 2.50e+03 ... (remaining 8159 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 11112 2.80 - 3.32: 43008 3.32 - 3.85: 80244 3.85 - 4.37: 95995 4.37 - 4.90: 158233 Nonbonded interactions: 388592 Sorted by model distance: nonbonded pdb=" OH TYR O 123 " pdb=" OH TYR U 126 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR D 126 " pdb=" OH TYR E 123 " model vdw 2.271 3.040 nonbonded pdb=" ND1 HIS I 28 " pdb=" OD2 ASP J 122 " model vdw 2.283 3.120 nonbonded pdb=" OH TYR T 126 " pdb=" OH TYR U 123 " model vdw 2.293 3.040 nonbonded pdb=" NE2 GLN P 97 " pdb=" OE2 GLU V 64 " model vdw 2.295 3.120 ... (remaining 388587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.760 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: 0.030 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.130 Process input model: 45.060 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.240 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: 0.000 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 47124 Z= 0.283 Angle : 0.741 12.389 63602 Z= 0.474 Chirality : 0.046 0.222 7406 Planarity : 0.005 0.041 8162 Dihedral : 19.003 88.223 17752 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.76 % Favored : 95.53 % Rotamer: Outliers : 3.94 % Allowed : 20.67 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.11), residues: 5950 helix: 1.33 (0.10), residues: 2380 sheet: 0.72 (0.13), residues: 1582 loop : -0.47 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 67 TYR 0.013 0.001 TYR O 8 PHE 0.036 0.002 PHE X 25 HIS 0.004 0.002 HIS J 109 Details of bonding type rmsd covalent geometry : bond 0.00401 (47124) covalent geometry : angle 0.74068 (63602) hydrogen bonds : bond 0.21770 ( 2772) hydrogen bonds : angle 7.04005 ( 7896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 893 time to evaluate : 1.947 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 outliers start: 197 outliers final: 43 residues processed: 1057 average time/residue: 1.0225 time to fit residues: 1280.1532 Evaluate side-chains 732 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 689 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 205 GLU Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 205 GLU Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain S residue 205 GLU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 205 GLU Chi-restraints excluded: chain T residue 207 LEU Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain b residue 120 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 0.1980 chunk 523 optimal weight: 0.8980 chunk 497 optimal weight: 0.2980 chunk 414 optimal weight: 0.9980 chunk 310 optimal weight: 0.6980 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN E 44 ASN ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN H 69 GLN H 89 GLN I 89 GLN I 141 GLN I 191 GLN J 30 ASN J 89 GLN K 30 ASN K 69 GLN L 30 ASN L 69 GLN L 89 GLN L 141 GLN M 89 GLN M 141 GLN N 30 ASN N 69 GLN N 89 GLN O 98 GLN O 122 GLN P 98 GLN ** Q 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 GLN V 30 ASN V 89 GLN W 69 GLN W 89 GLN W 141 GLN X 30 ASN Y 69 GLN Y 89 GLN Y 141 GLN Z 30 ASN Z 89 GLN Z 141 GLN Z 191 GLN a 89 GLN a 141 GLN b 30 ASN b 69 GLN b 141 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.090977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.068170 restraints weight = 79417.486| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.59 r_work: 0.2734 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 47124 Z= 0.122 Angle : 0.559 9.387 63602 Z= 0.313 Chirality : 0.045 0.205 7406 Planarity : 0.003 0.031 8162 Dihedral : 6.536 59.723 6692 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.69 % Allowed : 3.24 % Favored : 96.07 % Rotamer: Outliers : 3.90 % Allowed : 22.45 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.11), residues: 5950 helix: 2.56 (0.10), residues: 2352 sheet: 0.67 (0.13), residues: 1582 loop : -0.60 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 67 TYR 0.008 0.001 TYR Z 184 PHE 0.039 0.001 PHE Z 25 HIS 0.005 0.002 HIS L 109 Details of bonding type rmsd covalent geometry : bond 0.00241 (47124) covalent geometry : angle 0.55897 (63602) hydrogen bonds : bond 0.04216 ( 2772) hydrogen bonds : angle 4.73744 ( 7896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 736 time to evaluate : 1.900 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: G 66 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8538 (mmmm) REVERT: I 32 LYS cc_start: 0.9549 (OUTLIER) cc_final: 0.9250 (tttt) REVERT: L 96 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9069 (mtp) REVERT: M 141 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: Q 111 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8413 (m110) REVERT: V 198 LYS cc_start: 0.7884 (ttpt) cc_final: 0.7658 (ttpt) REVERT: W 96 MET cc_start: 0.9482 (OUTLIER) cc_final: 0.9193 (mmm) REVERT: Y 172 MET cc_start: 0.8566 (tpp) cc_final: 0.8322 (mmm) outliers start: 195 outliers final: 26 residues processed: 870 average time/residue: 0.9558 time to fit residues: 992.1280 Evaluate side-chains 693 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 661 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 141 GLN Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 205 GLU Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain Q residue 111 ASN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 205 GLU Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain Y residue 23 GLU Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Z residue 23 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 31 optimal weight: 7.9990 chunk 247 optimal weight: 3.9990 chunk 571 optimal weight: 0.0370 chunk 546 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 345 optimal weight: 2.9990 chunk 450 optimal weight: 7.9990 chunk 375 optimal weight: 9.9990 chunk 544 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN H 141 GLN K 191 GLN L 30 ASN L 191 GLN M 89 GLN N 30 ASN N 191 GLN ** O 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 ASN Q 122 GLN T 62 ASN V 30 ASN V 191 GLN W 89 GLN W 191 GLN Y 191 GLN Z 141 GLN Z 191 GLN a 141 GLN b 89 GLN b 191 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.082754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.060039 restraints weight = 81469.709| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.57 r_work: 0.2580 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9168 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 47124 Z= 0.198 Angle : 0.582 10.253 63602 Z= 0.326 Chirality : 0.047 0.340 7406 Planarity : 0.004 0.033 8162 Dihedral : 5.933 59.227 6653 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.39 % Favored : 96.08 % Rotamer: Outliers : 3.22 % Allowed : 21.21 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.11), residues: 5950 helix: 2.73 (0.10), residues: 2338 sheet: 1.11 (0.13), residues: 1428 loop : -0.70 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 197 TYR 0.012 0.001 TYR M 184 PHE 0.039 0.002 PHE a 25 HIS 0.005 0.002 HIS J 109 Details of bonding type rmsd covalent geometry : bond 0.00471 (47124) covalent geometry : angle 0.58184 (63602) hydrogen bonds : bond 0.05239 ( 2772) hydrogen bonds : angle 4.66787 ( 7896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 589 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.9508 (OUTLIER) cc_final: 0.8165 (t80) REVERT: B 221 TYR cc_start: 0.9507 (OUTLIER) cc_final: 0.8238 (t80) REVERT: C 68 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8336 (mm110) REVERT: D 221 TYR cc_start: 0.9501 (OUTLIER) cc_final: 0.8276 (t80) REVERT: E 111 ASN cc_start: 0.8823 (m110) cc_final: 0.8608 (m110) REVERT: E 221 TYR cc_start: 0.9528 (OUTLIER) cc_final: 0.8085 (t80) REVERT: F 68 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8348 (mm110) REVERT: G 68 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8418 (mm-40) REVERT: H 172 MET cc_start: 0.8830 (mmt) cc_final: 0.8606 (mmm) REVERT: H 198 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7812 (ttpt) REVERT: I 32 LYS cc_start: 0.9588 (OUTLIER) cc_final: 0.9301 (tttt) REVERT: L 96 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.9128 (mtp) REVERT: L 198 LYS cc_start: 0.7883 (ttpt) cc_final: 0.7633 (ttpt) REVERT: L 199 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7640 (mm) REVERT: M 198 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7881 (ttpt) REVERT: N 17 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8609 (pp20) REVERT: O 221 TYR cc_start: 0.9538 (OUTLIER) cc_final: 0.8016 (t80) REVERT: P 68 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8310 (mm110) REVERT: R 221 TYR cc_start: 0.9508 (OUTLIER) cc_final: 0.8185 (t80) REVERT: S 68 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8412 (mm110) REVERT: S 111 ASN cc_start: 0.8839 (m110) cc_final: 0.8610 (m110) REVERT: S 221 TYR cc_start: 0.9484 (OUTLIER) cc_final: 0.8207 (t80) REVERT: Y 172 MET cc_start: 0.8750 (tpp) cc_final: 0.8452 (mmm) REVERT: Y 198 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7692 (ttpt) REVERT: b 98 GLN cc_start: 0.9059 (mp10) cc_final: 0.8809 (mt0) outliers start: 161 outliers final: 41 residues processed: 724 average time/residue: 0.8137 time to fit residues: 705.3268 Evaluate side-chains 628 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 570 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 205 GLU Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 205 GLU Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 122 GLN Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 183 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 577 optimal weight: 5.9990 chunk 346 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 471 optimal weight: 2.9990 chunk 296 optimal weight: 10.0000 chunk 492 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN B 122 GLN E 122 GLN H 141 GLN H 191 GLN I 89 GLN I 141 GLN L 141 GLN L 191 GLN M 89 GLN M 141 GLN M 191 GLN V 30 ASN V 191 GLN W 89 GLN X 89 GLN Y 141 GLN Y 191 GLN Z 89 GLN Z 191 GLN a 89 GLN b 89 GLN b 191 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.057433 restraints weight = 82465.119| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.57 r_work: 0.2569 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9204 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 47124 Z= 0.241 Angle : 0.577 8.443 63602 Z= 0.323 Chirality : 0.047 0.232 7406 Planarity : 0.004 0.033 8162 Dihedral : 5.790 57.930 6650 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.50 % Favored : 96.03 % Rotamer: Outliers : 3.70 % Allowed : 21.63 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.11), residues: 5950 helix: 2.69 (0.10), residues: 2338 sheet: 1.13 (0.13), residues: 1428 loop : -0.72 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 67 TYR 0.013 0.001 TYR a 184 PHE 0.046 0.002 PHE I 25 HIS 0.005 0.002 HIS N 109 Details of bonding type rmsd covalent geometry : bond 0.00581 (47124) covalent geometry : angle 0.57710 (63602) hydrogen bonds : bond 0.05332 ( 2772) hydrogen bonds : angle 4.61413 ( 7896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 581 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8450 (mm-40) REVERT: A 221 TYR cc_start: 0.9568 (OUTLIER) cc_final: 0.8124 (t80) REVERT: B 68 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8467 (mm-40) REVERT: B 188 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8801 (tp30) REVERT: B 221 TYR cc_start: 0.9559 (OUTLIER) cc_final: 0.8094 (t80) REVERT: C 68 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8398 (mm110) REVERT: D 221 TYR cc_start: 0.9552 (OUTLIER) cc_final: 0.8203 (t80) REVERT: E 111 ASN cc_start: 0.8880 (m110) cc_final: 0.8657 (m110) REVERT: E 221 TYR cc_start: 0.9592 (OUTLIER) cc_final: 0.8092 (t80) REVERT: F 68 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8382 (mm110) REVERT: G 68 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8432 (mm-40) REVERT: H 144 GLU cc_start: 0.9116 (pm20) cc_final: 0.8856 (pm20) REVERT: H 199 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7836 (mm) REVERT: I 32 LYS cc_start: 0.9585 (OUTLIER) cc_final: 0.9283 (tttt) REVERT: J 199 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7887 (mm) REVERT: K 98 GLN cc_start: 0.9080 (mp10) cc_final: 0.8836 (mt0) REVERT: L 96 MET cc_start: 0.9505 (OUTLIER) cc_final: 0.9165 (mtp) REVERT: L 199 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7785 (mm) REVERT: M 144 GLU cc_start: 0.9206 (pm20) cc_final: 0.8881 (pm20) REVERT: M 199 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7903 (mm) REVERT: O 111 ASN cc_start: 0.8958 (m110) cc_final: 0.8749 (m110) REVERT: O 221 TYR cc_start: 0.9581 (OUTLIER) cc_final: 0.8021 (t80) REVERT: P 68 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8376 (mm110) REVERT: Q 68 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8440 (mm-40) REVERT: R 221 TYR cc_start: 0.9561 (OUTLIER) cc_final: 0.8134 (t80) REVERT: S 68 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8454 (mm110) REVERT: S 111 ASN cc_start: 0.8904 (m110) cc_final: 0.8672 (m110) REVERT: S 221 TYR cc_start: 0.9559 (OUTLIER) cc_final: 0.8093 (t80) REVERT: T 68 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8373 (mm110) REVERT: T 188 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8707 (tp30) REVERT: U 221 TYR cc_start: 0.9525 (OUTLIER) cc_final: 0.8221 (t80) REVERT: V 191 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: V 198 LYS cc_start: 0.8052 (ttpt) cc_final: 0.7822 (ttpt) REVERT: V 199 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7765 (mm) REVERT: W 199 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7833 (mm) REVERT: X 144 GLU cc_start: 0.9059 (pm20) cc_final: 0.8851 (pm20) REVERT: Y 172 MET cc_start: 0.8817 (tpp) cc_final: 0.8517 (mmm) REVERT: a 197 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7598 (mtp180) REVERT: a 199 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7734 (mm) REVERT: b 98 GLN cc_start: 0.9090 (mp10) cc_final: 0.8847 (mt0) outliers start: 185 outliers final: 49 residues processed: 751 average time/residue: 0.7371 time to fit residues: 662.8768 Evaluate side-chains 658 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 579 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 205 GLU Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 68 GLN Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 188 GLU Chi-restraints excluded: chain T residue 205 GLU Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 122 GLN Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 191 GLN Chi-restraints excluded: chain V residue 199 LEU Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain W residue 199 LEU Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 146 MET Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 197 ARG Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 146 optimal weight: 3.9990 chunk 317 optimal weight: 2.9990 chunk 419 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 386 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 336 optimal weight: 0.7980 chunk 306 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 191 GLN L 30 ASN L 141 GLN M 191 GLN V 89 GLN W 89 GLN X 141 GLN Y 141 GLN Y 191 GLN b 89 GLN b 191 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.079511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.056461 restraints weight = 80667.685| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 2.63 r_work: 0.2432 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2298 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 47124 Z= 0.160 Angle : 0.536 8.292 63602 Z= 0.297 Chirality : 0.045 0.201 7406 Planarity : 0.003 0.036 8162 Dihedral : 5.413 55.471 6644 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.34 % Favored : 96.18 % Rotamer: Outliers : 3.08 % Allowed : 22.23 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.11), residues: 5950 helix: 2.81 (0.10), residues: 2338 sheet: 1.15 (0.13), residues: 1428 loop : -0.78 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 195 TYR 0.011 0.001 TYR Y 184 PHE 0.044 0.002 PHE Z 25 HIS 0.005 0.002 HIS J 109 Details of bonding type rmsd covalent geometry : bond 0.00375 (47124) covalent geometry : angle 0.53552 (63602) hydrogen bonds : bond 0.04486 ( 2772) hydrogen bonds : angle 4.39466 ( 7896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 601 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8358 (mm-40) REVERT: A 221 TYR cc_start: 0.9444 (OUTLIER) cc_final: 0.8169 (t80) REVERT: B 68 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8287 (mm-40) REVERT: B 221 TYR cc_start: 0.9410 (OUTLIER) cc_final: 0.8168 (t80) REVERT: D 221 TYR cc_start: 0.9409 (OUTLIER) cc_final: 0.8195 (t80) REVERT: E 111 ASN cc_start: 0.8717 (m110) cc_final: 0.8496 (m110) REVERT: E 221 TYR cc_start: 0.9476 (OUTLIER) cc_final: 0.8024 (t80) REVERT: G 68 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8336 (mm-40) REVERT: H 144 GLU cc_start: 0.9095 (pm20) cc_final: 0.8806 (pm20) REVERT: H 199 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7539 (mm) REVERT: I 32 LYS cc_start: 0.9519 (OUTLIER) cc_final: 0.9243 (tttt) REVERT: J 199 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7693 (mm) REVERT: K 98 GLN cc_start: 0.8959 (mp10) cc_final: 0.8706 (mt0) REVERT: K 144 GLU cc_start: 0.9043 (pm20) cc_final: 0.8796 (pm20) REVERT: L 96 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.9108 (mtp) REVERT: L 199 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7468 (mm) REVERT: M 199 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7469 (mm) REVERT: O 111 ASN cc_start: 0.8816 (m110) cc_final: 0.8587 (m110) REVERT: O 221 TYR cc_start: 0.9472 (OUTLIER) cc_final: 0.8095 (t80) REVERT: P 68 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8223 (mm110) REVERT: P 223 ILE cc_start: 0.9684 (OUTLIER) cc_final: 0.9461 (mm) REVERT: R 68 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8321 (mm110) REVERT: R 221 TYR cc_start: 0.9435 (OUTLIER) cc_final: 0.8153 (t80) REVERT: S 68 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8284 (mm110) REVERT: S 111 ASN cc_start: 0.8745 (m110) cc_final: 0.8499 (m110) REVERT: S 221 TYR cc_start: 0.9422 (OUTLIER) cc_final: 0.8165 (t80) REVERT: U 221 TYR cc_start: 0.9372 (OUTLIER) cc_final: 0.8256 (t80) REVERT: V 60 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8885 (mttt) REVERT: V 199 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7581 (mm) REVERT: X 144 GLU cc_start: 0.9069 (pm20) cc_final: 0.8835 (pm20) REVERT: Y 144 GLU cc_start: 0.9057 (pm20) cc_final: 0.8833 (pm20) REVERT: Y 172 MET cc_start: 0.8648 (tpp) cc_final: 0.8299 (mmm) REVERT: Y 198 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7704 (ttpt) REVERT: a 197 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7514 (mtp180) REVERT: a 199 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7545 (mm) REVERT: b 98 GLN cc_start: 0.8959 (mp10) cc_final: 0.8717 (mt0) REVERT: b 144 GLU cc_start: 0.9051 (pm20) cc_final: 0.8795 (pm20) outliers start: 154 outliers final: 42 residues processed: 741 average time/residue: 0.5863 time to fit residues: 522.7835 Evaluate side-chains 660 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 593 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 223 ILE Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 122 GLN Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 60 LYS Chi-restraints excluded: chain V residue 199 LEU Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 146 MET Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 197 ARG Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain b residue 3 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 253 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 402 optimal weight: 4.9990 chunk 265 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 310 optimal weight: 9.9990 chunk 363 optimal weight: 0.2980 chunk 188 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 3 optimal weight: 0.0970 overall best weight: 1.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 89 GLN K 191 GLN N 141 GLN V 30 ASN W 89 GLN Y 141 GLN b 191 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.057724 restraints weight = 80273.476| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 2.62 r_work: 0.2473 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2341 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 47124 Z= 0.129 Angle : 0.534 10.134 63602 Z= 0.295 Chirality : 0.047 0.395 7406 Planarity : 0.004 0.042 8162 Dihedral : 5.068 53.857 6637 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.23 % Favored : 96.30 % Rotamer: Outliers : 2.28 % Allowed : 22.57 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.11), residues: 5950 helix: 2.88 (0.10), residues: 2338 sheet: 1.14 (0.13), residues: 1428 loop : -0.77 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 67 TYR 0.009 0.001 TYR H 184 PHE 0.045 0.002 PHE L 25 HIS 0.005 0.002 HIS J 109 Details of bonding type rmsd covalent geometry : bond 0.00293 (47124) covalent geometry : angle 0.53427 (63602) hydrogen bonds : bond 0.04018 ( 2772) hydrogen bonds : angle 4.29036 ( 7896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 601 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8416 (mm-40) REVERT: A 221 TYR cc_start: 0.9389 (OUTLIER) cc_final: 0.8235 (t80) REVERT: B 111 ASN cc_start: 0.8782 (m110) cc_final: 0.8559 (m110) REVERT: B 221 TYR cc_start: 0.9350 (OUTLIER) cc_final: 0.8219 (t80) REVERT: D 221 TYR cc_start: 0.9361 (OUTLIER) cc_final: 0.8312 (t80) REVERT: E 111 ASN cc_start: 0.8719 (m110) cc_final: 0.8512 (m110) REVERT: E 221 TYR cc_start: 0.9452 (OUTLIER) cc_final: 0.8133 (t80) REVERT: F 221 TYR cc_start: 0.9404 (OUTLIER) cc_final: 0.8236 (t80) REVERT: G 68 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8361 (mm-40) REVERT: G 221 TYR cc_start: 0.9369 (OUTLIER) cc_final: 0.8216 (t80) REVERT: H 144 GLU cc_start: 0.9128 (pm20) cc_final: 0.8837 (pm20) REVERT: H 199 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7552 (mm) REVERT: I 32 LYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9260 (tttt) REVERT: J 199 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7627 (mm) REVERT: K 98 GLN cc_start: 0.8973 (mp10) cc_final: 0.8736 (mt0) REVERT: K 144 GLU cc_start: 0.9066 (pm20) cc_final: 0.8811 (pm20) REVERT: L 96 MET cc_start: 0.9443 (OUTLIER) cc_final: 0.9122 (mtp) REVERT: L 199 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7441 (mm) REVERT: O 68 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8225 (mm110) REVERT: O 111 ASN cc_start: 0.8831 (m110) cc_final: 0.8621 (m110) REVERT: O 221 TYR cc_start: 0.9455 (OUTLIER) cc_final: 0.8090 (t80) REVERT: P 68 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8241 (mm110) REVERT: Q 68 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8408 (mm-40) REVERT: Q 221 TYR cc_start: 0.9345 (OUTLIER) cc_final: 0.8230 (t80) REVERT: R 221 TYR cc_start: 0.9377 (OUTLIER) cc_final: 0.8237 (t80) REVERT: S 111 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8525 (m110) REVERT: S 221 TYR cc_start: 0.9382 (OUTLIER) cc_final: 0.8210 (t80) REVERT: U 221 TYR cc_start: 0.9307 (OUTLIER) cc_final: 0.8322 (t80) REVERT: V 191 GLN cc_start: 0.8279 (tt0) cc_final: 0.7731 (tm-30) REVERT: V 198 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7649 (ttpt) REVERT: V 199 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7409 (mm) REVERT: W 199 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7637 (mm) REVERT: X 144 GLU cc_start: 0.9062 (pm20) cc_final: 0.8800 (pm20) REVERT: X 199 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7553 (mm) REVERT: Y 172 MET cc_start: 0.8648 (tpp) cc_final: 0.8253 (mmm) REVERT: Y 198 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7689 (ttpt) REVERT: a 197 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7539 (mtp180) REVERT: a 199 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7642 (mm) REVERT: b 98 GLN cc_start: 0.8967 (mp10) cc_final: 0.8720 (mt0) REVERT: b 144 GLU cc_start: 0.9067 (pm20) cc_final: 0.8815 (pm20) outliers start: 114 outliers final: 43 residues processed: 699 average time/residue: 0.6040 time to fit residues: 505.0689 Evaluate side-chains 656 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 586 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 111 ASN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 64 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 199 LEU Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 199 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 172 MET Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 197 ARG Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain b residue 3 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 545 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 470 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 538 optimal weight: 3.9990 chunk 528 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN N 89 GLN X 89 GLN Y 89 GLN Y 141 GLN Z 89 GLN b 191 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.078928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.055907 restraints weight = 80501.987| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 2.62 r_work: 0.2423 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2288 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 47124 Z= 0.183 Angle : 0.552 9.253 63602 Z= 0.306 Chirality : 0.047 0.317 7406 Planarity : 0.004 0.040 8162 Dihedral : 5.166 51.705 6636 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.43 % Favored : 96.10 % Rotamer: Outliers : 2.28 % Allowed : 22.87 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.11), residues: 5950 helix: 2.73 (0.10), residues: 2338 sheet: 1.11 (0.13), residues: 1428 loop : -0.78 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 115 TYR 0.012 0.001 TYR H 184 PHE 0.046 0.002 PHE a 25 HIS 0.004 0.002 HIS N 109 Details of bonding type rmsd covalent geometry : bond 0.00435 (47124) covalent geometry : angle 0.55185 (63602) hydrogen bonds : bond 0.04672 ( 2772) hydrogen bonds : angle 4.38590 ( 7896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 578 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8397 (mm-40) REVERT: A 221 TYR cc_start: 0.9453 (OUTLIER) cc_final: 0.8165 (t80) REVERT: B 68 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8332 (mm-40) REVERT: B 111 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8594 (m110) REVERT: B 221 TYR cc_start: 0.9424 (OUTLIER) cc_final: 0.8138 (t80) REVERT: D 221 TYR cc_start: 0.9417 (OUTLIER) cc_final: 0.8202 (t80) REVERT: E 111 ASN cc_start: 0.8759 (m110) cc_final: 0.8530 (m110) REVERT: E 221 TYR cc_start: 0.9496 (OUTLIER) cc_final: 0.8049 (t80) REVERT: F 68 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8202 (mm110) REVERT: G 68 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8345 (mm-40) REVERT: H 144 GLU cc_start: 0.9105 (pm20) cc_final: 0.8815 (pm20) REVERT: H 199 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7558 (mm) REVERT: I 32 LYS cc_start: 0.9540 (OUTLIER) cc_final: 0.9262 (tttt) REVERT: J 199 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7525 (mm) REVERT: K 98 GLN cc_start: 0.8995 (mp10) cc_final: 0.8754 (mt0) REVERT: K 144 GLU cc_start: 0.9068 (pm20) cc_final: 0.8793 (pm20) REVERT: L 96 MET cc_start: 0.9435 (OUTLIER) cc_final: 0.9118 (mtp) REVERT: L 191 GLN cc_start: 0.8244 (tt0) cc_final: 0.7708 (tm-30) REVERT: L 199 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7478 (mm) REVERT: O 68 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8202 (mm110) REVERT: O 111 ASN cc_start: 0.8854 (m110) cc_final: 0.8622 (m110) REVERT: O 221 TYR cc_start: 0.9499 (OUTLIER) cc_final: 0.8009 (t80) REVERT: P 68 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8230 (mm110) REVERT: P 223 ILE cc_start: 0.9687 (OUTLIER) cc_final: 0.9464 (mm) REVERT: Q 68 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8378 (mm-40) REVERT: R 68 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8355 (mm110) REVERT: R 221 TYR cc_start: 0.9453 (OUTLIER) cc_final: 0.8148 (t80) REVERT: S 111 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8529 (m110) REVERT: S 221 TYR cc_start: 0.9452 (OUTLIER) cc_final: 0.8143 (t80) REVERT: U 221 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.8229 (t80) REVERT: V 144 GLU cc_start: 0.8980 (pm20) cc_final: 0.8680 (pm20) REVERT: V 191 GLN cc_start: 0.8272 (tt0) cc_final: 0.7769 (tm-30) REVERT: V 199 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7537 (mm) REVERT: W 144 GLU cc_start: 0.9085 (pm20) cc_final: 0.8807 (pm20) REVERT: X 199 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7556 (mm) REVERT: Y 172 MET cc_start: 0.8674 (tpp) cc_final: 0.8285 (mmm) REVERT: a 197 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7518 (mtp180) REVERT: a 199 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7572 (mm) REVERT: b 98 GLN cc_start: 0.8980 (mp10) cc_final: 0.8739 (mt0) REVERT: b 144 GLU cc_start: 0.9085 (pm20) cc_final: 0.8813 (pm20) outliers start: 114 outliers final: 50 residues processed: 680 average time/residue: 0.6020 time to fit residues: 490.3351 Evaluate side-chains 654 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 576 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 223 ILE Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 111 ASN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 64 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 199 LEU Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 146 MET Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 197 ARG Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 537 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 323 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 383 optimal weight: 5.9990 chunk 371 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 191 GLN Y 141 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.057221 restraints weight = 80280.803| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 2.57 r_work: 0.2447 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2313 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 47124 Z= 0.148 Angle : 0.533 8.981 63602 Z= 0.295 Chirality : 0.046 0.285 7406 Planarity : 0.004 0.039 8162 Dihedral : 5.000 38.356 6633 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.38 % Favored : 96.15 % Rotamer: Outliers : 2.44 % Allowed : 22.99 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.11), residues: 5950 helix: 2.78 (0.10), residues: 2338 sheet: 1.09 (0.13), residues: 1428 loop : -0.79 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 115 TYR 0.010 0.001 TYR Y 184 PHE 0.044 0.002 PHE I 25 HIS 0.005 0.002 HIS I 109 Details of bonding type rmsd covalent geometry : bond 0.00347 (47124) covalent geometry : angle 0.53319 (63602) hydrogen bonds : bond 0.04265 ( 2772) hydrogen bonds : angle 4.31178 ( 7896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 576 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8392 (mm-40) REVERT: A 221 TYR cc_start: 0.9416 (OUTLIER) cc_final: 0.8193 (t80) REVERT: B 68 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8323 (mm-40) REVERT: B 111 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8579 (m110) REVERT: B 221 TYR cc_start: 0.9400 (OUTLIER) cc_final: 0.8185 (t80) REVERT: D 111 ASN cc_start: 0.8869 (m110) cc_final: 0.8653 (m110) REVERT: D 221 TYR cc_start: 0.9387 (OUTLIER) cc_final: 0.8258 (t80) REVERT: E 111 ASN cc_start: 0.8739 (m110) cc_final: 0.8516 (m110) REVERT: E 221 TYR cc_start: 0.9468 (OUTLIER) cc_final: 0.8097 (t80) REVERT: F 68 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8208 (mm110) REVERT: G 68 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8344 (mm-40) REVERT: H 144 GLU cc_start: 0.9103 (pm20) cc_final: 0.8812 (pm20) REVERT: H 199 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7541 (mm) REVERT: I 32 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.9245 (tttt) REVERT: J 199 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7521 (mm) REVERT: K 98 GLN cc_start: 0.8980 (mp10) cc_final: 0.8738 (mt0) REVERT: L 96 MET cc_start: 0.9432 (OUTLIER) cc_final: 0.9103 (mtp) REVERT: L 191 GLN cc_start: 0.8223 (tt0) cc_final: 0.7701 (tm-30) REVERT: L 199 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7427 (mm) REVERT: N 199 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7518 (mm) REVERT: O 68 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8184 (mm110) REVERT: O 111 ASN cc_start: 0.8841 (m110) cc_final: 0.8618 (m110) REVERT: O 221 TYR cc_start: 0.9464 (OUTLIER) cc_final: 0.8050 (t80) REVERT: P 68 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8234 (mm110) REVERT: P 223 ILE cc_start: 0.9675 (OUTLIER) cc_final: 0.9453 (mm) REVERT: Q 68 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8383 (mm-40) REVERT: R 68 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8348 (mm110) REVERT: R 221 TYR cc_start: 0.9419 (OUTLIER) cc_final: 0.8180 (t80) REVERT: S 111 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8517 (m110) REVERT: S 221 TYR cc_start: 0.9423 (OUTLIER) cc_final: 0.8201 (t80) REVERT: U 111 ASN cc_start: 0.8886 (m110) cc_final: 0.8674 (m110) REVERT: U 221 TYR cc_start: 0.9342 (OUTLIER) cc_final: 0.8279 (t80) REVERT: V 144 GLU cc_start: 0.8990 (pm20) cc_final: 0.8693 (pm20) REVERT: V 191 GLN cc_start: 0.8265 (tt0) cc_final: 0.7777 (tm-30) REVERT: V 199 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7524 (mm) REVERT: W 144 GLU cc_start: 0.9099 (pm20) cc_final: 0.8822 (pm20) REVERT: X 199 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7486 (mm) REVERT: Y 27 MET cc_start: 0.9165 (ttt) cc_final: 0.8857 (ttt) REVERT: Y 172 MET cc_start: 0.8673 (tpp) cc_final: 0.8254 (mmm) REVERT: Z 197 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7454 (mtp180) REVERT: a 197 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7499 (mtp180) REVERT: a 199 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7553 (mm) REVERT: b 98 GLN cc_start: 0.8969 (mp10) cc_final: 0.8721 (mt0) outliers start: 122 outliers final: 57 residues processed: 683 average time/residue: 0.5785 time to fit residues: 473.7623 Evaluate side-chains 660 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 573 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 223 ILE Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 111 ASN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 199 LEU Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 172 MET Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 146 MET Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 197 ARG Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 197 ARG Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 550 optimal weight: 2.9990 chunk 514 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 456 optimal weight: 0.9980 chunk 269 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 191 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 ASN I 89 GLN Q 62 ASN Y 141 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.081909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.059595 restraints weight = 79803.982| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 2.53 r_work: 0.2503 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2374 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 47124 Z= 0.119 Angle : 0.514 8.977 63602 Z= 0.283 Chirality : 0.045 0.263 7406 Planarity : 0.004 0.039 8162 Dihedral : 4.791 36.110 6633 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.18 % Favored : 96.35 % Rotamer: Outliers : 2.00 % Allowed : 23.25 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.11), residues: 5950 helix: 2.88 (0.10), residues: 2338 sheet: 1.06 (0.13), residues: 1428 loop : -0.80 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 115 TYR 0.009 0.001 TYR b 184 PHE 0.049 0.002 PHE X 25 HIS 0.005 0.002 HIS W 28 Details of bonding type rmsd covalent geometry : bond 0.00268 (47124) covalent geometry : angle 0.51439 (63602) hydrogen bonds : bond 0.03763 ( 2772) hydrogen bonds : angle 4.22108 ( 7896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 590 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8419 (mm-40) REVERT: A 221 TYR cc_start: 0.9400 (OUTLIER) cc_final: 0.8281 (t80) REVERT: B 111 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8630 (m110) REVERT: B 221 TYR cc_start: 0.9374 (OUTLIER) cc_final: 0.8281 (t80) REVERT: D 221 TYR cc_start: 0.9361 (OUTLIER) cc_final: 0.8353 (t80) REVERT: E 111 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8557 (m110) REVERT: E 221 TYR cc_start: 0.9433 (OUTLIER) cc_final: 0.8205 (t80) REVERT: F 68 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8245 (mm110) REVERT: F 221 TYR cc_start: 0.9404 (OUTLIER) cc_final: 0.8323 (t80) REVERT: G 221 TYR cc_start: 0.9379 (OUTLIER) cc_final: 0.8263 (t80) REVERT: I 191 GLN cc_start: 0.8338 (tt0) cc_final: 0.7873 (tm-30) REVERT: J 27 MET cc_start: 0.8888 (ttt) cc_final: 0.8511 (ttt) REVERT: J 199 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7669 (mm) REVERT: K 98 GLN cc_start: 0.9002 (mp10) cc_final: 0.8760 (mt0) REVERT: L 96 MET cc_start: 0.9456 (OUTLIER) cc_final: 0.9120 (mtp) REVERT: L 191 GLN cc_start: 0.8262 (tt0) cc_final: 0.7754 (tm-30) REVERT: L 199 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7585 (mm) REVERT: M 198 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7737 (ttpt) REVERT: N 139 GLU cc_start: 0.9239 (tp30) cc_final: 0.8957 (mm-30) REVERT: N 199 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7596 (mm) REVERT: O 68 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8234 (mm110) REVERT: O 111 ASN cc_start: 0.8864 (m110) cc_final: 0.8660 (m110) REVERT: O 221 TYR cc_start: 0.9436 (OUTLIER) cc_final: 0.8165 (t80) REVERT: P 68 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8267 (mm110) REVERT: P 221 TYR cc_start: 0.9390 (OUTLIER) cc_final: 0.8297 (t80) REVERT: Q 68 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8421 (mm-40) REVERT: Q 221 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.8271 (t80) REVERT: R 68 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8418 (mm110) REVERT: R 221 TYR cc_start: 0.9406 (OUTLIER) cc_final: 0.8269 (t80) REVERT: S 111 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8561 (m110) REVERT: S 221 TYR cc_start: 0.9398 (OUTLIER) cc_final: 0.8303 (t80) REVERT: U 221 TYR cc_start: 0.9323 (OUTLIER) cc_final: 0.8293 (t80) REVERT: V 144 GLU cc_start: 0.9003 (pm20) cc_final: 0.8706 (pm20) REVERT: V 191 GLN cc_start: 0.8287 (tt0) cc_final: 0.7806 (tm-30) REVERT: X 199 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7612 (mm) REVERT: Y 139 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8966 (mm-30) REVERT: Y 172 MET cc_start: 0.8716 (tpp) cc_final: 0.8337 (mmm) REVERT: a 27 MET cc_start: 0.8767 (ttt) cc_final: 0.8494 (ttt) REVERT: a 197 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7498 (mtp180) REVERT: a 199 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7601 (mm) REVERT: b 98 GLN cc_start: 0.8995 (mp10) cc_final: 0.8746 (mt0) outliers start: 100 outliers final: 46 residues processed: 676 average time/residue: 0.5658 time to fit residues: 456.0470 Evaluate side-chains 651 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 577 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 111 ASN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 172 MET Chi-restraints excluded: chain X residue 196 ILE Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 197 ARG Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 82 optimal weight: 7.9990 chunk 393 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 295 optimal weight: 0.0070 chunk 269 optimal weight: 0.7980 chunk 464 optimal weight: 4.9990 chunk 435 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 0.0050 chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 overall best weight: 1.1214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 122 GLN H 164 GLN M 89 GLN N 89 GLN U 62 ASN X 89 GLN X 141 GLN Y 141 GLN Y 164 GLN b 191 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.082306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.059941 restraints weight = 80481.082| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 2.55 r_work: 0.2514 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2385 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 47124 Z= 0.110 Angle : 0.511 8.978 63602 Z= 0.281 Chirality : 0.045 0.257 7406 Planarity : 0.003 0.038 8162 Dihedral : 4.646 35.215 6629 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.01 % Favored : 96.52 % Rotamer: Outliers : 1.60 % Allowed : 23.57 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.11), residues: 5950 helix: 2.93 (0.10), residues: 2338 sheet: 0.64 (0.13), residues: 1582 loop : -0.73 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 115 TYR 0.009 0.001 TYR K 66 PHE 0.043 0.002 PHE X 25 HIS 0.006 0.002 HIS b 28 Details of bonding type rmsd covalent geometry : bond 0.00245 (47124) covalent geometry : angle 0.51089 (63602) hydrogen bonds : bond 0.03640 ( 2772) hydrogen bonds : angle 4.18211 ( 7896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 599 time to evaluate : 1.038 Fit side-chains REVERT: A 68 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8417 (mm-40) REVERT: A 221 TYR cc_start: 0.9368 (OUTLIER) cc_final: 0.8289 (t80) REVERT: B 111 ASN cc_start: 0.8848 (m110) cc_final: 0.8636 (m110) REVERT: B 221 TYR cc_start: 0.9343 (OUTLIER) cc_final: 0.8225 (t80) REVERT: D 221 TYR cc_start: 0.9336 (OUTLIER) cc_final: 0.8363 (t80) REVERT: E 111 ASN cc_start: 0.8751 (m110) cc_final: 0.8545 (m110) REVERT: E 221 TYR cc_start: 0.9406 (OUTLIER) cc_final: 0.8241 (t80) REVERT: F 221 TYR cc_start: 0.9378 (OUTLIER) cc_final: 0.8345 (t80) REVERT: G 68 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8362 (mm-40) REVERT: G 221 TYR cc_start: 0.9355 (OUTLIER) cc_final: 0.8299 (t80) REVERT: I 191 GLN cc_start: 0.8328 (tt0) cc_final: 0.7872 (tm-30) REVERT: J 27 MET cc_start: 0.8922 (ttt) cc_final: 0.8565 (ttt) REVERT: J 141 GLN cc_start: 0.8988 (mt0) cc_final: 0.8575 (mt0) REVERT: J 191 GLN cc_start: 0.8332 (tt0) cc_final: 0.7807 (tm-30) REVERT: J 199 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7664 (mm) REVERT: K 98 GLN cc_start: 0.8995 (mp10) cc_final: 0.8753 (mt0) REVERT: K 139 GLU cc_start: 0.9267 (tp30) cc_final: 0.9052 (mm-30) REVERT: L 96 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.9097 (mtp) REVERT: L 191 GLN cc_start: 0.8252 (tt0) cc_final: 0.7751 (tm-30) REVERT: M 198 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7738 (ttpt) REVERT: N 139 GLU cc_start: 0.9227 (tp30) cc_final: 0.8857 (mm-30) REVERT: N 199 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7584 (mm) REVERT: O 68 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8227 (mm110) REVERT: O 221 TYR cc_start: 0.9420 (OUTLIER) cc_final: 0.8211 (t80) REVERT: P 221 TYR cc_start: 0.9337 (OUTLIER) cc_final: 0.8331 (t80) REVERT: Q 68 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8411 (mm-40) REVERT: Q 221 TYR cc_start: 0.9321 (OUTLIER) cc_final: 0.8307 (t80) REVERT: R 68 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8416 (mm110) REVERT: R 221 TYR cc_start: 0.9379 (OUTLIER) cc_final: 0.8288 (t80) REVERT: S 111 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8572 (m110) REVERT: S 221 TYR cc_start: 0.9372 (OUTLIER) cc_final: 0.8242 (t80) REVERT: U 221 TYR cc_start: 0.9297 (OUTLIER) cc_final: 0.8306 (t80) REVERT: V 144 GLU cc_start: 0.9009 (pm20) cc_final: 0.8709 (pm20) REVERT: V 191 GLN cc_start: 0.8267 (tt0) cc_final: 0.7809 (tm-30) REVERT: X 199 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7608 (mm) REVERT: Y 27 MET cc_start: 0.9306 (ttt) cc_final: 0.8915 (ttt) REVERT: Y 139 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8989 (mm-30) REVERT: Y 141 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8814 (mt0) REVERT: Y 172 MET cc_start: 0.8716 (tpp) cc_final: 0.8336 (mmm) REVERT: a 27 MET cc_start: 0.8762 (ttt) cc_final: 0.8459 (ttt) REVERT: a 199 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7604 (mm) REVERT: b 98 GLN cc_start: 0.8993 (mp10) cc_final: 0.8749 (mt0) outliers start: 80 outliers final: 41 residues processed: 672 average time/residue: 0.5807 time to fit residues: 465.1094 Evaluate side-chains 656 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 591 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 111 ASN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 141 GLN Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain b residue 3 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 151 optimal weight: 0.0170 chunk 214 optimal weight: 6.9990 chunk 366 optimal weight: 0.3980 chunk 157 optimal weight: 5.9990 chunk 404 optimal weight: 7.9990 chunk 583 optimal weight: 3.9990 chunk 459 optimal weight: 7.9990 chunk 360 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 overall best weight: 1.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN K 141 GLN Q 62 ASN Q 122 GLN ** U 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 141 GLN Z 141 GLN b 191 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.081289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.058910 restraints weight = 80183.736| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 2.53 r_work: 0.2489 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2360 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 47124 Z= 0.133 Angle : 0.522 8.759 63602 Z= 0.287 Chirality : 0.045 0.255 7406 Planarity : 0.004 0.038 8162 Dihedral : 4.683 36.078 6626 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.13 % Favored : 96.40 % Rotamer: Outliers : 1.58 % Allowed : 23.41 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.11), residues: 5950 helix: 2.88 (0.10), residues: 2338 sheet: 1.01 (0.13), residues: 1428 loop : -0.80 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 115 TYR 0.012 0.001 TYR K 66 PHE 0.041 0.002 PHE X 25 HIS 0.009 0.002 HIS W 28 Details of bonding type rmsd covalent geometry : bond 0.00307 (47124) covalent geometry : angle 0.52156 (63602) hydrogen bonds : bond 0.03942 ( 2772) hydrogen bonds : angle 4.21662 ( 7896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17898.92 seconds wall clock time: 303 minutes 24.55 seconds (18204.55 seconds total)