Starting phenix.real_space_refine on Thu Dec 26 14:45:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f66_28876/12_2024/8f66_28876_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f66_28876/12_2024/8f66_28876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f66_28876/12_2024/8f66_28876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f66_28876/12_2024/8f66_28876.map" model { file = "/net/cci-nas-00/data/ceres_data/8f66_28876/12_2024/8f66_28876_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f66_28876/12_2024/8f66_28876_neut.cif" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 29470 2.51 5 N 7868 2.21 5 O 8974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 183 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 46508 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "B" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "C" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "D" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "E" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "F" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "G" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "H" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "I" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "J" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "K" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "L" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "M" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "N" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "O" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "P" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "Q" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "R" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "S" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "T" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "U" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1773 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "V" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "W" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "X" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "Y" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "Z" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "a" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "b" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Time building chain proxies: 24.31, per 1000 atoms: 0.52 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: 10.93 Conformation dependent library (CDL) restraints added in 5.9 seconds 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11060 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 70 sheets defined 40.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.98 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: 26.98 Time building geometry restraints manager: 12.71 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: 0.00 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: 10.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.750 Check model and map are aligned: 0.330 Set scattering table: 0.430 Process input model: 107.650 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 47124 Z= 0.256 Angle : 0.741 12.389 63602 Z= 0.474 Chirality : 0.046 0.222 7406 Planarity : 0.005 0.041 8162 Dihedral : 19.003 88.223 17752 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.76 % Favored : 95.53 % Rotamer: Outliers : 3.94 % Allowed : 20.67 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.11), residues: 5950 helix: 1.33 (0.10), residues: 2380 sheet: 0.72 (0.13), residues: 1582 loop : -0.47 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 109 PHE 0.036 0.002 PHE X 25 TYR 0.013 0.001 TYR O 8 ARG 0.005 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 893 time to evaluate : 5.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 197 outliers final: 44 residues processed: 1057 average time/residue: 2.0906 time to fit residues: 2612.3258 Evaluate side-chains 732 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 688 time to evaluate : 6.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 205 GLU Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 205 GLU Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain S residue 205 GLU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 205 GLU Chi-restraints excluded: chain T residue 207 LEU Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain b residue 120 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 0.6980 chunk 445 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 460 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 280 optimal weight: 4.9990 chunk 343 optimal weight: 2.9990 chunk 533 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 J 191 GLN K 30 ASN K 69 GLN K 89 GLN L 30 ASN L 69 GLN L 89 GLN L 141 GLN M 89 GLN M 141 GLN N 30 ASN N 69 GLN O 98 GLN O 122 GLN P 98 GLN ** Q 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN ** 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 X 89 GLN 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 89 GLN b 141 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2388 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= 0.325 Angle : 0.608 8.487 63602 Z= 0.340 Chirality : 0.047 0.197 7406 Planarity : 0.004 0.029 8162 Dihedral : 6.936 59.878 6694 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.71 % Allowed : 2.67 % Favored : 96.62 % Rotamer: Outliers : 4.40 % Allowed : 21.51 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.11), residues: 5950 helix: 2.51 (0.10), residues: 2338 sheet: 1.16 (0.13), residues: 1428 loop : -0.69 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 109 PHE 0.042 0.002 PHE Z 25 TYR 0.013 0.001 TYR M 184 ARG 0.004 0.000 ARG V 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 634 time to evaluate : 5.615 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: A 221 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7069 (t80) REVERT: B 221 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7026 (t80) REVERT: D 221 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7134 (t80) REVERT: E 221 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.6982 (t80) REVERT: G 68 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.7029 (mm110) REVERT: L 96 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7269 (mtp) REVERT: O 221 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7020 (t80) REVERT: P 68 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6973 (mm110) REVERT: R 221 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.7076 (t80) REVERT: S 221 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7070 (t80) REVERT: U 221 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7170 (t80) REVERT: a 96 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7247 (mtp) outliers start: 220 outliers final: 45 residues processed: 816 average time/residue: 1.9293 time to fit residues: 1892.0107 Evaluate side-chains 638 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 581 time to evaluate : 5.963 ------------------------------------------------------------------------------- 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 205 GLU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 205 GLU 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 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 96 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 120 VAL 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 221 TYR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 205 GLU 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 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 Z residue 189 THR Chi-restraints excluded: chain a residue 96 MET Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain b residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 444 optimal weight: 8.9990 chunk 363 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 534 optimal weight: 2.9990 chunk 577 optimal weight: 5.9990 chunk 476 optimal weight: 4.9990 chunk 530 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 429 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 62 ASN D 62 ASN E 62 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 122 GLN J 89 GLN J 191 GLN L 191 GLN O 44 ASN O 122 GLN P 122 GLN Q 62 ASN S 62 ASN ** S 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 GLN T 62 ASN V 191 GLN W 89 GLN Y 141 GLN Y 191 GLN a 141 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 47124 Z= 0.316 Angle : 0.579 9.540 63602 Z= 0.325 Chirality : 0.047 0.295 7406 Planarity : 0.004 0.032 8162 Dihedral : 6.226 59.535 6670 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.39 % Favored : 95.90 % Rotamer: Outliers : 3.74 % Allowed : 20.93 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.11), residues: 5950 helix: 2.69 (0.10), residues: 2338 sheet: 1.06 (0.13), residues: 1428 loop : -0.68 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS N 109 PHE 0.039 0.002 PHE a 25 TYR 0.012 0.001 TYR M 184 ARG 0.003 0.000 ARG L 67 *********************** 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 758 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 571 time to evaluate : 5.822 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: A 68 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6978 (mm-40) REVERT: A 221 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.6990 (t80) REVERT: B 68 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6997 (mm-40) REVERT: B 221 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7042 (t80) REVERT: D 68 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6967 (mm-40) REVERT: D 221 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7108 (t80) REVERT: E 221 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.6969 (t80) REVERT: F 68 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.7015 (mm110) REVERT: G 68 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7057 (mm110) REVERT: I 32 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7748 (tttt) REVERT: M 96 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7199 (mtp) REVERT: O 221 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6951 (t80) REVERT: P 68 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.7004 (mm110) REVERT: Q 68 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7014 (mm-40) REVERT: R 221 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7004 (t80) REVERT: S 68 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6985 (mm-40) REVERT: S 221 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7045 (t80) REVERT: T 68 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6993 (mm110) REVERT: U 221 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7154 (t80) outliers start: 187 outliers final: 54 residues processed: 725 average time/residue: 2.0319 time to fit residues: 1756.9287 Evaluate side-chains 635 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 562 time to evaluate : 5.602 ------------------------------------------------------------------------------- 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 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 68 GLN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 62 ASN 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 120 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 32 LYS 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 96 MET Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 120 VAL 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 205 GLU 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 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 120 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain b residue 120 VAL 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 528 optimal weight: 3.9990 chunk 402 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 255 optimal weight: 3.9990 chunk 359 optimal weight: 3.9990 chunk 536 optimal weight: 3.9990 chunk 568 optimal weight: 5.9990 chunk 280 optimal weight: 0.8980 chunk 508 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 191 GLN I 89 GLN I 141 GLN J 89 GLN K 191 GLN L 30 ASN V 30 ASN V 191 GLN X 191 GLN Y 141 GLN Y 191 GLN Z 89 GLN a 89 GLN b 191 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2883 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= 0.318 Angle : 0.561 8.264 63602 Z= 0.313 Chirality : 0.046 0.207 7406 Planarity : 0.004 0.031 8162 Dihedral : 6.023 57.191 6665 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.31 % Favored : 96.22 % Rotamer: Outliers : 4.20 % Allowed : 21.11 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.11), residues: 5950 helix: 2.74 (0.10), residues: 2338 sheet: 1.06 (0.13), residues: 1428 loop : -0.76 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS J 109 PHE 0.043 0.002 PHE Z 25 TYR 0.012 0.001 TYR a 184 ARG 0.002 0.000 ARG M 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 575 time to evaluate : 5.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6998 (mm-40) REVERT: A 221 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7002 (t80) REVERT: B 68 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7006 (mm-40) REVERT: B 221 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7072 (t80) REVERT: C 68 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6970 (mm110) REVERT: D 221 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7111 (t80) REVERT: E 221 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6904 (t80) REVERT: F 68 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.7022 (mm110) REVERT: G 68 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7056 (mm110) REVERT: O 221 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6879 (t80) REVERT: P 68 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7034 (mm110) REVERT: Q 68 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7025 (mm-40) REVERT: R 221 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7009 (t80) REVERT: S 68 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.7002 (mm-40) REVERT: S 221 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.7034 (t80) REVERT: T 68 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7010 (mm110) REVERT: U 221 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7132 (t80) REVERT: Z 197 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.7006 (mtp180) outliers start: 210 outliers final: 62 residues processed: 750 average time/residue: 1.9122 time to fit residues: 1721.1812 Evaluate side-chains 658 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 578 time to evaluate : 5.902 ------------------------------------------------------------------------------- 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 221 TYR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 205 GLU 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 120 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 120 VAL 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 23 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 120 VAL 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 221 TYR Chi-restraints excluded: chain T residue 68 GLN 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 205 GLU Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 120 VAL 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 22 MET Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 120 VAL 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 120 VAL Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 4.9990 chunk 322 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 423 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 485 optimal weight: 3.9990 chunk 392 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 510 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN I 89 GLN J 89 GLN K 191 GLN L 30 ASN ** O 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN a 89 GLN b 191 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 47124 Z= 0.452 Angle : 0.604 8.945 63602 Z= 0.334 Chirality : 0.048 0.347 7406 Planarity : 0.004 0.035 8162 Dihedral : 5.978 55.369 6659 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.65 % Favored : 95.88 % Rotamer: Outliers : 3.54 % Allowed : 21.07 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.11), residues: 5950 helix: 2.59 (0.10), residues: 2338 sheet: 0.99 (0.13), residues: 1428 loop : -0.85 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS K 28 PHE 0.046 0.002 PHE I 25 TYR 0.013 0.002 TYR Y 184 ARG 0.003 0.000 ARG W 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 577 time to evaluate : 5.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7000 (t80) REVERT: B 68 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.7044 (mm-40) REVERT: B 221 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7008 (t80) REVERT: C 68 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7028 (mm110) REVERT: F 68 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.7063 (mm110) REVERT: G 68 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.7073 (mm110) REVERT: I 32 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7763 (tttt) REVERT: L 197 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7151 (mtp180) REVERT: P 68 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7092 (mm110) REVERT: Q 68 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.7056 (mm-40) REVERT: R 68 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7036 (mm110) REVERT: R 221 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.6948 (t80) REVERT: S 68 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7044 (mm-40) REVERT: S 221 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.6967 (t80) REVERT: T 68 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7057 (mm110) REVERT: U 64 ILE cc_start: 0.5714 (OUTLIER) cc_final: 0.5513 (mt) REVERT: Z 197 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7032 (mtp180) outliers start: 177 outliers final: 61 residues processed: 738 average time/residue: 1.8154 time to fit residues: 1610.6486 Evaluate side-chains 648 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 570 time to evaluate : 4.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 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 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 205 GLU 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 120 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 120 VAL 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 120 VAL Chi-restraints excluded: chain L residue 197 ARG Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 68 GLN 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 205 GLU Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 64 ILE 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 V residue 3 THR Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 120 VAL 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 120 VAL Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 3.9990 chunk 511 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 333 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 568 optimal weight: 4.9990 chunk 472 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 89 GLN N 30 ASN O 44 ASN R 44 ASN V 30 ASN V 89 GLN X 30 ASN Z 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3096 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= 0.319 Angle : 0.570 9.204 63602 Z= 0.316 Chirality : 0.048 0.388 7406 Planarity : 0.004 0.040 8162 Dihedral : 5.669 55.609 6653 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.39 % Favored : 96.13 % Rotamer: Outliers : 3.10 % Allowed : 21.53 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.11), residues: 5950 helix: 2.66 (0.10), residues: 2338 sheet: 0.99 (0.13), residues: 1428 loop : -0.90 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.003 HIS J 109 PHE 0.044 0.002 PHE Z 25 TYR 0.012 0.001 TYR Y 184 ARG 0.002 0.000 ARG W 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 566 time to evaluate : 5.104 Fit side-chains REVERT: A 68 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6978 (mm110) REVERT: A 221 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.7020 (t80) REVERT: B 68 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7045 (mm-40) REVERT: B 221 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7035 (t80) REVERT: C 68 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7003 (mm110) REVERT: D 64 ILE cc_start: 0.5500 (OUTLIER) cc_final: 0.5270 (mt) REVERT: D 221 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7141 (t80) REVERT: E 64 ILE cc_start: 0.5605 (OUTLIER) cc_final: 0.5399 (mt) REVERT: E 221 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.6879 (t80) REVERT: F 68 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7047 (mm110) REVERT: G 64 ILE cc_start: 0.5715 (OUTLIER) cc_final: 0.5449 (mt) REVERT: G 68 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.7065 (mm110) REVERT: L 197 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7136 (mtp180) REVERT: O 221 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.6875 (t80) REVERT: P 68 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7057 (mm110) REVERT: Q 68 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.7037 (mm-40) REVERT: R 64 ILE cc_start: 0.5440 (OUTLIER) cc_final: 0.5198 (mt) REVERT: R 68 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6992 (mm110) REVERT: R 221 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.7004 (t80) REVERT: S 68 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7025 (mm-40) REVERT: S 221 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.7034 (t80) REVERT: U 68 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6990 (mm110) REVERT: U 221 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7143 (t80) outliers start: 155 outliers final: 61 residues processed: 706 average time/residue: 1.7666 time to fit residues: 1503.5433 Evaluate side-chains 646 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 562 time to evaluate : 4.204 ------------------------------------------------------------------------------- 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 64 ILE Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 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 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 120 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 120 VAL 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 120 VAL Chi-restraints excluded: chain L residue 197 ARG Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 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 64 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 68 GLN Chi-restraints excluded: chain U residue 122 GLN Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 120 VAL 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 89 GLN Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 120 VAL Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 189 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 324 optimal weight: 3.9990 chunk 415 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 478 optimal weight: 0.0980 chunk 317 optimal weight: 0.2980 chunk 566 optimal weight: 1.9990 chunk 354 optimal weight: 4.9990 chunk 345 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 89 GLN N 141 GLN R 44 ASN V 89 GLN X 141 GLN Y 191 GLN b 191 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 47124 Z= 0.147 Angle : 0.515 8.910 63602 Z= 0.284 Chirality : 0.045 0.326 7406 Planarity : 0.003 0.037 8162 Dihedral : 5.025 36.832 6644 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.45 % Favored : 96.08 % Rotamer: Outliers : 2.48 % Allowed : 22.35 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.11), residues: 5950 helix: 2.88 (0.10), residues: 2338 sheet: 1.00 (0.13), residues: 1428 loop : -0.87 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS X 109 PHE 0.042 0.001 PHE a 25 TYR 0.009 0.001 TYR Z 66 ARG 0.002 0.000 ARG L 71 *********************** 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 722 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 598 time to evaluate : 4.340 Fit side-chains REVERT: A 221 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7168 (t80) REVERT: B 68 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6938 (mm-40) REVERT: B 221 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7108 (t80) REVERT: C 68 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6897 (mm110) REVERT: D 64 ILE cc_start: 0.5384 (OUTLIER) cc_final: 0.5143 (mt) REVERT: D 221 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.7205 (t80) REVERT: E 221 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.6957 (t80) REVERT: F 68 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6911 (mm110) REVERT: F 221 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7140 (t80) REVERT: G 64 ILE cc_start: 0.5661 (OUTLIER) cc_final: 0.5376 (mt) REVERT: G 68 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6974 (mm110) REVERT: G 221 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.7111 (t80) REVERT: O 221 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7018 (t80) REVERT: P 68 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6933 (mm110) REVERT: P 221 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7152 (t80) REVERT: Q 64 ILE cc_start: 0.5554 (OUTLIER) cc_final: 0.5290 (mt) REVERT: Q 221 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.7140 (t80) REVERT: R 64 ILE cc_start: 0.5298 (OUTLIER) cc_final: 0.5067 (mt) REVERT: R 221 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.7156 (t80) REVERT: S 68 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6942 (mm-40) REVERT: S 221 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.7149 (t80) REVERT: U 68 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6935 (mm110) REVERT: U 221 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7220 (t80) REVERT: V 96 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7186 (mtp) outliers start: 124 outliers final: 31 residues processed: 706 average time/residue: 1.7392 time to fit residues: 1485.7398 Evaluate side-chains 623 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 568 time to evaluate : 4.140 ------------------------------------------------------------------------------- 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 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 64 ILE Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 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 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 I residue 3 THR Chi-restraints excluded: chain I residue 22 MET Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain K 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 Q residue 64 ILE Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 64 ILE 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 68 GLN 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 96 MET Chi-restraints excluded: chain X residue 196 ILE Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain b residue 3 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 338 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 360 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 445 optimal weight: 4.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 122 GLN G 122 GLN H 89 GLN H 191 GLN N 89 GLN P 122 GLN Q 122 GLN ** S 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 164 GLN Y 191 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 47124 Z= 0.410 Angle : 0.589 8.398 63602 Z= 0.325 Chirality : 0.048 0.294 7406 Planarity : 0.004 0.036 8162 Dihedral : 5.258 40.855 6630 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.31 % Favored : 96.22 % Rotamer: Outliers : 2.00 % Allowed : 22.61 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.11), residues: 5950 helix: 2.65 (0.10), residues: 2338 sheet: 1.01 (0.13), residues: 1428 loop : -0.89 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS K 109 PHE 0.050 0.002 PHE Z 25 TYR 0.013 0.002 TYR b 66 ARG 0.003 0.000 ARG S 115 *********************** 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 660 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 560 time to evaluate : 4.201 Fit side-chains REVERT: A 221 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.6992 (t80) REVERT: B 68 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7027 (mm-40) REVERT: B 221 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7004 (t80) REVERT: C 68 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.7011 (mm110) REVERT: E 221 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.6869 (t80) REVERT: F 68 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7037 (mm110) REVERT: G 68 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7057 (mm110) REVERT: O 221 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6857 (t80) REVERT: P 68 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7086 (mm110) REVERT: Q 68 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.7016 (mm-40) REVERT: R 68 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.7024 (mm110) REVERT: R 221 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.6993 (t80) REVERT: S 68 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7024 (mm-40) REVERT: S 221 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6999 (t80) REVERT: U 68 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.7024 (mm110) REVERT: U 221 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7104 (t80) outliers start: 100 outliers final: 40 residues processed: 652 average time/residue: 1.6005 time to fit residues: 1238.7488 Evaluate side-chains 609 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 553 time to evaluate : 3.998 ------------------------------------------------------------------------------- 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 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 64 ILE Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 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 I residue 3 THR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain L 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 Q residue 64 ILE Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 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 64 ILE 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 68 GLN 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 Z residue 3 THR Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain b residue 3 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 4.9990 chunk 542 optimal weight: 2.9990 chunk 495 optimal weight: 2.9990 chunk 528 optimal weight: 3.9990 chunk 317 optimal weight: 0.8980 chunk 230 optimal weight: 1.9990 chunk 414 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 477 optimal weight: 6.9990 chunk 499 optimal weight: 1.9990 chunk 526 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 30 ASN ** O 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 47124 Z= 0.179 Angle : 0.529 10.114 63602 Z= 0.291 Chirality : 0.046 0.443 7406 Planarity : 0.003 0.038 8162 Dihedral : 4.885 37.515 6630 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.45 % Favored : 96.08 % Rotamer: Outliers : 1.52 % Allowed : 23.13 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.11), residues: 5950 helix: 2.82 (0.10), residues: 2338 sheet: 1.05 (0.13), residues: 1428 loop : -0.89 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS N 28 PHE 0.040 0.002 PHE I 25 TYR 0.009 0.001 TYR Y 184 ARG 0.004 0.000 ARG S 115 *********************** 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 643 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 567 time to evaluate : 3.997 Fit side-chains REVERT: A 221 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7140 (t80) REVERT: B 68 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6992 (mm-40) REVERT: B 221 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.7114 (t80) REVERT: C 68 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6924 (mm110) REVERT: D 221 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.7155 (t80) REVERT: E 221 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.6933 (t80) REVERT: F 64 ILE cc_start: 0.5327 (OUTLIER) cc_final: 0.5123 (mt) REVERT: G 64 ILE cc_start: 0.5618 (OUTLIER) cc_final: 0.5350 (mt) REVERT: G 68 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.7003 (mm110) REVERT: L 197 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.7099 (mtp180) REVERT: O 221 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.6979 (t80) REVERT: P 64 ILE cc_start: 0.5392 (OUTLIER) cc_final: 0.5176 (mt) REVERT: P 68 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.7019 (mm110) REVERT: R 68 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6957 (mm110) REVERT: R 221 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.7147 (t80) REVERT: S 68 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6983 (mm-40) REVERT: S 221 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.7102 (t80) REVERT: U 68 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6928 (mm110) REVERT: U 221 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7189 (t80) outliers start: 76 outliers final: 36 residues processed: 639 average time/residue: 1.5303 time to fit residues: 1163.1516 Evaluate side-chains 617 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 562 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 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 64 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain L residue 197 ARG Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 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 64 ILE 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 68 GLN 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 64 ILE Chi-restraints excluded: chain U residue 68 GLN Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain a residue 3 THR 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 346 optimal weight: 4.9990 chunk 558 optimal weight: 6.9990 chunk 340 optimal weight: 4.9990 chunk 264 optimal weight: 0.9980 chunk 388 optimal weight: 8.9990 chunk 585 optimal weight: 8.9990 chunk 539 optimal weight: 0.6980 chunk 466 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 360 optimal weight: 9.9990 chunk 286 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 191 GLN Q 62 ASN W 89 GLN Y 191 GLN b 191 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 47124 Z= 0.298 Angle : 0.561 8.975 63602 Z= 0.308 Chirality : 0.047 0.401 7406 Planarity : 0.004 0.037 8162 Dihedral : 5.060 39.273 6630 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.23 % Favored : 96.32 % Rotamer: Outliers : 1.40 % Allowed : 23.13 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.11), residues: 5950 helix: 2.73 (0.10), residues: 2338 sheet: 1.05 (0.13), residues: 1428 loop : -0.89 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 109 PHE 0.042 0.002 PHE Z 25 TYR 0.011 0.001 TYR Y 184 ARG 0.005 0.000 ARG S 115 ********************** 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 634 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 564 time to evaluate : 3.912 Fit side-chains REVERT: A 68 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6974 (mm110) REVERT: A 221 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7034 (t80) REVERT: B 68 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6986 (mm-40) REVERT: B 221 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7054 (t80) REVERT: C 68 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6968 (mm110) REVERT: D 221 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7130 (t80) REVERT: E 221 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6923 (t80) REVERT: F 64 ILE cc_start: 0.5404 (OUTLIER) cc_final: 0.5194 (mt) REVERT: G 68 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.7053 (mm110) REVERT: L 197 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.7117 (mtp180) REVERT: O 221 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.6920 (t80) REVERT: P 64 ILE cc_start: 0.5509 (OUTLIER) cc_final: 0.5288 (mt) REVERT: P 68 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.7064 (mm110) REVERT: R 68 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6990 (mm110) REVERT: R 221 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7038 (t80) REVERT: S 68 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6995 (mm-40) REVERT: S 221 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7070 (t80) REVERT: U 68 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6992 (mm110) REVERT: U 221 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.7153 (t80) outliers start: 70 outliers final: 38 residues processed: 631 average time/residue: 1.4915 time to fit residues: 1117.5498 Evaluate side-chains 618 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 561 time to evaluate : 3.652 ------------------------------------------------------------------------------- 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 221 TYR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 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 64 ILE Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain L residue 197 ARG Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 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 64 ILE 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 68 GLN 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 64 ILE Chi-restraints excluded: chain U residue 68 GLN Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 167 SER Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 22 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 4.9990 chunk 496 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 430 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 467 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 479 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.080627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.058175 restraints weight = 80588.246| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 2.56 r_work: 0.2472 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2343 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 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 0.035 47124 Z= 0.199 Angle : 0.517 9.504 63602 Z= 0.285 Chirality : 0.045 0.232 7406 Planarity : 0.003 0.038 8162 Dihedral : 4.904 37.653 6630 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.66 % Favored : 96.07 % Rotamer: Outliers : 1.28 % Allowed : 23.33 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.11), residues: 5950 helix: 2.81 (0.10), residues: 2338 sheet: 1.05 (0.13), residues: 1428 loop : -0.90 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS X 109 PHE 0.041 0.001 PHE K 25 TYR 0.010 0.001 TYR I 66 ARG 0.005 0.000 ARG S 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21235.12 seconds wall clock time: 373 minutes 8.34 seconds (22388.34 seconds total)