Starting phenix.real_space_refine on Thu Mar 5 02:25:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7box_30135/03_2026/7box_30135.cif Found real_map, /net/cci-nas-00/data/ceres_data/7box_30135/03_2026/7box_30135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7box_30135/03_2026/7box_30135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7box_30135/03_2026/7box_30135.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7box_30135/03_2026/7box_30135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7box_30135/03_2026/7box_30135.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 sd= 0.574 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 96 5.16 5 C 11556 2.51 5 N 3168 2.21 5 O 3798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18618 Number of models: 1 Model: "" Number of chains: 12 Chain: "M" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain: "N" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 187} Chain: "O" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain: "P" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain: "R" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 187} Chain: "S" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain: "T" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 187} Chain: "U" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain: "V" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 187} Chain: "W" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain: "X" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 187} Time building chain proxies: 3.89, per 1000 atoms: 0.21 Number of scatterers: 18618 At special positions: 0 Unit cell: (168.91, 168.91, 87.63, 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 96 16.00 O 3798 8.00 N 3168 7.00 C 11556 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: 1.52 Conformation dependent library (CDL) restraints added in 801.0 milliseconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 24 sheets defined 42.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'M' and resid 10 through 25 removed outlier: 4.073A pdb=" N ALA M 16 " --> pdb=" O ALA M 12 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE M 24 " --> pdb=" O ILE M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 55 removed outlier: 4.142A pdb=" N GLN M 53 " --> pdb=" O LYS M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 150 removed outlier: 3.580A pdb=" N VAL M 139 " --> pdb=" O ARG M 135 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG M 144 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE M 150 " --> pdb=" O PHE M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 179 removed outlier: 3.552A pdb=" N GLU M 157 " --> pdb=" O ALA M 153 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU M 160 " --> pdb=" O VAL M 156 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU M 162 " --> pdb=" O GLY M 158 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU M 175 " --> pdb=" O CYS M 171 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET M 176 " --> pdb=" O MET M 172 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP M 177 " --> pdb=" O GLU M 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 25 Processing helix chain 'N' and resid 37 through 55 removed outlier: 3.649A pdb=" N ALA N 43 " --> pdb=" O ASP N 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN N 53 " --> pdb=" O LYS N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 150 removed outlier: 3.621A pdb=" N VAL N 139 " --> pdb=" O ARG N 135 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG N 144 " --> pdb=" O THR N 140 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 179 removed outlier: 3.741A pdb=" N GLU N 157 " --> pdb=" O ALA N 153 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU N 162 " --> pdb=" O GLY N 158 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR N 174 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU N 175 " --> pdb=" O CYS N 171 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET N 176 " --> pdb=" O MET N 172 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP N 177 " --> pdb=" O GLU N 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 25 removed outlier: 4.004A pdb=" N ALA O 16 " --> pdb=" O ALA O 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 55 removed outlier: 3.502A pdb=" N LEU O 47 " --> pdb=" O ALA O 43 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN O 53 " --> pdb=" O LYS O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 150 removed outlier: 3.508A pdb=" N VAL O 139 " --> pdb=" O ARG O 135 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG O 144 " --> pdb=" O THR O 140 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 153 through 180 removed outlier: 3.504A pdb=" N GLU O 157 " --> pdb=" O ALA O 153 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL O 159 " --> pdb=" O GLU O 155 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU O 160 " --> pdb=" O VAL O 156 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU O 162 " --> pdb=" O GLY O 158 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR O 174 " --> pdb=" O LEU O 170 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU O 175 " --> pdb=" O CYS O 171 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET O 176 " --> pdb=" O MET O 172 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP O 177 " --> pdb=" O GLU O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 194 removed outlier: 3.676A pdb=" N LEU O 193 " --> pdb=" O PHE O 189 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU O 194 " --> pdb=" O THR O 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 189 through 194' Processing helix chain 'P' and resid 11 through 25 Processing helix chain 'P' and resid 37 through 57 removed outlier: 3.678A pdb=" N ALA P 43 " --> pdb=" O ASP P 39 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG P 44 " --> pdb=" O ALA P 40 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN P 53 " --> pdb=" O LYS P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 150 removed outlier: 3.589A pdb=" N VAL P 139 " --> pdb=" O ARG P 135 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG P 144 " --> pdb=" O THR P 140 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN P 147 " --> pdb=" O SER P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 180 removed outlier: 3.715A pdb=" N GLU P 157 " --> pdb=" O ALA P 153 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU P 162 " --> pdb=" O GLY P 158 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU P 175 " --> pdb=" O CYS P 171 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET P 176 " --> pdb=" O MET P 172 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP P 177 " --> pdb=" O GLU P 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 25 removed outlier: 3.923A pdb=" N ALA Q 16 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE Q 24 " --> pdb=" O ILE Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 57 removed outlier: 3.527A pdb=" N LEU Q 47 " --> pdb=" O ALA Q 43 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN Q 53 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 131 through 150 removed outlier: 3.524A pdb=" N VAL Q 139 " --> pdb=" O ARG Q 135 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG Q 144 " --> pdb=" O THR Q 140 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN Q 147 " --> pdb=" O SER Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 153 through 180 removed outlier: 3.629A pdb=" N VAL Q 159 " --> pdb=" O GLU Q 155 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU Q 160 " --> pdb=" O VAL Q 156 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU Q 162 " --> pdb=" O GLY Q 158 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU Q 175 " --> pdb=" O CYS Q 171 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET Q 176 " --> pdb=" O MET Q 172 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP Q 177 " --> pdb=" O GLU Q 173 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY Q 180 " --> pdb=" O MET Q 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 25 Processing helix chain 'R' and resid 37 through 57 removed outlier: 4.057A pdb=" N GLN R 53 " --> pdb=" O LYS R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 150 removed outlier: 3.543A pdb=" N VAL R 139 " --> pdb=" O ARG R 135 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG R 144 " --> pdb=" O THR R 140 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN R 147 " --> pdb=" O SER R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 180 removed outlier: 3.811A pdb=" N GLU R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU R 162 " --> pdb=" O GLY R 158 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU R 175 " --> pdb=" O CYS R 171 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET R 176 " --> pdb=" O MET R 172 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP R 177 " --> pdb=" O GLU R 173 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 25 removed outlier: 3.893A pdb=" N ALA S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE S 24 " --> pdb=" O ILE S 20 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY S 25 " --> pdb=" O LEU S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 55 removed outlier: 4.080A pdb=" N GLN S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 150 removed outlier: 3.510A pdb=" N VAL S 139 " --> pdb=" O ARG S 135 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG S 144 " --> pdb=" O THR S 140 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN S 147 " --> pdb=" O SER S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 153 through 180 removed outlier: 3.522A pdb=" N VAL S 159 " --> pdb=" O GLU S 155 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU S 160 " --> pdb=" O VAL S 156 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU S 162 " --> pdb=" O GLY S 158 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU S 175 " --> pdb=" O CYS S 171 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET S 176 " --> pdb=" O MET S 172 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP S 177 " --> pdb=" O GLU S 173 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY S 180 " --> pdb=" O MET S 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 25 Processing helix chain 'T' and resid 37 through 55 removed outlier: 3.581A pdb=" N ALA T 41 " --> pdb=" O ASN T 37 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN T 53 " --> pdb=" O LYS T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 151 removed outlier: 3.631A pdb=" N VAL T 139 " --> pdb=" O ARG T 135 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG T 144 " --> pdb=" O THR T 140 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN T 147 " --> pdb=" O SER T 143 " (cutoff:3.500A) Processing helix chain 'T' and resid 153 through 179 removed outlier: 3.608A pdb=" N GLU T 157 " --> pdb=" O ALA T 153 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU T 162 " --> pdb=" O GLY T 158 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU T 175 " --> pdb=" O CYS T 171 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET T 176 " --> pdb=" O MET T 172 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 25 removed outlier: 3.921A pdb=" N ALA U 16 " --> pdb=" O ALA U 12 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE U 24 " --> pdb=" O ILE U 20 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY U 25 " --> pdb=" O LEU U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 55 removed outlier: 4.129A pdb=" N GLN U 53 " --> pdb=" O LYS U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 131 through 150 removed outlier: 3.563A pdb=" N VAL U 139 " --> pdb=" O ARG U 135 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG U 144 " --> pdb=" O THR U 140 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN U 147 " --> pdb=" O SER U 143 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE U 150 " --> pdb=" O PHE U 146 " (cutoff:3.500A) Processing helix chain 'U' and resid 153 through 179 removed outlier: 3.583A pdb=" N GLU U 157 " --> pdb=" O ALA U 153 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU U 160 " --> pdb=" O VAL U 156 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU U 162 " --> pdb=" O GLY U 158 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR U 174 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU U 175 " --> pdb=" O CYS U 171 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET U 176 " --> pdb=" O MET U 172 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP U 177 " --> pdb=" O GLU U 173 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 25 Processing helix chain 'V' and resid 37 through 55 removed outlier: 3.805A pdb=" N ALA V 41 " --> pdb=" O ASN V 37 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN V 53 " --> pdb=" O LYS V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 131 through 151 removed outlier: 3.669A pdb=" N VAL V 139 " --> pdb=" O ARG V 135 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG V 144 " --> pdb=" O THR V 140 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN V 147 " --> pdb=" O SER V 143 " (cutoff:3.500A) Processing helix chain 'V' and resid 153 through 179 removed outlier: 3.508A pdb=" N GLU V 157 " --> pdb=" O ALA V 153 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU V 162 " --> pdb=" O GLY V 158 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR V 174 " --> pdb=" O LEU V 170 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU V 175 " --> pdb=" O CYS V 171 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET V 176 " --> pdb=" O MET V 172 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP V 177 " --> pdb=" O GLU V 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 25 removed outlier: 4.004A pdb=" N ALA W 16 " --> pdb=" O ALA W 12 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE W 24 " --> pdb=" O ILE W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 55 removed outlier: 4.174A pdb=" N GLN W 53 " --> pdb=" O LYS W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 131 through 150 removed outlier: 3.590A pdb=" N VAL W 139 " --> pdb=" O ARG W 135 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG W 144 " --> pdb=" O THR W 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN W 147 " --> pdb=" O SER W 143 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE W 150 " --> pdb=" O PHE W 146 " (cutoff:3.500A) Processing helix chain 'W' and resid 153 through 179 removed outlier: 3.620A pdb=" N GLU W 157 " --> pdb=" O ALA W 153 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU W 160 " --> pdb=" O VAL W 156 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU W 162 " --> pdb=" O GLY W 158 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR W 174 " --> pdb=" O LEU W 170 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU W 175 " --> pdb=" O CYS W 171 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET W 176 " --> pdb=" O MET W 172 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP W 177 " --> pdb=" O GLU W 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 191 through 195 removed outlier: 3.564A pdb=" N LEU W 194 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR W 195 " --> pdb=" O GLY W 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 191 through 195' Processing helix chain 'X' and resid 11 through 25 Processing helix chain 'X' and resid 37 through 55 removed outlier: 3.501A pdb=" N ALA X 41 " --> pdb=" O ASN X 37 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA X 43 " --> pdb=" O ASP X 39 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN X 53 " --> pdb=" O LYS X 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 150 removed outlier: 3.649A pdb=" N VAL X 139 " --> pdb=" O ARG X 135 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG X 144 " --> pdb=" O THR X 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN X 147 " --> pdb=" O SER X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 153 through 179 removed outlier: 3.596A pdb=" N GLU X 157 " --> pdb=" O ALA X 153 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU X 162 " --> pdb=" O GLY X 158 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR X 174 " --> pdb=" O LEU X 170 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU X 175 " --> pdb=" O CYS X 171 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET X 176 " --> pdb=" O MET X 172 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP X 177 " --> pdb=" O GLU X 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 63 through 67 removed outlier: 3.550A pdb=" N ILE M 121 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY M 66 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL M 119 " --> pdb=" O GLY M 66 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN M 120 " --> pdb=" O LEU M 87 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU M 87 " --> pdb=" O ASN M 120 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE M 122 " --> pdb=" O LEU M 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'N' and resid 63 through 67 removed outlier: 3.508A pdb=" N ILE N 121 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY N 66 " --> pdb=" O VAL N 119 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL N 119 " --> pdb=" O GLY N 66 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN N 120 " --> pdb=" O LEU N 87 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU N 87 " --> pdb=" O ASN N 120 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE N 122 " --> pdb=" O LEU N 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 96 through 99 Processing sheet with id=AA5, first strand: chain 'O' and resid 63 through 67 removed outlier: 3.698A pdb=" N GLY O 66 " --> pdb=" O VAL O 119 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL O 119 " --> pdb=" O GLY O 66 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN O 120 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU O 87 " --> pdb=" O ASN O 120 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE O 122 " --> pdb=" O LEU O 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 96 through 98 Processing sheet with id=AA7, first strand: chain 'P' and resid 63 through 67 removed outlier: 3.741A pdb=" N GLY P 66 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL P 119 " --> pdb=" O GLY P 66 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN P 120 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU P 87 " --> pdb=" O ASN P 120 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE P 122 " --> pdb=" O LEU P 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 96 through 99 Processing sheet with id=AA9, first strand: chain 'Q' and resid 63 through 67 removed outlier: 3.709A pdb=" N GLY Q 66 " --> pdb=" O VAL Q 119 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL Q 119 " --> pdb=" O GLY Q 66 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN Q 120 " --> pdb=" O LEU Q 87 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU Q 87 " --> pdb=" O ASN Q 120 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE Q 122 " --> pdb=" O LEU Q 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'R' and resid 63 through 67 removed outlier: 3.795A pdb=" N GLY R 66 " --> pdb=" O VAL R 119 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL R 119 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN R 120 " --> pdb=" O LEU R 87 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU R 87 " --> pdb=" O ASN R 120 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE R 122 " --> pdb=" O LEU R 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 96 through 99 Processing sheet with id=AB4, first strand: chain 'S' and resid 63 through 67 removed outlier: 3.505A pdb=" N ILE S 121 " --> pdb=" O GLU S 64 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY S 66 " --> pdb=" O VAL S 119 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL S 119 " --> pdb=" O GLY S 66 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN S 120 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU S 87 " --> pdb=" O ASN S 120 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE S 122 " --> pdb=" O LEU S 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 96 through 98 Processing sheet with id=AB6, first strand: chain 'T' and resid 63 through 67 removed outlier: 3.604A pdb=" N ILE T 121 " --> pdb=" O GLU T 64 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY T 66 " --> pdb=" O VAL T 119 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL T 119 " --> pdb=" O GLY T 66 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN T 120 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU T 87 " --> pdb=" O ASN T 120 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE T 122 " --> pdb=" O LEU T 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 96 through 98 Processing sheet with id=AB8, first strand: chain 'U' and resid 63 through 67 removed outlier: 3.573A pdb=" N ILE U 121 " --> pdb=" O GLU U 64 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY U 66 " --> pdb=" O VAL U 119 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL U 119 " --> pdb=" O GLY U 66 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN U 120 " --> pdb=" O LEU U 87 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU U 87 " --> pdb=" O ASN U 120 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE U 122 " --> pdb=" O LEU U 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 96 through 98 Processing sheet with id=AC1, first strand: chain 'V' and resid 63 through 67 removed outlier: 3.651A pdb=" N ILE V 121 " --> pdb=" O GLU V 64 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY V 66 " --> pdb=" O VAL V 119 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL V 119 " --> pdb=" O GLY V 66 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN V 120 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU V 87 " --> pdb=" O ASN V 120 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE V 122 " --> pdb=" O LEU V 85 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 96 through 99 Processing sheet with id=AC3, first strand: chain 'W' and resid 63 through 67 removed outlier: 3.603A pdb=" N ILE W 121 " --> pdb=" O GLU W 64 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY W 66 " --> pdb=" O VAL W 119 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL W 119 " --> pdb=" O GLY W 66 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN W 120 " --> pdb=" O LEU W 87 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU W 87 " --> pdb=" O ASN W 120 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE W 122 " --> pdb=" O LEU W 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 96 through 98 Processing sheet with id=AC5, first strand: chain 'X' and resid 63 through 67 removed outlier: 3.626A pdb=" N ILE X 121 " --> pdb=" O GLU X 64 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY X 66 " --> pdb=" O VAL X 119 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL X 119 " --> pdb=" O GLY X 66 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN X 120 " --> pdb=" O LEU X 87 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU X 87 " --> pdb=" O ASN X 120 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE X 122 " --> pdb=" O LEU X 85 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 96 through 99 710 hydrogen bonds defined for protein. 2115 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: 2.47 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5289 1.33 - 1.45: 3590 1.45 - 1.57: 9895 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 18942 Sorted by residual: bond pdb=" CB ILE Q 24 " pdb=" CG2 ILE Q 24 " ideal model delta sigma weight residual 1.521 1.406 0.115 3.30e-02 9.18e+02 1.21e+01 bond pdb=" CG MET O 176 " pdb=" SD MET O 176 " ideal model delta sigma weight residual 1.803 1.724 0.079 2.50e-02 1.60e+03 9.98e+00 bond pdb=" CB ILE M 24 " pdb=" CG2 ILE M 24 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.04e+00 bond pdb=" CB ASN P 42 " pdb=" CG ASN P 42 " ideal model delta sigma weight residual 1.516 1.441 0.075 2.50e-02 1.60e+03 9.01e+00 bond pdb=" CB ILE O 24 " pdb=" CG2 ILE O 24 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.80e+00 ... (remaining 18937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 24233 2.83 - 5.66: 1181 5.66 - 8.49: 202 8.49 - 11.32: 27 11.32 - 14.15: 13 Bond angle restraints: 25656 Sorted by residual: angle pdb=" C SER R 75 " pdb=" N ASN R 76 " pdb=" CA ASN R 76 " ideal model delta sigma weight residual 121.70 131.98 -10.28 1.80e+00 3.09e-01 3.26e+01 angle pdb=" C SER P 75 " pdb=" N ASN P 76 " pdb=" CA ASN P 76 " ideal model delta sigma weight residual 121.70 131.97 -10.27 1.80e+00 3.09e-01 3.25e+01 angle pdb=" C GLY P 58 " pdb=" N TRP P 59 " pdb=" CA TRP P 59 " ideal model delta sigma weight residual 120.82 129.01 -8.19 1.47e+00 4.63e-01 3.11e+01 angle pdb=" C SER N 75 " pdb=" N ASN N 76 " pdb=" CA ASN N 76 " ideal model delta sigma weight residual 121.70 131.67 -9.97 1.80e+00 3.09e-01 3.07e+01 angle pdb=" C SER T 75 " pdb=" N ASN T 76 " pdb=" CA ASN T 76 " ideal model delta sigma weight residual 121.70 131.52 -9.82 1.80e+00 3.09e-01 2.98e+01 ... (remaining 25651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 10356 15.63 - 31.26: 792 31.26 - 46.89: 149 46.89 - 62.52: 31 62.52 - 78.14: 36 Dihedral angle restraints: 11364 sinusoidal: 4566 harmonic: 6798 Sorted by residual: dihedral pdb=" CA ARG T 57 " pdb=" C ARG T 57 " pdb=" N GLY T 58 " pdb=" CA GLY T 58 " ideal model delta harmonic sigma weight residual 180.00 125.79 54.21 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA ARG Q 57 " pdb=" C ARG Q 57 " pdb=" N GLY Q 58 " pdb=" CA GLY Q 58 " ideal model delta harmonic sigma weight residual 180.00 125.94 54.06 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA ARG S 57 " pdb=" C ARG S 57 " pdb=" N GLY S 58 " pdb=" CA GLY S 58 " ideal model delta harmonic sigma weight residual 180.00 126.64 53.36 0 5.00e+00 4.00e-02 1.14e+02 ... (remaining 11361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2322 0.088 - 0.176: 399 0.176 - 0.264: 26 0.264 - 0.352: 2 0.352 - 0.440: 5 Chirality restraints: 2754 Sorted by residual: chirality pdb=" CA ASN P 37 " pdb=" N ASN P 37 " pdb=" C ASN P 37 " pdb=" CB ASN P 37 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA ASN R 37 " pdb=" N ASN R 37 " pdb=" C ASN R 37 " pdb=" CB ASN R 37 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA ASN N 37 " pdb=" N ASN N 37 " pdb=" C ASN N 37 " pdb=" CB ASN N 37 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 2751 not shown) Planarity restraints: 3444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE X 150 " -0.023 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C PHE X 150 " 0.077 2.00e-02 2.50e+03 pdb=" O PHE X 150 " -0.028 2.00e-02 2.50e+03 pdb=" N PHE X 151 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA P 38 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.79e+01 pdb=" C ALA P 38 " 0.073 2.00e-02 2.50e+03 pdb=" O ALA P 38 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP P 39 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE P 150 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C PHE P 150 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE P 150 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE P 151 " -0.025 2.00e-02 2.50e+03 ... (remaining 3441 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3962 2.77 - 3.30: 17954 3.30 - 3.83: 30222 3.83 - 4.37: 35747 4.37 - 4.90: 56740 Nonbonded interactions: 144625 Sorted by model distance: nonbonded pdb=" O ARG R 52 " pdb=" OG SER R 56 " model vdw 2.236 3.040 nonbonded pdb=" O ARG P 52 " pdb=" OG SER P 56 " model vdw 2.239 3.040 nonbonded pdb=" O ARG N 52 " pdb=" OG SER N 56 " model vdw 2.244 3.040 nonbonded pdb=" O ARG T 52 " pdb=" OG SER T 56 " model vdw 2.250 3.040 nonbonded pdb=" O ARG O 52 " pdb=" OG SER O 56 " model vdw 2.264 3.040 ... (remaining 144620 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: 0.01 Found NCS groups: ncs_group { reference = chain 'M' selection = (chain 'N' and resid 3 through 196) selection = chain 'O' selection = (chain 'P' and resid 3 through 196) selection = chain 'Q' selection = (chain 'R' and resid 3 through 196) selection = chain 'S' selection = (chain 'T' and resid 3 through 196) selection = chain 'U' selection = (chain 'V' and resid 3 through 196) selection = chain 'W' selection = (chain 'X' and resid 3 through 196) } 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=0.10 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.490 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.770 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.012 0.115 18942 Z= 0.496 Angle : 1.462 14.155 25656 Z= 0.815 Chirality : 0.067 0.440 2754 Planarity : 0.007 0.045 3444 Dihedral : 12.930 78.145 7032 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.05 % Favored : 91.47 % Rotamer: Outliers : 0.05 % Allowed : 7.91 % Favored : 92.04 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.62 % Twisted Proline : 0.00 % Twisted General : 2.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.94 (0.12), residues: 2310 helix: -3.45 (0.11), residues: 912 sheet: -2.71 (0.57), residues: 72 loop : -3.30 (0.12), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 196 TYR 0.026 0.005 TYR P 136 PHE 0.056 0.007 PHE P 150 TRP 0.029 0.008 TRP R 59 Details of bonding type rmsd covalent geometry : bond 0.01182 (18942) covalent geometry : angle 1.46238 (25656) hydrogen bonds : bond 0.30613 ( 710) hydrogen bonds : angle 9.40771 ( 2115) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1065 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: M 166 GLU cc_start: 0.8015 (tt0) cc_final: 0.7750 (tt0) REVERT: M 172 MET cc_start: 0.7536 (tpp) cc_final: 0.6840 (ptt) REVERT: N 47 LEU cc_start: 0.9235 (tt) cc_final: 0.8999 (tt) REVERT: N 64 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7953 (mt-10) REVERT: N 67 ILE cc_start: 0.8697 (pp) cc_final: 0.8235 (pt) REVERT: O 145 GLN cc_start: 0.7841 (mt0) cc_final: 0.6952 (mt0) REVERT: P 172 MET cc_start: 0.7369 (tpp) cc_final: 0.6088 (ptt) REVERT: R 172 MET cc_start: 0.7679 (tpp) cc_final: 0.6248 (ptt) REVERT: S 82 ASP cc_start: 0.7987 (m-30) cc_final: 0.7787 (m-30) REVERT: S 112 ARG cc_start: 0.8043 (mpt-90) cc_final: 0.7793 (mtt90) REVERT: S 172 MET cc_start: 0.7979 (tpp) cc_final: 0.6630 (ptt) REVERT: U 50 ILE cc_start: 0.8678 (mt) cc_final: 0.8175 (mt) REVERT: U 127 TYR cc_start: 0.8948 (t80) cc_final: 0.8569 (t80) REVERT: U 145 GLN cc_start: 0.7673 (mt0) cc_final: 0.6897 (mt0) REVERT: V 9 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6885 (mt-10) REVERT: V 67 ILE cc_start: 0.7573 (pp) cc_final: 0.7316 (pt) REVERT: V 121 ILE cc_start: 0.9531 (mt) cc_final: 0.9097 (mt) REVERT: V 172 MET cc_start: 0.7724 (tpp) cc_final: 0.6753 (ptt) REVERT: W 50 ILE cc_start: 0.8887 (mt) cc_final: 0.8666 (mt) REVERT: W 145 GLN cc_start: 0.7903 (mt0) cc_final: 0.7675 (mt0) REVERT: W 169 ARG cc_start: 0.7551 (ttp-110) cc_final: 0.6764 (tpt170) REVERT: W 183 MET cc_start: 0.7908 (mtm) cc_final: 0.7290 (mtp) REVERT: X 15 SER cc_start: 0.8283 (t) cc_final: 0.8031 (p) REVERT: X 54 ILE cc_start: 0.8825 (mm) cc_final: 0.8547 (mm) REVERT: X 145 GLN cc_start: 0.7747 (mt0) cc_final: 0.7493 (mt0) outliers start: 1 outliers final: 0 residues processed: 1065 average time/residue: 0.1367 time to fit residues: 219.3740 Evaluate side-chains 505 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.2980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 7 ASN ** M 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 GLN M 62 ASN ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN N 18 ASN N 42 ASN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 ASN N 182 ASN O 7 ASN ** O 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 ASN P 18 ASN P 42 ASN ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 ASN Q 7 ASN Q 42 ASN ** Q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 GLN Q 182 ASN R 42 ASN R 48 ASN ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 182 ASN S 7 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN T 42 ASN ** T 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 GLN ** T 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 182 ASN U 7 ASN ** U 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 182 ASN V 42 ASN V 48 ASN ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 109 GLN ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 182 ASN W 7 ASN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 182 ASN X 18 ASN X 48 ASN ** X 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.100222 restraints weight = 34737.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.102654 restraints weight = 17311.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.104231 restraints weight = 10454.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.105264 restraints weight = 7211.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105983 restraints weight = 5443.200| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18942 Z= 0.171 Angle : 0.821 10.862 25656 Z= 0.442 Chirality : 0.047 0.227 2754 Planarity : 0.005 0.031 3444 Dihedral : 7.704 44.872 2664 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.23 % Allowed : 20.25 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.88 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.14), residues: 2310 helix: -1.11 (0.15), residues: 888 sheet: -2.46 (0.41), residues: 144 loop : -2.66 (0.14), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 2 TYR 0.024 0.002 TYR W 136 PHE 0.032 0.002 PHE P 150 TRP 0.021 0.003 TRP T 137 Details of bonding type rmsd covalent geometry : bond 0.00374 (18942) covalent geometry : angle 0.82084 (25656) hydrogen bonds : bond 0.05158 ( 710) hydrogen bonds : angle 5.05265 ( 2115) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 566 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: M 5 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8193 (m-30) REVERT: M 112 ARG cc_start: 0.8471 (ptp-170) cc_final: 0.8180 (mpt-90) REVERT: M 161 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7860 (tm-30) REVERT: M 165 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7903 (t70) REVERT: M 172 MET cc_start: 0.7823 (tpp) cc_final: 0.6773 (ptt) REVERT: M 176 MET cc_start: 0.8050 (mmm) cc_final: 0.6788 (ptm) REVERT: M 184 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8732 (pp) REVERT: N 6 MET cc_start: 0.8506 (tpt) cc_final: 0.8215 (tpt) REVERT: N 55 GLN cc_start: 0.9102 (mp10) cc_final: 0.8516 (mp10) REVERT: N 68 THR cc_start: 0.8927 (t) cc_final: 0.8176 (p) REVERT: O 161 GLN cc_start: 0.8313 (tp40) cc_final: 0.7429 (tp40) REVERT: O 184 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8771 (pp) REVERT: P 49 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8491 (ttpp) REVERT: P 160 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8674 (tm) REVERT: P 164 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8564 (tm-30) REVERT: P 172 MET cc_start: 0.7926 (tpp) cc_final: 0.6285 (ptt) REVERT: P 184 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8607 (pp) REVERT: P 194 LEU cc_start: 0.9039 (mp) cc_final: 0.8797 (mp) REVERT: Q 19 ASP cc_start: 0.7842 (m-30) cc_final: 0.7536 (m-30) REVERT: Q 157 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7938 (tm-30) REVERT: Q 172 MET cc_start: 0.8292 (mmm) cc_final: 0.6868 (ptt) REVERT: R 29 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7914 (m) REVERT: R 172 MET cc_start: 0.7998 (tpp) cc_final: 0.6570 (ptt) REVERT: S 157 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7590 (tm-30) REVERT: S 162 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6689 (mp0) REVERT: S 172 MET cc_start: 0.8240 (tpp) cc_final: 0.6809 (ptt) REVERT: S 183 MET cc_start: 0.8148 (mtt) cc_final: 0.7915 (mtm) REVERT: T 29 VAL cc_start: 0.9132 (p) cc_final: 0.8894 (m) REVERT: T 64 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7685 (mt-10) REVERT: T 163 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7071 (tt0) REVERT: T 172 MET cc_start: 0.8496 (tpp) cc_final: 0.7077 (ptm) REVERT: T 187 ASP cc_start: 0.6826 (p0) cc_final: 0.6139 (p0) REVERT: U 19 ASP cc_start: 0.8127 (m-30) cc_final: 0.7856 (m-30) REVERT: U 145 GLN cc_start: 0.7895 (mt0) cc_final: 0.7490 (mt0) REVERT: U 172 MET cc_start: 0.8905 (tpp) cc_final: 0.8373 (tpp) REVERT: V 49 LYS cc_start: 0.9098 (tttp) cc_final: 0.8828 (tttm) REVERT: V 62 ASN cc_start: 0.8228 (t0) cc_final: 0.7872 (t0) REVERT: V 163 GLU cc_start: 0.7772 (tt0) cc_final: 0.7238 (tt0) REVERT: V 164 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8397 (tm-30) REVERT: V 172 MET cc_start: 0.8253 (tpp) cc_final: 0.6676 (ptt) REVERT: V 184 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8559 (pp) REVERT: V 194 LEU cc_start: 0.8890 (mp) cc_final: 0.8670 (mp) REVERT: W 169 ARG cc_start: 0.7950 (ttp-110) cc_final: 0.7196 (tpp-160) REVERT: W 172 MET cc_start: 0.8834 (tpp) cc_final: 0.8474 (tpp) REVERT: W 184 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8485 (pp) REVERT: X 55 GLN cc_start: 0.8939 (mp10) cc_final: 0.8697 (mp10) REVERT: X 172 MET cc_start: 0.8433 (tpp) cc_final: 0.6611 (ptt) outliers start: 85 outliers final: 34 residues processed: 623 average time/residue: 0.1135 time to fit residues: 113.9467 Evaluate side-chains 454 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 410 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 5 ASP Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 165 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 161 GLN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 148 ASN Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 49 LYS Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 108 SER Chi-restraints excluded: chain X residue 184 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 150 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 226 optimal weight: 0.0570 chunk 155 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 48 ASN M 55 GLN ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 ASN ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 ASN ** P 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN Q 55 GLN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 GLN S 109 GLN ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 55 GLN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 ASN W 53 GLN W 55 GLN ** X 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 147 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.097220 restraints weight = 35170.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099794 restraints weight = 16222.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101488 restraints weight = 9360.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102617 restraints weight = 6252.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103403 restraints weight = 4626.105| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18942 Z= 0.186 Angle : 0.724 7.523 25656 Z= 0.393 Chirality : 0.046 0.214 2754 Planarity : 0.004 0.038 3444 Dihedral : 6.893 42.940 2664 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.57 % Allowed : 21.54 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.97 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.15), residues: 2310 helix: -0.06 (0.16), residues: 936 sheet: -2.88 (0.44), residues: 108 loop : -2.52 (0.14), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG T 168 TYR 0.017 0.002 TYR X 136 PHE 0.027 0.002 PHE N 150 TRP 0.023 0.003 TRP Q 137 Details of bonding type rmsd covalent geometry : bond 0.00427 (18942) covalent geometry : angle 0.72359 (25656) hydrogen bonds : bond 0.04893 ( 710) hydrogen bonds : angle 4.54899 ( 2115) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 489 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: M 129 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8300 (mt-10) REVERT: M 157 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8398 (tm-30) REVERT: M 161 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7904 (tm-30) REVERT: M 163 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7699 (mt-10) REVERT: M 165 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8051 (t70) REVERT: M 181 TYR cc_start: 0.8122 (m-80) cc_final: 0.7852 (m-80) REVERT: N 55 GLN cc_start: 0.9175 (mp10) cc_final: 0.8715 (mp10) REVERT: N 68 THR cc_start: 0.9032 (t) cc_final: 0.8712 (p) REVERT: N 113 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8676 (p90) REVERT: O 77 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8939 (pp) REVERT: O 161 GLN cc_start: 0.8522 (tp40) cc_final: 0.8153 (tp40) REVERT: O 172 MET cc_start: 0.8913 (mmm) cc_final: 0.8512 (tpp) REVERT: P 49 LYS cc_start: 0.8975 (ttpp) cc_final: 0.8722 (ttpp) REVERT: P 164 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: P 172 MET cc_start: 0.8374 (tpp) cc_final: 0.6631 (ptt) REVERT: P 184 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8371 (pp) REVERT: P 194 LEU cc_start: 0.8987 (mp) cc_final: 0.8623 (mp) REVERT: Q 112 ARG cc_start: 0.7530 (mtp85) cc_final: 0.7182 (mtp180) REVERT: Q 184 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8965 (pp) REVERT: R 29 VAL cc_start: 0.8853 (p) cc_final: 0.8617 (m) REVERT: R 172 MET cc_start: 0.8300 (tpp) cc_final: 0.6624 (ptt) REVERT: S 13 GLU cc_start: 0.8392 (pt0) cc_final: 0.8011 (pm20) REVERT: S 70 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8374 (mt) REVERT: S 162 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6708 (mp0) REVERT: S 172 MET cc_start: 0.8606 (tpp) cc_final: 0.7005 (ptt) REVERT: S 183 MET cc_start: 0.8100 (mtt) cc_final: 0.7829 (mtm) REVERT: T 64 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7519 (mt-10) REVERT: T 95 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8819 (mt) REVERT: U 88 MET cc_start: 0.8043 (mtp) cc_final: 0.7628 (mtp) REVERT: U 105 ASP cc_start: 0.8867 (m-30) cc_final: 0.8592 (t0) REVERT: U 112 ARG cc_start: 0.8032 (mpt-90) cc_final: 0.7739 (mtt90) REVERT: U 145 GLN cc_start: 0.8417 (mt0) cc_final: 0.7854 (mt0) REVERT: U 172 MET cc_start: 0.9060 (tpp) cc_final: 0.8418 (tpp) REVERT: U 184 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8780 (pp) REVERT: V 55 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8757 (mm110) REVERT: V 132 GLU cc_start: 0.8989 (tp30) cc_final: 0.8628 (tp30) REVERT: V 157 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7916 (tm-30) REVERT: V 172 MET cc_start: 0.8458 (tpp) cc_final: 0.6923 (ptt) REVERT: W 10 THR cc_start: 0.8066 (t) cc_final: 0.7120 (t) REVERT: W 145 GLN cc_start: 0.8215 (mt0) cc_final: 0.7968 (mt0) REVERT: W 169 ARG cc_start: 0.8327 (ttp-110) cc_final: 0.7121 (tpp-160) REVERT: W 184 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8749 (pp) REVERT: W 185 ASP cc_start: 0.7710 (m-30) cc_final: 0.7465 (m-30) REVERT: X 10 THR cc_start: 0.8848 (t) cc_final: 0.8599 (t) REVERT: X 157 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7719 (tm-30) REVERT: X 163 GLU cc_start: 0.8237 (tt0) cc_final: 0.8012 (tt0) REVERT: X 170 LEU cc_start: 0.8882 (mm) cc_final: 0.8615 (tp) REVERT: X 172 MET cc_start: 0.8603 (tpp) cc_final: 0.6861 (ptt) outliers start: 112 outliers final: 57 residues processed: 571 average time/residue: 0.1091 time to fit residues: 100.9898 Evaluate side-chains 463 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 396 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 165 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 63 ILE Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 78 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 161 optimal weight: 0.4980 chunk 203 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 48 ASN M 53 GLN M 109 GLN ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 ASN O 48 ASN ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 55 GLN U 62 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 ASN W 55 GLN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.097893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.088162 restraints weight = 36042.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.090598 restraints weight = 16790.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.092204 restraints weight = 9788.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.093268 restraints weight = 6575.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.093994 restraints weight = 4860.058| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18942 Z= 0.201 Angle : 0.711 7.785 25656 Z= 0.386 Chirality : 0.046 0.205 2754 Planarity : 0.004 0.039 3444 Dihedral : 6.617 42.273 2664 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 6.92 % Allowed : 20.60 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.93 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.16), residues: 2310 helix: 0.51 (0.16), residues: 936 sheet: -2.58 (0.47), residues: 108 loop : -2.40 (0.14), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 149 TYR 0.021 0.002 TYR Q 136 PHE 0.027 0.002 PHE P 150 TRP 0.018 0.003 TRP W 137 Details of bonding type rmsd covalent geometry : bond 0.00461 (18942) covalent geometry : angle 0.71114 (25656) hydrogen bonds : bond 0.04475 ( 710) hydrogen bonds : angle 4.46752 ( 2115) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 439 time to evaluate : 0.710 Fit side-chains REVERT: M 161 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8108 (tm-30) REVERT: M 163 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7782 (mt-10) REVERT: M 165 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8087 (t70) REVERT: M 172 MET cc_start: 0.8712 (tpp) cc_final: 0.6410 (ptt) REVERT: M 184 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8872 (pp) REVERT: N 68 THR cc_start: 0.9183 (t) cc_final: 0.8964 (p) REVERT: N 113 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8675 (p90) REVERT: N 172 MET cc_start: 0.8363 (tpp) cc_final: 0.8148 (mmm) REVERT: O 136 TYR cc_start: 0.9198 (t80) cc_final: 0.8736 (t80) REVERT: O 145 GLN cc_start: 0.8001 (mt0) cc_final: 0.7597 (mt0) REVERT: O 172 MET cc_start: 0.8824 (mmm) cc_final: 0.8346 (tpp) REVERT: P 49 LYS cc_start: 0.9175 (ttpp) cc_final: 0.8917 (ttpp) REVERT: P 75 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8201 (m) REVERT: P 172 MET cc_start: 0.8473 (tpp) cc_final: 0.7037 (ptt) REVERT: P 184 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8598 (pp) REVERT: P 194 LEU cc_start: 0.8966 (mp) cc_final: 0.8564 (mp) REVERT: Q 112 ARG cc_start: 0.7536 (mtp85) cc_final: 0.7206 (mtp180) REVERT: Q 163 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7695 (mt-10) REVERT: Q 176 MET cc_start: 0.8406 (mmm) cc_final: 0.7412 (ptm) REVERT: Q 184 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8717 (pp) REVERT: Q 185 ASP cc_start: 0.7646 (m-30) cc_final: 0.7334 (m-30) REVERT: R 39 ASP cc_start: 0.8404 (m-30) cc_final: 0.7894 (m-30) REVERT: R 172 MET cc_start: 0.8330 (tpp) cc_final: 0.6918 (ptt) REVERT: S 13 GLU cc_start: 0.8309 (pt0) cc_final: 0.7878 (pm20) REVERT: S 70 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8245 (mt) REVERT: S 172 MET cc_start: 0.8767 (tpp) cc_final: 0.8408 (tpp) REVERT: T 64 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7788 (mt-10) REVERT: T 87 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9072 (tm) REVERT: T 95 ILE cc_start: 0.9237 (mt) cc_final: 0.8936 (mt) REVERT: T 163 GLU cc_start: 0.7797 (tt0) cc_final: 0.7594 (tt0) REVERT: U 13 GLU cc_start: 0.8276 (pt0) cc_final: 0.7945 (pm20) REVERT: U 172 MET cc_start: 0.9093 (tpp) cc_final: 0.8507 (tpp) REVERT: U 176 MET cc_start: 0.8486 (mmt) cc_final: 0.7078 (ptm) REVERT: U 184 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8772 (pp) REVERT: V 124 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9103 (tt) REVERT: V 157 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7832 (tm-30) REVERT: V 163 GLU cc_start: 0.8074 (tt0) cc_final: 0.7588 (tt0) REVERT: V 172 MET cc_start: 0.8445 (tpp) cc_final: 0.6829 (ptt) REVERT: V 184 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8723 (pp) REVERT: V 194 LEU cc_start: 0.8854 (mp) cc_final: 0.8570 (mp) REVERT: W 10 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.7541 (t) REVERT: W 13 GLU cc_start: 0.8059 (pt0) cc_final: 0.7763 (pm20) REVERT: W 19 ASP cc_start: 0.8254 (m-30) cc_final: 0.7904 (m-30) REVERT: W 53 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8765 (tp40) REVERT: W 145 GLN cc_start: 0.8247 (mt0) cc_final: 0.7885 (mt0) REVERT: W 169 ARG cc_start: 0.8340 (ttp-110) cc_final: 0.6997 (tpp-160) REVERT: W 172 MET cc_start: 0.8871 (mmm) cc_final: 0.8339 (tpp) REVERT: W 184 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8717 (pp) REVERT: W 185 ASP cc_start: 0.7661 (m-30) cc_final: 0.7433 (m-30) REVERT: X 163 GLU cc_start: 0.8092 (tt0) cc_final: 0.7823 (tt0) REVERT: X 172 MET cc_start: 0.8610 (tpp) cc_final: 0.7011 (ptt) outliers start: 139 outliers final: 78 residues processed: 543 average time/residue: 0.1083 time to fit residues: 95.6329 Evaluate side-chains 477 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 386 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 165 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 191 SER Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 161 GLN Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 161 GLN Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain S residue 5 ASP Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 63 ILE Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 78 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 156 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 164 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 7 ASN M 109 GLN ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 93 GLN W 161 GLN ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.088541 restraints weight = 35643.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.090944 restraints weight = 16663.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.092522 restraints weight = 9695.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.093581 restraints weight = 6496.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.094266 restraints weight = 4793.604| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18942 Z= 0.176 Angle : 0.681 7.942 25656 Z= 0.367 Chirality : 0.045 0.195 2754 Planarity : 0.003 0.031 3444 Dihedral : 6.400 41.331 2664 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 6.37 % Allowed : 21.74 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.93 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.16), residues: 2310 helix: 0.94 (0.16), residues: 930 sheet: -2.34 (0.50), residues: 96 loop : -2.27 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 2 TYR 0.022 0.001 TYR M 136 PHE 0.024 0.002 PHE P 150 TRP 0.014 0.002 TRP P 137 Details of bonding type rmsd covalent geometry : bond 0.00404 (18942) covalent geometry : angle 0.68140 (25656) hydrogen bonds : bond 0.04161 ( 710) hydrogen bonds : angle 4.34554 ( 2115) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 419 time to evaluate : 0.703 Fit side-chains REVERT: M 161 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8131 (tm-30) REVERT: M 163 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7740 (mt-10) REVERT: M 165 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8100 (t70) REVERT: M 172 MET cc_start: 0.8492 (tpp) cc_final: 0.6585 (ptt) REVERT: M 184 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8689 (pp) REVERT: N 87 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8993 (tm) REVERT: N 113 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8660 (p90) REVERT: N 130 MET cc_start: 0.8745 (mmm) cc_final: 0.8310 (mtp) REVERT: N 172 MET cc_start: 0.8399 (tpp) cc_final: 0.8036 (mmm) REVERT: O 145 GLN cc_start: 0.8049 (mt0) cc_final: 0.7819 (mt0) REVERT: O 163 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: O 172 MET cc_start: 0.8805 (mmm) cc_final: 0.8399 (tpp) REVERT: P 75 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8182 (m) REVERT: P 109 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8761 (mm-40) REVERT: P 164 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: P 172 MET cc_start: 0.8479 (tpp) cc_final: 0.6972 (ptt) REVERT: Q 163 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7661 (mt-10) REVERT: Q 176 MET cc_start: 0.8384 (mmm) cc_final: 0.7569 (ptm) REVERT: Q 184 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8727 (pp) REVERT: Q 185 ASP cc_start: 0.7615 (m-30) cc_final: 0.7346 (m-30) REVERT: R 39 ASP cc_start: 0.8468 (m-30) cc_final: 0.7959 (m-30) REVERT: R 172 MET cc_start: 0.8241 (tpp) cc_final: 0.6961 (ptt) REVERT: S 13 GLU cc_start: 0.8313 (pt0) cc_final: 0.7870 (pm20) REVERT: S 70 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8202 (mt) REVERT: S 172 MET cc_start: 0.8769 (tpp) cc_final: 0.8378 (tpp) REVERT: T 64 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7848 (mt-10) REVERT: T 95 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8937 (mt) REVERT: T 112 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7809 (ptp-110) REVERT: U 13 GLU cc_start: 0.8270 (pt0) cc_final: 0.8069 (pm20) REVERT: U 62 ASN cc_start: 0.9032 (t0) cc_final: 0.8624 (t0) REVERT: U 172 MET cc_start: 0.8967 (tpp) cc_final: 0.8535 (tpp) REVERT: U 184 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8761 (pp) REVERT: V 172 MET cc_start: 0.8479 (tpp) cc_final: 0.7081 (ptt) REVERT: V 184 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8476 (pp) REVERT: V 194 LEU cc_start: 0.8849 (mp) cc_final: 0.8364 (mp) REVERT: W 10 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.7754 (m) REVERT: W 19 ASP cc_start: 0.7808 (m-30) cc_final: 0.7564 (m-30) REVERT: W 53 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8657 (tp40) REVERT: W 62 ASN cc_start: 0.8891 (t0) cc_final: 0.8685 (t0) REVERT: W 145 GLN cc_start: 0.8266 (mt0) cc_final: 0.7939 (mt0) REVERT: W 169 ARG cc_start: 0.8359 (ttp-110) cc_final: 0.6963 (tpp-160) REVERT: W 172 MET cc_start: 0.8770 (mmm) cc_final: 0.8230 (tpp) REVERT: X 163 GLU cc_start: 0.8024 (tt0) cc_final: 0.7790 (tt0) REVERT: X 172 MET cc_start: 0.8618 (tpp) cc_final: 0.7033 (ptt) outliers start: 128 outliers final: 81 residues processed: 517 average time/residue: 0.1142 time to fit residues: 96.8276 Evaluate side-chains 493 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 398 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 165 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 163 GLU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 91 SER Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain S residue 5 ASP Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 MET Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 112 ARG Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 63 ILE Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 112 ARG Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 93 GLN Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain X residue 184 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 114 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 93 GLN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 147 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.087362 restraints weight = 35793.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.089756 restraints weight = 16798.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.091322 restraints weight = 9772.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.092344 restraints weight = 6538.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.093067 restraints weight = 4868.151| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 47 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18942 Z= 0.188 Angle : 0.684 7.891 25656 Z= 0.368 Chirality : 0.045 0.199 2754 Planarity : 0.003 0.034 3444 Dihedral : 6.343 41.131 2664 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 6.82 % Allowed : 22.59 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.93 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.16), residues: 2310 helix: 1.17 (0.16), residues: 912 sheet: -2.19 (0.68), residues: 60 loop : -2.15 (0.15), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 168 TYR 0.017 0.001 TYR O 136 PHE 0.022 0.002 PHE P 150 TRP 0.013 0.002 TRP M 137 Details of bonding type rmsd covalent geometry : bond 0.00433 (18942) covalent geometry : angle 0.68430 (25656) hydrogen bonds : bond 0.04145 ( 710) hydrogen bonds : angle 4.32317 ( 2115) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 417 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: M 161 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8250 (tm-30) REVERT: M 163 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7774 (mt-10) REVERT: M 172 MET cc_start: 0.8400 (tpp) cc_final: 0.6379 (ptt) REVERT: M 184 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8800 (pp) REVERT: N 87 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9089 (tm) REVERT: N 113 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8638 (p90) REVERT: O 163 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: O 172 MET cc_start: 0.8798 (mmm) cc_final: 0.8383 (tpp) REVERT: P 6 MET cc_start: 0.9233 (tpp) cc_final: 0.8620 (tpp) REVERT: P 77 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8986 (pp) REVERT: P 111 ASP cc_start: 0.9513 (t0) cc_final: 0.8949 (t0) REVERT: P 172 MET cc_start: 0.8480 (tpp) cc_final: 0.6960 (ptt) REVERT: P 184 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8676 (pp) REVERT: P 194 LEU cc_start: 0.8736 (mp) cc_final: 0.8511 (mp) REVERT: Q 163 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7691 (mt-10) REVERT: Q 176 MET cc_start: 0.8287 (mmm) cc_final: 0.7527 (ptm) REVERT: Q 184 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8899 (pp) REVERT: R 39 ASP cc_start: 0.8496 (m-30) cc_final: 0.7963 (m-30) REVERT: R 172 MET cc_start: 0.8223 (tpp) cc_final: 0.6930 (ptt) REVERT: S 70 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8157 (mt) REVERT: S 161 GLN cc_start: 0.8479 (tm130) cc_final: 0.7856 (tm-30) REVERT: S 172 MET cc_start: 0.8800 (tpp) cc_final: 0.8395 (tpp) REVERT: T 95 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8988 (mt) REVERT: T 112 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7864 (ptp-110) REVERT: U 112 ARG cc_start: 0.8437 (mtt90) cc_final: 0.8145 (mtt-85) REVERT: U 172 MET cc_start: 0.8791 (tpp) cc_final: 0.8521 (tpp) REVERT: U 176 MET cc_start: 0.8229 (mmt) cc_final: 0.7353 (ptm) REVERT: U 184 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8561 (pp) REVERT: V 172 MET cc_start: 0.8424 (tpp) cc_final: 0.6867 (ptt) REVERT: V 184 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8559 (pp) REVERT: V 194 LEU cc_start: 0.8868 (mp) cc_final: 0.8441 (mp) REVERT: W 13 GLU cc_start: 0.8421 (pm20) cc_final: 0.8206 (pm20) REVERT: W 19 ASP cc_start: 0.7765 (m-30) cc_final: 0.7558 (m-30) REVERT: W 75 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8123 (p) REVERT: W 169 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.6906 (tpp-160) REVERT: W 184 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8777 (pp) REVERT: X 163 GLU cc_start: 0.8070 (tt0) cc_final: 0.7758 (tt0) REVERT: X 164 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8527 (tm-30) REVERT: X 172 MET cc_start: 0.8647 (tpp) cc_final: 0.7220 (ptt) outliers start: 137 outliers final: 90 residues processed: 519 average time/residue: 0.1072 time to fit residues: 91.8643 Evaluate side-chains 487 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 382 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 161 GLN Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 194 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 163 GLU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 59 TRP Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 MET Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 112 ARG Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain X residue 161 GLN Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain X residue 184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 9 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 85 optimal weight: 0.0980 chunk 62 optimal weight: 0.4980 chunk 210 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN ** N 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 ASN Q 109 GLN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 145 GLN U 145 GLN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 147 ASN W 7 ASN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.098683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.089345 restraints weight = 35632.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.091757 restraints weight = 16687.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.093316 restraints weight = 9696.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.094367 restraints weight = 6450.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.095071 restraints weight = 4729.945| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 47 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.7294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18942 Z= 0.147 Angle : 0.665 8.034 25656 Z= 0.358 Chirality : 0.044 0.191 2754 Planarity : 0.003 0.040 3444 Dihedral : 6.170 40.886 2664 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.97 % Allowed : 23.83 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.84 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.17), residues: 2310 helix: 1.51 (0.16), residues: 888 sheet: -2.35 (0.66), residues: 60 loop : -2.04 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 168 TYR 0.014 0.001 TYR U 80 PHE 0.018 0.002 PHE P 150 TRP 0.011 0.002 TRP Q 59 Details of bonding type rmsd covalent geometry : bond 0.00336 (18942) covalent geometry : angle 0.66513 (25656) hydrogen bonds : bond 0.03817 ( 710) hydrogen bonds : angle 4.19158 ( 2115) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 407 time to evaluate : 0.798 Fit side-chains REVERT: M 53 GLN cc_start: 0.9138 (tp40) cc_final: 0.8142 (tm-30) REVERT: M 140 THR cc_start: 0.9594 (t) cc_final: 0.9362 (t) REVERT: M 161 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8203 (tm-30) REVERT: M 163 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7810 (mt-10) REVERT: M 172 MET cc_start: 0.8452 (tpp) cc_final: 0.6433 (ptt) REVERT: M 184 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8751 (pp) REVERT: N 87 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9042 (tm) REVERT: N 113 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8582 (p90) REVERT: N 130 MET cc_start: 0.8757 (mmm) cc_final: 0.8274 (mtp) REVERT: O 136 TYR cc_start: 0.9147 (t80) cc_final: 0.8560 (t80) REVERT: O 145 GLN cc_start: 0.8223 (mt0) cc_final: 0.7859 (mt0) REVERT: O 163 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: O 172 MET cc_start: 0.8791 (mmm) cc_final: 0.8382 (tpp) REVERT: P 21 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9189 (mm) REVERT: P 111 ASP cc_start: 0.9482 (t0) cc_final: 0.8950 (t0) REVERT: P 164 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: P 172 MET cc_start: 0.8446 (tpp) cc_final: 0.7010 (ptt) REVERT: P 184 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8717 (pp) REVERT: P 194 LEU cc_start: 0.8780 (mp) cc_final: 0.8419 (mp) REVERT: Q 95 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8674 (mt) REVERT: Q 109 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7968 (mp10) REVERT: Q 176 MET cc_start: 0.8188 (mmm) cc_final: 0.7456 (ptm) REVERT: Q 184 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8829 (pp) REVERT: R 39 ASP cc_start: 0.8060 (m-30) cc_final: 0.7643 (m-30) REVERT: R 172 MET cc_start: 0.8137 (tpp) cc_final: 0.6975 (ptt) REVERT: R 176 MET cc_start: 0.8326 (mmt) cc_final: 0.6912 (ptm) REVERT: S 172 MET cc_start: 0.8686 (tpp) cc_final: 0.8151 (tpp) REVERT: T 95 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8972 (mt) REVERT: T 112 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7763 (ptp-110) REVERT: U 13 GLU cc_start: 0.8564 (pm20) cc_final: 0.8316 (pm20) REVERT: U 62 ASN cc_start: 0.9027 (t0) cc_final: 0.8561 (t0) REVERT: U 112 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7988 (mtt180) REVERT: U 172 MET cc_start: 0.9021 (tpp) cc_final: 0.8451 (tpp) REVERT: U 176 MET cc_start: 0.8133 (mmt) cc_final: 0.7334 (ptm) REVERT: U 184 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8799 (pp) REVERT: V 172 MET cc_start: 0.8385 (tpp) cc_final: 0.7111 (ptt) REVERT: V 184 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8212 (pp) REVERT: V 194 LEU cc_start: 0.8908 (mp) cc_final: 0.8503 (mp) REVERT: W 13 GLU cc_start: 0.8311 (pm20) cc_final: 0.7970 (pm20) REVERT: W 75 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8088 (p) REVERT: W 145 GLN cc_start: 0.8267 (mt0) cc_final: 0.8004 (mt0) REVERT: W 169 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.6804 (tpp-160) REVERT: W 184 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8704 (pp) REVERT: X 164 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8202 (tm-30) REVERT: X 172 MET cc_start: 0.8586 (tpp) cc_final: 0.7240 (ptt) outliers start: 120 outliers final: 82 residues processed: 506 average time/residue: 0.1108 time to fit residues: 92.1094 Evaluate side-chains 489 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 391 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 163 GLU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 59 TRP Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 5 ASP Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 59 TRP Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 MET Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 112 ARG Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 77 LEU Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain X residue 184 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 214 optimal weight: 0.2980 chunk 110 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 222 optimal weight: 0.6980 chunk 203 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 147 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.089527 restraints weight = 35640.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091929 restraints weight = 16796.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.093502 restraints weight = 9739.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.094521 restraints weight = 6484.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.095237 restraints weight = 4791.702| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.7430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18942 Z= 0.145 Angle : 0.662 7.773 25656 Z= 0.356 Chirality : 0.044 0.190 2754 Planarity : 0.003 0.040 3444 Dihedral : 6.013 40.054 2664 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.92 % Allowed : 23.63 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.84 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.17), residues: 2310 helix: 1.66 (0.16), residues: 912 sheet: -2.40 (0.66), residues: 60 loop : -1.98 (0.15), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 168 TYR 0.013 0.001 TYR U 80 PHE 0.017 0.002 PHE P 150 TRP 0.011 0.002 TRP Q 59 Details of bonding type rmsd covalent geometry : bond 0.00330 (18942) covalent geometry : angle 0.66164 (25656) hydrogen bonds : bond 0.03778 ( 710) hydrogen bonds : angle 4.11931 ( 2115) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 401 time to evaluate : 0.642 Fit side-chains REVERT: M 53 GLN cc_start: 0.9151 (tp40) cc_final: 0.8136 (tm-30) REVERT: M 161 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8212 (tm-30) REVERT: M 163 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7730 (mt-10) REVERT: M 172 MET cc_start: 0.8461 (tpp) cc_final: 0.6409 (ptt) REVERT: M 184 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8831 (pp) REVERT: N 42 ASN cc_start: 0.8369 (t0) cc_final: 0.7946 (t0) REVERT: N 87 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9078 (tm) REVERT: N 113 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8596 (p90) REVERT: O 49 LYS cc_start: 0.8968 (tttp) cc_final: 0.8644 (tttm) REVERT: O 145 GLN cc_start: 0.8408 (mt0) cc_final: 0.7956 (mt0) REVERT: O 163 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: P 21 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9205 (mm) REVERT: P 77 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8968 (pp) REVERT: P 87 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9178 (tm) REVERT: P 111 ASP cc_start: 0.9405 (t0) cc_final: 0.8790 (t0) REVERT: P 164 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: P 172 MET cc_start: 0.8393 (tpp) cc_final: 0.6714 (ptt) REVERT: P 184 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8698 (pp) REVERT: P 194 LEU cc_start: 0.8780 (mp) cc_final: 0.8399 (mp) REVERT: Q 109 GLN cc_start: 0.8305 (mm-40) cc_final: 0.8064 (mp10) REVERT: Q 176 MET cc_start: 0.8091 (mmm) cc_final: 0.7406 (ptm) REVERT: Q 184 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8737 (pp) REVERT: R 172 MET cc_start: 0.8140 (tpp) cc_final: 0.6159 (ptt) REVERT: S 157 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8072 (tm-30) REVERT: S 172 MET cc_start: 0.8708 (tpp) cc_final: 0.8498 (mmm) REVERT: T 95 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8980 (mt) REVERT: T 172 MET cc_start: 0.8466 (tpp) cc_final: 0.8245 (mpp) REVERT: U 13 GLU cc_start: 0.8632 (pm20) cc_final: 0.8393 (pm20) REVERT: U 62 ASN cc_start: 0.9013 (t0) cc_final: 0.8528 (t0) REVERT: U 112 ARG cc_start: 0.8353 (mtt90) cc_final: 0.8021 (mtt180) REVERT: U 172 MET cc_start: 0.8957 (tpp) cc_final: 0.8507 (tpp) REVERT: U 184 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8952 (pp) REVERT: V 50 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8463 (mm) REVERT: V 64 GLU cc_start: 0.7784 (mp0) cc_final: 0.7547 (mp0) REVERT: V 157 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7684 (tm-30) REVERT: V 172 MET cc_start: 0.8361 (tpp) cc_final: 0.6996 (ptt) REVERT: V 184 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8371 (pp) REVERT: V 194 LEU cc_start: 0.8890 (mp) cc_final: 0.8450 (mp) REVERT: W 53 GLN cc_start: 0.9093 (tp40) cc_final: 0.8560 (tm-30) REVERT: W 75 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.8133 (p) REVERT: W 169 ARG cc_start: 0.8477 (ttp-110) cc_final: 0.6818 (tpp-160) REVERT: W 184 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8776 (pp) REVERT: X 111 ASP cc_start: 0.9393 (t0) cc_final: 0.8839 (t0) REVERT: X 130 MET cc_start: 0.8090 (mtp) cc_final: 0.7873 (mmm) REVERT: X 164 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: X 172 MET cc_start: 0.8647 (tpp) cc_final: 0.7153 (ptt) outliers start: 119 outliers final: 90 residues processed: 500 average time/residue: 0.1061 time to fit residues: 87.5883 Evaluate side-chains 478 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 371 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 5 ASP Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 161 GLN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 194 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 163 GLU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 59 TRP Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 91 SER Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 5 ASP Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 59 TRP Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 MET Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 77 LEU Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 50 ILE Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain X residue 164 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 174 optimal weight: 0.0030 chunk 0 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 189 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 ASN ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 93 GLN ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 ASN ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.088629 restraints weight = 35625.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.091032 restraints weight = 16796.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.092609 restraints weight = 9744.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.093600 restraints weight = 6486.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.094320 restraints weight = 4815.889| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.7549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18942 Z= 0.153 Angle : 0.666 7.793 25656 Z= 0.359 Chirality : 0.044 0.190 2754 Planarity : 0.003 0.037 3444 Dihedral : 5.943 40.185 2664 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.02 % Allowed : 23.88 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.80 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2310 helix: 1.55 (0.16), residues: 942 sheet: -2.56 (0.66), residues: 60 loop : -1.95 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 168 TYR 0.018 0.001 TYR W 178 PHE 0.022 0.002 PHE W 189 TRP 0.010 0.002 TRP Q 59 Details of bonding type rmsd covalent geometry : bond 0.00351 (18942) covalent geometry : angle 0.66614 (25656) hydrogen bonds : bond 0.03782 ( 710) hydrogen bonds : angle 4.11878 ( 2115) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 387 time to evaluate : 0.719 Fit side-chains REVERT: M 53 GLN cc_start: 0.9145 (tp40) cc_final: 0.8162 (tm-30) REVERT: M 161 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8196 (tm-30) REVERT: M 163 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7749 (mt-10) REVERT: M 172 MET cc_start: 0.8453 (tpp) cc_final: 0.6355 (ptt) REVERT: M 184 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8795 (pp) REVERT: N 42 ASN cc_start: 0.8366 (t0) cc_final: 0.7977 (t0) REVERT: N 87 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9106 (tm) REVERT: N 113 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8595 (p90) REVERT: O 49 LYS cc_start: 0.8976 (tttp) cc_final: 0.8674 (tttm) REVERT: O 145 GLN cc_start: 0.8421 (mt0) cc_final: 0.7914 (mt0) REVERT: O 163 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: O 172 MET cc_start: 0.8831 (mmm) cc_final: 0.8395 (tpp) REVERT: P 21 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9197 (mm) REVERT: P 77 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9006 (pp) REVERT: P 87 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9095 (tm) REVERT: P 111 ASP cc_start: 0.9435 (t0) cc_final: 0.8853 (t0) REVERT: P 164 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: P 172 MET cc_start: 0.8415 (tpp) cc_final: 0.6791 (ptt) REVERT: P 184 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8670 (pp) REVERT: P 194 LEU cc_start: 0.8785 (mp) cc_final: 0.8404 (mp) REVERT: Q 109 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8060 (mp10) REVERT: Q 176 MET cc_start: 0.8093 (mmm) cc_final: 0.7460 (ptm) REVERT: Q 184 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8779 (pp) REVERT: R 88 MET cc_start: 0.8802 (mmm) cc_final: 0.8578 (mtp) REVERT: R 130 MET cc_start: 0.8275 (mtp) cc_final: 0.7973 (mtp) REVERT: R 172 MET cc_start: 0.7808 (tpp) cc_final: 0.6437 (ptt) REVERT: T 95 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8945 (mt) REVERT: T 172 MET cc_start: 0.8500 (tpp) cc_final: 0.6701 (ptt) REVERT: U 13 GLU cc_start: 0.8627 (pm20) cc_final: 0.8396 (pm20) REVERT: U 62 ASN cc_start: 0.9064 (t0) cc_final: 0.8517 (t0) REVERT: U 112 ARG cc_start: 0.8417 (mtt90) cc_final: 0.8061 (mtt180) REVERT: U 172 MET cc_start: 0.8803 (tpp) cc_final: 0.8382 (tpp) REVERT: U 184 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8854 (pp) REVERT: V 50 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8541 (mm) REVERT: V 172 MET cc_start: 0.8412 (tpp) cc_final: 0.7113 (ptt) REVERT: V 184 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8397 (pp) REVERT: V 194 LEU cc_start: 0.8810 (mp) cc_final: 0.8369 (mp) REVERT: W 75 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8141 (p) REVERT: W 169 ARG cc_start: 0.8497 (ttp-110) cc_final: 0.6794 (tpp-160) REVERT: W 184 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8788 (pp) REVERT: X 130 MET cc_start: 0.8167 (mtp) cc_final: 0.7933 (mmm) REVERT: X 164 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: X 172 MET cc_start: 0.8589 (tpp) cc_final: 0.7157 (ptt) outliers start: 121 outliers final: 96 residues processed: 489 average time/residue: 0.1073 time to fit residues: 87.0392 Evaluate side-chains 484 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 371 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 5 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 161 GLN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 194 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 163 GLU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 59 TRP Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 5 ASP Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 59 TRP Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 MET Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 77 LEU Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 50 ILE Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain X residue 161 GLN Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain X residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 137 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 ASN ** N 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.096832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.087345 restraints weight = 35550.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.089717 restraints weight = 16938.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.091279 restraints weight = 9936.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.092306 restraints weight = 6684.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092986 restraints weight = 4960.313| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.7633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18942 Z= 0.176 Angle : 0.685 7.909 25656 Z= 0.368 Chirality : 0.045 0.177 2754 Planarity : 0.003 0.050 3444 Dihedral : 6.013 41.130 2664 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 6.02 % Allowed : 24.18 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.88 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.17), residues: 2310 helix: 1.52 (0.16), residues: 954 sheet: -2.70 (0.65), residues: 60 loop : -1.93 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 168 TYR 0.025 0.001 TYR X 96 PHE 0.016 0.002 PHE Q 150 TRP 0.012 0.002 TRP N 137 Details of bonding type rmsd covalent geometry : bond 0.00407 (18942) covalent geometry : angle 0.68454 (25656) hydrogen bonds : bond 0.03970 ( 710) hydrogen bonds : angle 4.17661 ( 2115) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 381 time to evaluate : 0.686 Fit side-chains REVERT: M 53 GLN cc_start: 0.9095 (tp40) cc_final: 0.8247 (tm-30) REVERT: M 161 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8136 (tm-30) REVERT: M 163 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7738 (mt-10) REVERT: M 165 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8082 (t70) REVERT: M 172 MET cc_start: 0.8512 (tpp) cc_final: 0.6472 (ptt) REVERT: M 184 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8789 (pp) REVERT: N 42 ASN cc_start: 0.8471 (t0) cc_final: 0.8063 (t0) REVERT: N 87 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9172 (tm) REVERT: N 113 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8620 (p90) REVERT: O 49 LYS cc_start: 0.9010 (tttp) cc_final: 0.8520 (tttm) REVERT: O 145 GLN cc_start: 0.8426 (mt0) cc_final: 0.7931 (mt0) REVERT: O 163 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: O 172 MET cc_start: 0.8767 (mmm) cc_final: 0.8324 (tpp) REVERT: P 21 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9230 (mm) REVERT: P 87 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9094 (tm) REVERT: P 111 ASP cc_start: 0.9447 (t0) cc_final: 0.8834 (t0) REVERT: P 172 MET cc_start: 0.8445 (tpp) cc_final: 0.6836 (ptt) REVERT: P 184 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8767 (pp) REVERT: Q 176 MET cc_start: 0.7960 (mmm) cc_final: 0.7424 (ptm) REVERT: Q 184 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8834 (pp) REVERT: R 39 ASP cc_start: 0.8551 (m-30) cc_final: 0.7965 (m-30) REVERT: R 88 MET cc_start: 0.8699 (mmm) cc_final: 0.8297 (mtp) REVERT: R 130 MET cc_start: 0.8327 (mtp) cc_final: 0.8087 (mtp) REVERT: R 172 MET cc_start: 0.7854 (tpp) cc_final: 0.6580 (ptt) REVERT: S 161 GLN cc_start: 0.8473 (tm130) cc_final: 0.7858 (tm-30) REVERT: S 172 MET cc_start: 0.8768 (mmm) cc_final: 0.8430 (tpp) REVERT: T 95 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8981 (mt) REVERT: T 172 MET cc_start: 0.8521 (tpp) cc_final: 0.6719 (ptt) REVERT: U 161 GLN cc_start: 0.8230 (tm130) cc_final: 0.7741 (tm-30) REVERT: U 172 MET cc_start: 0.8819 (tpp) cc_final: 0.8423 (tpp) REVERT: U 184 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8722 (pp) REVERT: V 50 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8562 (mm) REVERT: V 172 MET cc_start: 0.8457 (tpp) cc_final: 0.7214 (ptt) REVERT: V 184 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8338 (pp) REVERT: V 194 LEU cc_start: 0.8797 (mp) cc_final: 0.8433 (mp) REVERT: W 75 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8128 (p) REVERT: W 172 MET cc_start: 0.8757 (mmm) cc_final: 0.7273 (ptt) REVERT: W 184 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8817 (pp) REVERT: X 111 ASP cc_start: 0.9363 (t0) cc_final: 0.8754 (t0) REVERT: X 130 MET cc_start: 0.8223 (mtp) cc_final: 0.8013 (mmm) REVERT: X 164 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: X 172 MET cc_start: 0.8581 (tpp) cc_final: 0.7174 (ptt) outliers start: 121 outliers final: 92 residues processed: 482 average time/residue: 0.1024 time to fit residues: 82.3283 Evaluate side-chains 470 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 362 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 5 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 165 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 161 GLN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 163 GLU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 59 TRP Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 91 SER Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 59 TRP Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 77 LEU Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 50 ILE Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain X residue 108 SER Chi-restraints excluded: chain X residue 161 GLN Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain X residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 49 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 209 optimal weight: 0.5980 chunk 195 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 91 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 147 ASN ** N 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.098107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.088730 restraints weight = 35705.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.091122 restraints weight = 16911.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.092678 restraints weight = 9861.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.093717 restraints weight = 6584.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.094420 restraints weight = 4831.853| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.7722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18942 Z= 0.153 Angle : 0.672 7.906 25656 Z= 0.360 Chirality : 0.044 0.177 2754 Planarity : 0.003 0.049 3444 Dihedral : 5.940 41.260 2664 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.67 % Allowed : 24.78 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.84 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2310 helix: 1.61 (0.16), residues: 948 sheet: -2.80 (0.65), residues: 60 loop : -1.87 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 168 TYR 0.022 0.001 TYR X 96 PHE 0.023 0.002 PHE W 189 TRP 0.010 0.002 TRP N 137 Details of bonding type rmsd covalent geometry : bond 0.00352 (18942) covalent geometry : angle 0.67201 (25656) hydrogen bonds : bond 0.03753 ( 710) hydrogen bonds : angle 4.13034 ( 2115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3033.31 seconds wall clock time: 53 minutes 33.04 seconds (3213.04 seconds total)