Starting phenix.real_space_refine on Thu Mar 5 01:11:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y9x_10740/03_2026/6y9x_10740.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y9x_10740/03_2026/6y9x_10740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y9x_10740/03_2026/6y9x_10740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y9x_10740/03_2026/6y9x_10740.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y9x_10740/03_2026/6y9x_10740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y9x_10740/03_2026/6y9x_10740.map" } resolution = 4.4 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 11607 2.51 5 N 3207 2.21 5 O 3466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s 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: 18418 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1132 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 134} Chain: "B" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "C" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "G" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "H" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "J" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1258 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "N" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 584 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "Y" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1132 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 134} Chain: "d" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "e" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "j" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 584 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "k" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Time building chain proxies: 4.05, per 1000 atoms: 0.22 Number of scatterers: 18418 At special positions: 0 Unit cell: (136.74, 179.14, 106, 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 138 16.00 O 3466 8.00 N 3207 7.00 C 11607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.04 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS G 198 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS H 198 " - pdb=" SG CYS H 218 " distance=2.03 Simple disulfide: pdb=" SG CYS N 198 " - pdb=" SG CYS N 218 " distance=2.04 Simple disulfide: pdb=" SG CYS d 198 " - pdb=" SG CYS d 218 " distance=2.03 Simple disulfide: pdb=" SG CYS e 198 " - pdb=" SG CYS e 218 " distance=2.03 Simple disulfide: pdb=" SG CYS j 198 " - pdb=" SG CYS j 218 " distance=2.03 Simple disulfide: pdb=" SG CYS k 198 " - pdb=" SG CYS k 218 " distance=2.03 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: 1.58 Conformation dependent library (CDL) restraints added in 773.9 milliseconds 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB ARG C 18 " Number of C-beta restraints generated: 4400 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 8 sheets defined 64.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.527A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.791A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.596A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.804A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 36 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 removed outlier: 4.006A pdb=" N ALA C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 160 through 174 Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.537A pdb=" N GLU C 187 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.870A pdb=" N CYS C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.675A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 83 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.700A pdb=" N GLN D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 146 removed outlier: 3.602A pdb=" N ARG D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.765A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 145 Processing helix chain 'G' and resid 160 through 175 Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.897A pdb=" N TRP G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'G' and resid 210 through 218 Processing helix chain 'H' and resid 16 through 31 Processing helix chain 'H' and resid 35 through 44 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 62 through 84 Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'H' and resid 160 through 175 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.895A pdb=" N TRP H 184 " --> pdb=" O GLU H 180 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 206 Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'J' and resid 29 through 42 Processing helix chain 'J' and resid 119 through 123 Processing helix chain 'J' and resid 135 through 144 removed outlier: 4.122A pdb=" N ARG J 144 " --> pdb=" O GLU J 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 153 removed outlier: 3.526A pdb=" N ILE N 153 " --> pdb=" O ILE N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 175 Processing helix chain 'N' and resid 178 through 190 removed outlier: 3.791A pdb=" N TRP N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N 187 " --> pdb=" O ASN N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 206 removed outlier: 3.593A pdb=" N LEU N 205 " --> pdb=" O ILE N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 removed outlier: 3.800A pdb=" N CYS N 218 " --> pdb=" O MET N 214 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 30 removed outlier: 3.675A pdb=" N LEU Y 20 " --> pdb=" O SER Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 44 Processing helix chain 'Y' and resid 48 through 58 Processing helix chain 'Y' and resid 62 through 83 Processing helix chain 'Y' and resid 100 through 105 Processing helix chain 'Y' and resid 110 through 118 removed outlier: 3.699A pdb=" N GLN Y 114 " --> pdb=" O THR Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 126 through 146 removed outlier: 3.601A pdb=" N ARG Y 132 " --> pdb=" O GLU Y 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 30 removed outlier: 3.674A pdb=" N LEU d 20 " --> pdb=" O SER d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 44 Processing helix chain 'd' and resid 48 through 58 Processing helix chain 'd' and resid 62 through 83 Processing helix chain 'd' and resid 100 through 105 Processing helix chain 'd' and resid 110 through 118 removed outlier: 3.700A pdb=" N GLN d 114 " --> pdb=" O THR d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 146 removed outlier: 3.603A pdb=" N ARG d 132 " --> pdb=" O GLU d 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 174 Processing helix chain 'd' and resid 178 through 193 removed outlier: 4.765A pdb=" N LEU d 190 " --> pdb=" O THR d 186 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 206 Processing helix chain 'd' and resid 210 through 218 Processing helix chain 'e' and resid 16 through 31 Processing helix chain 'e' and resid 35 through 44 Processing helix chain 'e' and resid 48 through 58 Processing helix chain 'e' and resid 62 through 84 Processing helix chain 'e' and resid 100 through 105 Processing helix chain 'e' and resid 110 through 120 Processing helix chain 'e' and resid 125 through 145 Processing helix chain 'e' and resid 149 through 153 Processing helix chain 'e' and resid 160 through 175 Processing helix chain 'e' and resid 178 through 189 removed outlier: 3.692A pdb=" N GLU e 187 " --> pdb=" O ASN e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 195 through 206 removed outlier: 3.906A pdb=" N ILE e 201 " --> pdb=" O ASP e 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 210 through 218 removed outlier: 3.510A pdb=" N MET e 214 " --> pdb=" O THR e 210 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 153 Processing helix chain 'j' and resid 160 through 175 Processing helix chain 'j' and resid 178 through 189 removed outlier: 3.690A pdb=" N GLU j 187 " --> pdb=" O ASN j 183 " (cutoff:3.500A) Processing helix chain 'j' and resid 195 through 206 removed outlier: 3.904A pdb=" N ILE j 201 " --> pdb=" O ASP j 197 " (cutoff:3.500A) Processing helix chain 'j' and resid 210 through 218 removed outlier: 3.511A pdb=" N MET j 214 " --> pdb=" O THR j 210 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 31 removed outlier: 3.524A pdb=" N LEU k 20 " --> pdb=" O SER k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 36 through 44 Processing helix chain 'k' and resid 48 through 58 Processing helix chain 'k' and resid 62 through 84 Processing helix chain 'k' and resid 100 through 105 Processing helix chain 'k' and resid 110 through 119 Processing helix chain 'k' and resid 125 through 145 Processing helix chain 'k' and resid 160 through 176 Processing helix chain 'k' and resid 179 through 193 removed outlier: 4.359A pdb=" N LEU k 190 " --> pdb=" O THR k 186 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL k 191 " --> pdb=" O GLU k 187 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN k 193 " --> pdb=" O LEU k 189 " (cutoff:3.500A) Processing helix chain 'k' and resid 195 through 204 Processing helix chain 'k' and resid 210 through 219 removed outlier: 3.923A pdb=" N CYS k 218 " --> pdb=" O MET k 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.668A pdb=" N VAL B 3 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 11 " --> pdb=" O VAL B 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.600A pdb=" N VAL C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 11 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'H' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'J' and resid 53 through 57 removed outlier: 4.395A pdb=" N ILE J 97 " --> pdb=" O CYS J 115 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET J 100 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL J 128 " --> pdb=" O MET J 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER J 21 " --> pdb=" O LYS J 133 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL J 12 " --> pdb=" O PRO J 16 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY J 18 " --> pdb=" O ILE J 10 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP J 160 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA J 11 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE J 158 " --> pdb=" O ALA J 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 2 through 3 removed outlier: 3.665A pdb=" N VAL e 3 " --> pdb=" O VAL e 11 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL e 11 " --> pdb=" O VAL e 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'k' and resid 3 through 4 removed outlier: 3.540A pdb=" N VAL k 3 " --> pdb=" O VAL k 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL k 11 " --> pdb=" O VAL k 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 1037 hydrogen bonds defined for protein. 3081 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: 2.50 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.44: 7785 1.44 - 1.67: 10784 1.67 - 1.90: 252 1.90 - 2.14: 0 2.14 - 2.37: 3 Bond restraints: 18824 Sorted by residual: bond pdb=" C PRO C 147 " pdb=" N THR C 148 " ideal model delta sigma weight residual 1.331 2.237 -0.906 1.23e-02 6.61e+03 5.43e+03 bond pdb=" CA ARG C 18 " pdb=" C ARG C 18 " ideal model delta sigma weight residual 1.522 2.366 -0.844 1.37e-02 5.33e+03 3.80e+03 bond pdb=" N ARG C 18 " pdb=" CA ARG C 18 " ideal model delta sigma weight residual 1.456 2.274 -0.818 1.33e-02 5.65e+03 3.78e+03 bond pdb=" C HIS e 84 " pdb=" N PRO e 85 " ideal model delta sigma weight residual 1.330 1.514 -0.184 1.22e-02 6.72e+03 2.28e+02 bond pdb=" CD2 HIS J 54 " pdb=" NE2 HIS J 54 " ideal model delta sigma weight residual 1.374 1.296 0.078 1.10e-02 8.26e+03 5.06e+01 ... (remaining 18819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.81: 25549 9.81 - 19.63: 14 19.63 - 29.44: 3 29.44 - 39.25: 0 39.25 - 49.07: 1 Bond angle restraints: 25567 Sorted by residual: angle pdb=" N ARG C 18 " pdb=" CA ARG C 18 " pdb=" C ARG C 18 " ideal model delta sigma weight residual 113.23 64.16 49.07 1.24e+00 6.50e-01 1.57e+03 angle pdb=" CA ARG C 18 " pdb=" C ARG C 18 " pdb=" O ARG C 18 " ideal model delta sigma weight residual 119.27 92.00 27.27 1.17e+00 7.31e-01 5.43e+02 angle pdb=" CA ARG C 18 " pdb=" C ARG C 18 " pdb=" N THR C 19 " ideal model delta sigma weight residual 118.21 145.56 -27.35 1.36e+00 5.41e-01 4.04e+02 angle pdb=" O PRO C 147 " pdb=" C PRO C 147 " pdb=" N THR C 148 " ideal model delta sigma weight residual 122.30 108.80 13.50 1.36e+00 5.41e-01 9.85e+01 angle pdb=" C ARG e 97 " pdb=" CA ARG e 97 " pdb=" CB ARG e 97 " ideal model delta sigma weight residual 111.30 133.23 -21.93 2.23e+00 2.01e-01 9.67e+01 ... (remaining 25562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10634 17.94 - 35.87: 711 35.87 - 53.81: 180 53.81 - 71.75: 19 71.75 - 89.69: 13 Dihedral angle restraints: 11557 sinusoidal: 4764 harmonic: 6793 Sorted by residual: dihedral pdb=" C ARG e 97 " pdb=" N ARG e 97 " pdb=" CA ARG e 97 " pdb=" CB ARG e 97 " ideal model delta harmonic sigma weight residual -122.60 -163.07 40.47 0 2.50e+00 1.60e-01 2.62e+02 dihedral pdb=" N ARG e 97 " pdb=" C ARG e 97 " pdb=" CA ARG e 97 " pdb=" CB ARG e 97 " ideal model delta harmonic sigma weight residual 122.80 158.61 -35.81 0 2.50e+00 1.60e-01 2.05e+02 dihedral pdb=" CB CYS B 198 " pdb=" SG CYS B 198 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -134.76 48.76 1 1.00e+01 1.00e-02 3.27e+01 ... (remaining 11554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.947: 2846 0.947 - 1.893: 1 1.893 - 2.839: 0 2.839 - 3.786: 0 3.786 - 4.732: 1 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA ARG C 18 " pdb=" N ARG C 18 " pdb=" C ARG C 18 " pdb=" CB ARG C 18 " both_signs ideal model delta sigma weight residual False 2.51 7.24 -4.73 2.00e-01 2.50e+01 5.60e+02 chirality pdb=" CA ARG e 97 " pdb=" N ARG e 97 " pdb=" C ARG e 97 " pdb=" CB ARG e 97 " both_signs ideal model delta sigma weight residual False 2.51 0.89 1.62 2.00e-01 2.50e+01 6.54e+01 chirality pdb=" CA PRO J 30 " pdb=" N PRO J 30 " pdb=" C PRO J 30 " pdb=" CB PRO J 30 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 2845 not shown) Planarity restraints: 3345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 60 " 0.124 2.00e-02 2.50e+03 7.90e-02 1.09e+02 pdb=" CG PHE J 60 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE J 60 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 PHE J 60 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE J 60 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE J 60 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE J 60 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 147 " -0.064 2.00e-02 2.50e+03 9.94e-02 9.89e+01 pdb=" C PRO C 147 " 0.171 2.00e-02 2.50e+03 pdb=" O PRO C 147 " -0.068 2.00e-02 2.50e+03 pdb=" N THR C 148 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG e 97 " 0.039 2.00e-02 2.50e+03 7.89e-02 6.23e+01 pdb=" C ARG e 97 " -0.136 2.00e-02 2.50e+03 pdb=" O ARG e 97 " 0.053 2.00e-02 2.50e+03 pdb=" N GLU e 98 " 0.044 2.00e-02 2.50e+03 ... (remaining 3342 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.06: 6 2.06 - 2.77: 3418 2.77 - 3.48: 26032 3.48 - 4.19: 40619 4.19 - 4.90: 71418 Nonbonded interactions: 141493 Sorted by model distance: nonbonded pdb=" OE1 GLN G 7 " pdb=" NE2 GLN k 9 " model vdw 1.344 3.120 nonbonded pdb=" OE1 GLN D 192 " pdb=" CD1 LEU H 151 " model vdw 1.514 3.460 nonbonded pdb=" CG2 VAL G 181 " pdb=" OE1 GLU d 180 " model vdw 1.586 3.460 nonbonded pdb=" OE1 GLN G 192 " pdb=" CD1 LEU d 151 " model vdw 1.748 3.460 nonbonded pdb=" CD GLN G 7 " pdb=" NE2 GLN k 9 " model vdw 1.920 3.350 ... (remaining 141488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'Y' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'd' selection = chain 'e' selection = chain 'k' } ncs_group { reference = chain 'N' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.780 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 0.906 18834 Z= 0.921 Angle : 1.068 49.068 25587 Z= 0.726 Chirality : 0.108 4.732 2848 Planarity : 0.007 0.099 3345 Dihedral : 13.054 89.686 7127 Min Nonbonded Distance : 1.344 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.99 % Rotamer: Outliers : 0.45 % Allowed : 3.00 % Favored : 96.55 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.16), residues: 2336 helix: -0.33 (0.13), residues: 1402 sheet: -1.56 (0.60), residues: 65 loop : -0.85 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 37 TYR 0.100 0.003 TYR J 48 PHE 0.124 0.009 PHE J 60 TRP 0.019 0.001 TRP J 121 HIS 0.009 0.001 HIS J 70 Details of bonding type rmsd covalent geometry : bond 0.01239 (18824) covalent geometry : angle 1.06771 (25567) SS BOND : bond 0.00304 ( 10) SS BOND : angle 0.96509 ( 20) hydrogen bonds : bond 0.13584 ( 1037) hydrogen bonds : angle 5.13706 ( 3081) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1139 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.9407 (m-30) cc_final: 0.9091 (m-30) REVERT: A 56 LEU cc_start: 0.9588 (mt) cc_final: 0.9325 (mt) REVERT: A 96 MET cc_start: -0.1411 (mpp) cc_final: -0.1634 (mmt) REVERT: B 2 ILE cc_start: 0.7622 (pt) cc_final: 0.7366 (tt) REVERT: B 24 VAL cc_start: 0.9458 (t) cc_final: 0.9226 (p) REVERT: B 25 LYS cc_start: 0.9575 (mttt) cc_final: 0.9080 (ttmt) REVERT: B 35 GLU cc_start: 0.9493 (pm20) cc_final: 0.9099 (mp0) REVERT: B 39 MET cc_start: 0.9296 (tpp) cc_final: 0.9067 (tpp) REVERT: B 66 MET cc_start: 0.8800 (mmt) cc_final: 0.8173 (mmm) REVERT: B 67 GLN cc_start: 0.8821 (tp40) cc_final: 0.8398 (mm-40) REVERT: B 68 MET cc_start: 0.9518 (mtp) cc_final: 0.9024 (mtt) REVERT: B 75 GLU cc_start: 0.9166 (tt0) cc_final: 0.8956 (tt0) REVERT: B 114 GLN cc_start: 0.8780 (mt0) cc_final: 0.8516 (mt0) REVERT: B 118 MET cc_start: 0.8863 (mtm) cc_final: 0.8467 (ptp) REVERT: B 131 LYS cc_start: 0.9563 (ttmt) cc_final: 0.9147 (mmmt) REVERT: C 113 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8806 (tt0) REVERT: C 129 ILE cc_start: 0.9095 (mt) cc_final: 0.8043 (mt) REVERT: C 131 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8117 (mtpt) REVERT: C 187 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8897 (mp0) REVERT: C 189 LEU cc_start: 0.9100 (mm) cc_final: 0.8739 (mp) REVERT: D 27 VAL cc_start: 0.9377 (p) cc_final: 0.8620 (m) REVERT: D 35 GLU cc_start: 0.9093 (pm20) cc_final: 0.8539 (pm20) REVERT: D 55 MET cc_start: 0.9194 (mtp) cc_final: 0.8977 (ttm) REVERT: D 56 LEU cc_start: 0.9715 (mt) cc_final: 0.9315 (mt) REVERT: D 118 MET cc_start: 0.9032 (mtm) cc_final: 0.8543 (ppp) REVERT: D 130 TYR cc_start: 0.9155 (t80) cc_final: 0.8813 (t80) REVERT: D 140 LYS cc_start: 0.9600 (mttt) cc_final: 0.9301 (tptp) REVERT: D 141 ILE cc_start: 0.9212 (mt) cc_final: 0.8795 (mt) REVERT: G 23 TRP cc_start: 0.9468 (t-100) cc_final: 0.8839 (t-100) REVERT: G 35 GLU cc_start: 0.9512 (pm20) cc_final: 0.9206 (pm20) REVERT: G 39 MET cc_start: 0.9541 (ttm) cc_final: 0.9291 (ttm) REVERT: G 57 ASN cc_start: 0.9590 (m-40) cc_final: 0.9367 (m110) REVERT: G 58 THR cc_start: 0.9434 (p) cc_final: 0.9125 (p) REVERT: G 96 MET cc_start: 0.0872 (mpp) cc_final: -0.1168 (mtt) REVERT: G 111 LEU cc_start: 0.8486 (tp) cc_final: 0.8217 (mp) REVERT: G 141 ILE cc_start: 0.9550 (mt) cc_final: 0.9316 (mt) REVERT: G 152 ASP cc_start: 0.8923 (m-30) cc_final: 0.8632 (p0) REVERT: G 186 THR cc_start: 0.7960 (t) cc_final: 0.7708 (t) REVERT: G 199 LYS cc_start: 0.8953 (tttp) cc_final: 0.8696 (ttmt) REVERT: G 214 MET cc_start: 0.9364 (mtm) cc_final: 0.8335 (tpt) REVERT: H 39 MET cc_start: 0.8553 (ttm) cc_final: 0.8118 (tpt) REVERT: H 70 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8591 (ptpp) REVERT: H 135 ILE cc_start: 0.9569 (mt) cc_final: 0.9140 (pt) REVERT: H 139 ASN cc_start: 0.9158 (m-40) cc_final: 0.8824 (m-40) REVERT: J 34 GLU cc_start: 0.9506 (tp30) cc_final: 0.9115 (tp30) REVERT: J 115 CYS cc_start: 0.8642 (m) cc_final: 0.8037 (m) REVERT: J 120 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8737 (pm20) REVERT: J 129 PHE cc_start: 0.7261 (p90) cc_final: 0.5511 (p90) REVERT: J 161 CYS cc_start: 0.5318 (p) cc_final: 0.4957 (p) REVERT: N 189 LEU cc_start: 0.8913 (mm) cc_final: 0.8712 (mm) REVERT: Y 13 GLN cc_start: 0.8983 (tt0) cc_final: 0.8733 (pm20) REVERT: Y 21 ASN cc_start: 0.9541 (t0) cc_final: 0.9122 (t0) REVERT: Y 25 LYS cc_start: 0.9585 (tttt) cc_final: 0.9328 (mtpp) REVERT: Y 49 PRO cc_start: 0.9450 (Cg_exo) cc_final: 0.9213 (Cg_endo) REVERT: Y 52 LEU cc_start: 0.9691 (mt) cc_final: 0.9263 (mp) REVERT: Y 104 ILE cc_start: 0.7685 (tt) cc_final: 0.7202 (pt) REVERT: Y 110 THR cc_start: 0.9234 (t) cc_final: 0.8948 (t) REVERT: Y 114 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8663 (mm-40) REVERT: Y 117 TRP cc_start: 0.7666 (m-10) cc_final: 0.6995 (m-10) REVERT: Y 131 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8727 (tptt) REVERT: Y 139 ASN cc_start: 0.9600 (m-40) cc_final: 0.9222 (m110) REVERT: d 39 MET cc_start: 0.7384 (ttm) cc_final: 0.7071 (tpt) REVERT: d 67 GLN cc_start: 0.9152 (tp-100) cc_final: 0.8875 (mt0) REVERT: d 68 MET cc_start: 0.8221 (mtp) cc_final: 0.8001 (mtp) REVERT: d 130 TYR cc_start: 0.6904 (t80) cc_final: 0.6532 (t80) REVERT: d 139 ASN cc_start: 0.9541 (m-40) cc_final: 0.9254 (m-40) REVERT: d 140 LYS cc_start: 0.9348 (mttt) cc_final: 0.9100 (tptp) REVERT: d 162 ARG cc_start: 0.8611 (mtt180) cc_final: 0.8375 (tpt-90) REVERT: d 163 ASP cc_start: 0.8555 (m-30) cc_final: 0.8347 (t0) REVERT: e 35 GLU cc_start: 0.9478 (pm20) cc_final: 0.8983 (pp20) REVERT: e 39 MET cc_start: 0.9551 (tpp) cc_final: 0.9287 (tpp) REVERT: e 51 ASP cc_start: 0.9267 (m-30) cc_final: 0.8866 (m-30) REVERT: e 66 MET cc_start: 0.8748 (mmm) cc_final: 0.8494 (mmm) REVERT: e 74 ASN cc_start: 0.9583 (m-40) cc_final: 0.9269 (m110) REVERT: e 79 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8492 (pp20) REVERT: e 104 ILE cc_start: 0.8897 (mt) cc_final: 0.8620 (mt) REVERT: e 114 GLN cc_start: 0.8259 (mt0) cc_final: 0.8051 (mt0) REVERT: e 173 ARG cc_start: 0.8552 (ttt180) cc_final: 0.8320 (tpm170) REVERT: e 178 SER cc_start: 0.8082 (p) cc_final: 0.6969 (t) REVERT: j 213 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9179 (mt-10) REVERT: k 21 ASN cc_start: 0.9536 (m110) cc_final: 0.9325 (t0) REVERT: k 52 LEU cc_start: 0.9680 (mt) cc_final: 0.9367 (mt) REVERT: k 67 GLN cc_start: 0.9275 (tp40) cc_final: 0.9035 (tp-100) REVERT: k 68 MET cc_start: 0.9334 (mtp) cc_final: 0.9133 (mtt) REVERT: k 83 VAL cc_start: 0.9195 (p) cc_final: 0.8798 (p) REVERT: k 96 MET cc_start: 0.5134 (ttm) cc_final: 0.4393 (ptp) REVERT: k 129 ILE cc_start: 0.9525 (mt) cc_final: 0.8870 (tt) REVERT: k 159 GLU cc_start: 0.8064 (tt0) cc_final: 0.7829 (tt0) REVERT: k 173 ARG cc_start: 0.9376 (ttt180) cc_final: 0.8935 (ttm170) outliers start: 9 outliers final: 2 residues processed: 1144 average time/residue: 0.1640 time to fit residues: 265.8876 Evaluate side-chains 699 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 696 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 40.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 0.5980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN B 53 ASN B 179 GLN B 183 ASN B 219 GLN C 53 ASN C 219 GLN D 4 GLN D 95 GLN D 179 GLN G 4 GLN H 4 GLN H 193 ASN J 108 ASN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 GLN Y 4 GLN Y 67 GLN d 4 GLN d 95 GLN e 53 ASN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 219 GLN k 9 GLN k 21 ASN k 53 ASN ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.109556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.083842 restraints weight = 70139.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.086241 restraints weight = 49929.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.088009 restraints weight = 38547.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.089268 restraints weight = 31533.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.090298 restraints weight = 27073.703| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18834 Z= 0.160 Angle : 0.663 7.348 25587 Z= 0.347 Chirality : 0.046 0.239 2848 Planarity : 0.005 0.089 3345 Dihedral : 4.131 26.171 2500 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.25 % Allowed : 5.24 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2338 helix: 0.27 (0.13), residues: 1442 sheet: -1.21 (0.68), residues: 59 loop : -0.60 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 97 TYR 0.016 0.002 TYR D 169 PHE 0.025 0.002 PHE B 161 TRP 0.024 0.002 TRP Y 133 HIS 0.004 0.001 HIS k 62 Details of bonding type rmsd covalent geometry : bond 0.00345 (18824) covalent geometry : angle 0.66205 (25567) SS BOND : bond 0.00207 ( 10) SS BOND : angle 1.10134 ( 20) hydrogen bonds : bond 0.04595 ( 1037) hydrogen bonds : angle 4.45842 ( 3081) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 879 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.9497 (t-100) cc_final: 0.9238 (t-100) REVERT: A 40 PHE cc_start: 0.9610 (t80) cc_final: 0.9241 (t80) REVERT: A 41 SER cc_start: 0.9499 (m) cc_final: 0.9161 (t) REVERT: A 45 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7999 (mm-30) REVERT: A 50 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8812 (tm-30) REVERT: A 51 ASP cc_start: 0.9292 (m-30) cc_final: 0.9066 (m-30) REVERT: A 71 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8800 (tm-30) REVERT: A 113 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8802 (mt-10) REVERT: B 21 ASN cc_start: 0.9553 (t0) cc_final: 0.9343 (t0) REVERT: B 24 VAL cc_start: 0.9562 (t) cc_final: 0.9129 (p) REVERT: B 25 LYS cc_start: 0.9583 (mttt) cc_final: 0.9138 (ttmt) REVERT: B 74 ASN cc_start: 0.9368 (m-40) cc_final: 0.9086 (m110) REVERT: B 129 ILE cc_start: 0.9423 (pt) cc_final: 0.8677 (pt) REVERT: B 131 LYS cc_start: 0.9513 (ttmt) cc_final: 0.9273 (mmmt) REVERT: C 53 ASN cc_start: 0.9316 (m-40) cc_final: 0.8938 (m110) REVERT: C 62 HIS cc_start: 0.8947 (m-70) cc_final: 0.8571 (m90) REVERT: C 131 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8139 (mtpt) REVERT: C 187 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8935 (mp0) REVERT: C 189 LEU cc_start: 0.9137 (mm) cc_final: 0.8830 (mp) REVERT: C 215 MET cc_start: 0.8822 (mtm) cc_final: 0.8581 (mtm) REVERT: D 48 THR cc_start: 0.9410 (t) cc_final: 0.9146 (t) REVERT: D 56 LEU cc_start: 0.9529 (mt) cc_final: 0.9263 (mt) REVERT: D 117 TRP cc_start: 0.8326 (m-10) cc_final: 0.8113 (m-10) REVERT: D 130 TYR cc_start: 0.9124 (t80) cc_final: 0.8890 (t80) REVERT: D 131 LYS cc_start: 0.8978 (tttt) cc_final: 0.8569 (tttt) REVERT: D 140 LYS cc_start: 0.9548 (mttt) cc_final: 0.9319 (tptp) REVERT: D 141 ILE cc_start: 0.8967 (mt) cc_final: 0.8760 (mt) REVERT: D 163 ASP cc_start: 0.8629 (m-30) cc_final: 0.8383 (m-30) REVERT: D 164 TYR cc_start: 0.8007 (t80) cc_final: 0.7682 (t80) REVERT: D 193 ASN cc_start: 0.9227 (m-40) cc_final: 0.8019 (p0) REVERT: D 215 MET cc_start: 0.7850 (ttt) cc_final: 0.7482 (ttm) REVERT: G 23 TRP cc_start: 0.9429 (t-100) cc_final: 0.9186 (t-100) REVERT: G 35 GLU cc_start: 0.9375 (pm20) cc_final: 0.8978 (pm20) REVERT: G 39 MET cc_start: 0.9533 (ttm) cc_final: 0.9266 (ttm) REVERT: G 57 ASN cc_start: 0.9558 (m-40) cc_final: 0.9323 (m110) REVERT: G 96 MET cc_start: 0.1441 (mpp) cc_final: -0.0734 (mtt) REVERT: G 131 LYS cc_start: 0.9423 (ttmt) cc_final: 0.9151 (mttt) REVERT: G 161 PHE cc_start: 0.7879 (t80) cc_final: 0.7374 (t80) REVERT: G 187 GLU cc_start: 0.9100 (pt0) cc_final: 0.8557 (pt0) REVERT: G 215 MET cc_start: 0.8729 (mmt) cc_final: 0.8157 (mmm) REVERT: H 30 LYS cc_start: 0.6707 (tptt) cc_final: 0.6425 (mttt) REVERT: H 129 ILE cc_start: 0.8893 (tt) cc_final: 0.8216 (tt) REVERT: H 133 TRP cc_start: 0.8605 (m-10) cc_final: 0.7990 (m-10) REVERT: H 135 ILE cc_start: 0.9519 (mt) cc_final: 0.9285 (mt) REVERT: H 161 PHE cc_start: 0.7868 (t80) cc_final: 0.7439 (t80) REVERT: J 10 ILE cc_start: 0.9204 (tp) cc_final: 0.8638 (tp) REVERT: J 24 LEU cc_start: 0.8618 (mp) cc_final: 0.8055 (mm) REVERT: J 36 PHE cc_start: 0.8292 (t80) cc_final: 0.8080 (t80) REVERT: J 48 TYR cc_start: 0.8374 (m-10) cc_final: 0.7759 (m-10) REVERT: J 100 MET cc_start: 0.5641 (mmm) cc_final: 0.4540 (tpt) REVERT: J 122 LEU cc_start: 0.8202 (mt) cc_final: 0.7842 (mp) REVERT: J 129 PHE cc_start: 0.7401 (p90) cc_final: 0.6488 (p90) REVERT: J 157 THR cc_start: 0.9441 (t) cc_final: 0.9230 (m) REVERT: J 158 ILE cc_start: 0.8810 (mp) cc_final: 0.8598 (tt) REVERT: J 161 CYS cc_start: 0.3701 (p) cc_final: 0.3055 (p) REVERT: N 150 ILE cc_start: 0.7723 (tp) cc_final: 0.7467 (tp) REVERT: N 153 ILE cc_start: 0.8693 (mt) cc_final: 0.8492 (mp) REVERT: Y 5 ASN cc_start: 0.8146 (t0) cc_final: 0.7813 (t0) REVERT: Y 13 GLN cc_start: 0.9011 (tt0) cc_final: 0.8740 (pm20) REVERT: Y 20 LEU cc_start: 0.9593 (pp) cc_final: 0.9285 (pp) REVERT: Y 45 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8402 (mm-30) REVERT: Y 49 PRO cc_start: 0.9405 (Cg_exo) cc_final: 0.8980 (Cg_endo) REVERT: Y 55 MET cc_start: 0.9453 (ttm) cc_final: 0.9095 (ttm) REVERT: Y 56 LEU cc_start: 0.9456 (mt) cc_final: 0.9132 (mt) REVERT: Y 63 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8693 (mm-40) REVERT: Y 131 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8304 (tptt) REVERT: Y 139 ASN cc_start: 0.9522 (m-40) cc_final: 0.9223 (m110) REVERT: d 63 GLN cc_start: 0.6438 (tt0) cc_final: 0.6172 (pm20) REVERT: d 114 GLN cc_start: 0.8745 (mp-120) cc_final: 0.7512 (pt0) REVERT: d 130 TYR cc_start: 0.7187 (t80) cc_final: 0.6392 (t80) REVERT: d 133 TRP cc_start: 0.8499 (m-10) cc_final: 0.7644 (m-10) REVERT: d 139 ASN cc_start: 0.9567 (m-40) cc_final: 0.9281 (m-40) REVERT: d 140 LYS cc_start: 0.9429 (mttt) cc_final: 0.9075 (tptp) REVERT: d 144 MET cc_start: 0.8499 (tmm) cc_final: 0.8168 (tmm) REVERT: d 203 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8675 (mttm) REVERT: e 35 GLU cc_start: 0.9473 (pm20) cc_final: 0.9233 (pm20) REVERT: e 39 MET cc_start: 0.9477 (tpp) cc_final: 0.9051 (tpp) REVERT: e 55 MET cc_start: 0.8772 (ttt) cc_final: 0.8492 (ttt) REVERT: e 57 ASN cc_start: 0.9287 (m-40) cc_final: 0.8930 (m110) REVERT: e 66 MET cc_start: 0.9050 (mmm) cc_final: 0.8686 (mmm) REVERT: e 70 LYS cc_start: 0.9227 (ptpp) cc_final: 0.8965 (ptpt) REVERT: e 74 ASN cc_start: 0.9592 (m-40) cc_final: 0.9291 (m-40) REVERT: e 79 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8445 (pp20) REVERT: e 104 ILE cc_start: 0.9116 (mt) cc_final: 0.8894 (mt) REVERT: e 138 LEU cc_start: 0.9573 (mt) cc_final: 0.9367 (mt) REVERT: e 178 SER cc_start: 0.7340 (p) cc_final: 0.6778 (t) REVERT: j 155 GLN cc_start: 0.5752 (mt0) cc_final: 0.5486 (pm20) REVERT: k 25 LYS cc_start: 0.9681 (ptmt) cc_final: 0.9343 (ptmm) REVERT: k 57 ASN cc_start: 0.9556 (m-40) cc_final: 0.9265 (m110) REVERT: k 70 LYS cc_start: 0.9115 (mtmt) cc_final: 0.8871 (mtmm) REVERT: k 96 MET cc_start: 0.4879 (ttm) cc_final: 0.4321 (ptp) REVERT: k 173 ARG cc_start: 0.8872 (ttt180) cc_final: 0.8568 (ttp80) outliers start: 5 outliers final: 2 residues processed: 882 average time/residue: 0.1479 time to fit residues: 188.1975 Evaluate side-chains 667 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 665 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 21 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 31 optimal weight: 30.0000 chunk 78 optimal weight: 40.0000 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN B 176 GLN G 114 GLN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 GLN N 155 GLN d 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.104728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.079529 restraints weight = 72209.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.081767 restraints weight = 51466.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.083454 restraints weight = 39836.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.084709 restraints weight = 32605.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.085654 restraints weight = 27927.572| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18834 Z= 0.194 Angle : 0.687 10.250 25587 Z= 0.360 Chirality : 0.046 0.258 2848 Planarity : 0.005 0.058 3345 Dihedral : 4.422 29.874 2500 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.10 % Allowed : 5.04 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2338 helix: 0.40 (0.13), residues: 1440 sheet: -1.59 (0.59), residues: 68 loop : -0.39 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 97 TYR 0.025 0.002 TYR C 130 PHE 0.015 0.002 PHE N 168 TRP 0.024 0.002 TRP d 23 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00417 (18824) covalent geometry : angle 0.68623 (25567) SS BOND : bond 0.00626 ( 10) SS BOND : angle 1.13587 ( 20) hydrogen bonds : bond 0.04503 ( 1037) hydrogen bonds : angle 4.51193 ( 3081) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 831 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.9676 (t80) cc_final: 0.9054 (t80) REVERT: A 41 SER cc_start: 0.9511 (m) cc_final: 0.9027 (t) REVERT: A 50 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8997 (tm-30) REVERT: A 51 ASP cc_start: 0.9387 (m-30) cc_final: 0.9066 (m-30) REVERT: A 52 LEU cc_start: 0.9796 (mm) cc_final: 0.9536 (mm) REVERT: A 55 MET cc_start: 0.9278 (ttt) cc_final: 0.8971 (tmm) REVERT: A 56 LEU cc_start: 0.9550 (mt) cc_final: 0.9323 (mt) REVERT: A 57 ASN cc_start: 0.9645 (m110) cc_final: 0.9422 (m110) REVERT: A 68 MET cc_start: 0.8798 (mtt) cc_final: 0.8458 (mtt) REVERT: A 71 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8737 (tm-30) REVERT: A 113 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8819 (mt-10) REVERT: A 119 THR cc_start: 0.8399 (t) cc_final: 0.7609 (t) REVERT: B 21 ASN cc_start: 0.9606 (t0) cc_final: 0.8654 (t0) REVERT: B 25 LYS cc_start: 0.9689 (mttt) cc_final: 0.9257 (mttp) REVERT: B 30 LYS cc_start: 0.9160 (mmpt) cc_final: 0.8832 (mmmt) REVERT: B 50 GLN cc_start: 0.9235 (mt0) cc_final: 0.8803 (mt0) REVERT: B 74 ASN cc_start: 0.9402 (m-40) cc_final: 0.9123 (m110) REVERT: B 104 ILE cc_start: 0.9190 (mt) cc_final: 0.8935 (mt) REVERT: B 111 LEU cc_start: 0.9126 (tp) cc_final: 0.8782 (tp) REVERT: B 114 GLN cc_start: 0.8728 (mt0) cc_final: 0.7352 (mt0) REVERT: B 131 LYS cc_start: 0.9590 (ttmt) cc_final: 0.9309 (tttt) REVERT: B 167 ARG cc_start: 0.9410 (ptm160) cc_final: 0.9181 (ptp90) REVERT: C 18 ARG cc_start: 0.8975 (mtm-85) cc_final: 0.8443 (ttm110) REVERT: C 53 ASN cc_start: 0.9426 (m-40) cc_final: 0.9182 (m110) REVERT: C 62 HIS cc_start: 0.8774 (m-70) cc_final: 0.8363 (m-70) REVERT: C 74 ASN cc_start: 0.9411 (m110) cc_final: 0.9199 (m110) REVERT: C 100 ARG cc_start: 0.8236 (mpp-170) cc_final: 0.7787 (mpp-170) REVERT: C 128 GLU cc_start: 0.9160 (mp0) cc_final: 0.8819 (mp0) REVERT: C 131 LYS cc_start: 0.8713 (ttmt) cc_final: 0.8248 (mtpt) REVERT: C 187 GLU cc_start: 0.9269 (mt-10) cc_final: 0.9023 (mp0) REVERT: C 189 LEU cc_start: 0.9243 (mm) cc_final: 0.8928 (mp) REVERT: C 215 MET cc_start: 0.9036 (mtm) cc_final: 0.8692 (mtm) REVERT: D 56 LEU cc_start: 0.9688 (mt) cc_final: 0.9353 (mt) REVERT: D 57 ASN cc_start: 0.9632 (m110) cc_final: 0.9372 (m110) REVERT: D 117 TRP cc_start: 0.8210 (m-10) cc_final: 0.7965 (m-10) REVERT: D 130 TYR cc_start: 0.9240 (t80) cc_final: 0.8934 (t80) REVERT: D 131 LYS cc_start: 0.8997 (tttt) cc_final: 0.8777 (tttt) REVERT: D 141 ILE cc_start: 0.8983 (mt) cc_final: 0.8750 (mt) REVERT: D 144 MET cc_start: 0.7734 (ttt) cc_final: 0.7342 (ttm) REVERT: D 164 TYR cc_start: 0.7971 (t80) cc_final: 0.7443 (t80) REVERT: D 193 ASN cc_start: 0.9301 (m-40) cc_final: 0.7882 (p0) REVERT: D 203 LYS cc_start: 0.9139 (mptt) cc_final: 0.8774 (mmtm) REVERT: D 211 LEU cc_start: 0.8426 (tp) cc_final: 0.8087 (tp) REVERT: D 215 MET cc_start: 0.7830 (ttt) cc_final: 0.7330 (ttm) REVERT: G 39 MET cc_start: 0.9588 (ttm) cc_final: 0.9354 (ttm) REVERT: G 57 ASN cc_start: 0.9549 (m-40) cc_final: 0.9325 (m110) REVERT: G 96 MET cc_start: 0.1376 (mpp) cc_final: -0.0143 (mmm) REVERT: G 164 TYR cc_start: 0.8634 (t80) cc_final: 0.8413 (t80) REVERT: G 185 MET cc_start: 0.9159 (mtt) cc_final: 0.8491 (mtt) REVERT: G 214 MET cc_start: 0.9174 (mtm) cc_final: 0.8955 (ptp) REVERT: G 215 MET cc_start: 0.8688 (mmt) cc_final: 0.8402 (mmm) REVERT: H 132 ARG cc_start: 0.9239 (mmp80) cc_final: 0.9002 (mmm160) REVERT: H 161 PHE cc_start: 0.8203 (t80) cc_final: 0.7554 (t80) REVERT: H 215 MET cc_start: 0.9036 (tpt) cc_final: 0.8704 (mmm) REVERT: J 24 LEU cc_start: 0.8853 (mp) cc_final: 0.8287 (mm) REVERT: J 25 PHE cc_start: 0.8516 (m-80) cc_final: 0.7861 (m-80) REVERT: J 48 TYR cc_start: 0.8561 (m-10) cc_final: 0.7826 (m-10) REVERT: J 76 LYS cc_start: 0.5126 (mttt) cc_final: 0.4584 (tppp) REVERT: J 100 MET cc_start: 0.5669 (mmm) cc_final: 0.4645 (tpt) REVERT: J 122 LEU cc_start: 0.8218 (mt) cc_final: 0.7939 (mp) REVERT: J 129 PHE cc_start: 0.7350 (p90) cc_final: 0.6901 (p90) REVERT: N 150 ILE cc_start: 0.7557 (tp) cc_final: 0.7272 (tp) REVERT: N 153 ILE cc_start: 0.8741 (mt) cc_final: 0.8519 (mp) REVERT: N 181 VAL cc_start: 0.8921 (p) cc_final: 0.8702 (p) REVERT: N 185 MET cc_start: 0.8692 (ptp) cc_final: 0.8272 (ptp) REVERT: Y 5 ASN cc_start: 0.8154 (t0) cc_final: 0.7631 (t0) REVERT: Y 20 LEU cc_start: 0.9639 (pp) cc_final: 0.9346 (pp) REVERT: Y 40 PHE cc_start: 0.9306 (t80) cc_final: 0.8974 (t80) REVERT: Y 50 GLN cc_start: 0.8656 (mp10) cc_final: 0.8449 (mp10) REVERT: Y 56 LEU cc_start: 0.9508 (mt) cc_final: 0.9153 (mt) REVERT: Y 62 HIS cc_start: 0.8171 (m-70) cc_final: 0.7818 (m-70) REVERT: Y 63 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8708 (mm-40) REVERT: Y 113 GLU cc_start: 0.8917 (pm20) cc_final: 0.8477 (pm20) REVERT: Y 139 ASN cc_start: 0.9551 (m-40) cc_final: 0.9237 (m110) REVERT: d 39 MET cc_start: 0.7239 (tpp) cc_final: 0.7022 (tpp) REVERT: d 139 ASN cc_start: 0.9579 (m-40) cc_final: 0.9312 (m-40) REVERT: d 140 LYS cc_start: 0.9473 (mttt) cc_final: 0.9015 (tptp) REVERT: d 144 MET cc_start: 0.8885 (tmm) cc_final: 0.8564 (tmm) REVERT: e 10 MET cc_start: 0.8202 (mmp) cc_final: 0.7948 (mmp) REVERT: e 39 MET cc_start: 0.9452 (tpp) cc_final: 0.9125 (tpp) REVERT: e 51 ASP cc_start: 0.9448 (m-30) cc_final: 0.9204 (m-30) REVERT: e 57 ASN cc_start: 0.9370 (m-40) cc_final: 0.9112 (m110) REVERT: e 66 MET cc_start: 0.9006 (mmm) cc_final: 0.8721 (mmm) REVERT: e 79 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8543 (pp20) REVERT: e 82 ARG cc_start: 0.9001 (tmm160) cc_final: 0.8776 (ttp80) REVERT: e 111 LEU cc_start: 0.9243 (pt) cc_final: 0.8968 (pt) REVERT: e 114 GLN cc_start: 0.8835 (mt0) cc_final: 0.7900 (mt0) REVERT: e 118 MET cc_start: 0.8587 (mtt) cc_final: 0.8365 (mtt) REVERT: e 128 GLU cc_start: 0.9258 (pm20) cc_final: 0.8760 (pm20) REVERT: e 132 ARG cc_start: 0.9384 (ptp-170) cc_final: 0.8820 (ptp-170) REVERT: e 185 MET cc_start: 0.9098 (mtm) cc_final: 0.8897 (mtp) REVERT: j 155 GLN cc_start: 0.5924 (mt0) cc_final: 0.5590 (pm20) REVERT: k 66 MET cc_start: 0.9296 (mmm) cc_final: 0.8916 (ptp) REVERT: k 96 MET cc_start: 0.4832 (ttm) cc_final: 0.3594 (mpp) REVERT: k 104 ILE cc_start: 0.8556 (mm) cc_final: 0.8005 (mm) REVERT: k 118 MET cc_start: 0.8688 (mmm) cc_final: 0.7808 (ptp) REVERT: k 129 ILE cc_start: 0.9531 (tt) cc_final: 0.9111 (pt) REVERT: k 132 ARG cc_start: 0.9234 (ttp-110) cc_final: 0.9001 (ttp-110) REVERT: k 173 ARG cc_start: 0.9004 (ttt180) cc_final: 0.8667 (ttp80) REVERT: k 185 MET cc_start: 0.9266 (mtm) cc_final: 0.8974 (mtm) REVERT: k 187 GLU cc_start: 0.9304 (mt-10) cc_final: 0.9098 (mt-10) outliers start: 2 outliers final: 0 residues processed: 832 average time/residue: 0.1498 time to fit residues: 180.7744 Evaluate side-chains 634 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 47 optimal weight: 20.0000 chunk 14 optimal weight: 40.0000 chunk 85 optimal weight: 10.0000 chunk 147 optimal weight: 50.0000 chunk 206 optimal weight: 0.3980 chunk 182 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 chunk 35 optimal weight: 50.0000 chunk 228 optimal weight: 8.9990 chunk 198 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 overall best weight: 6.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN H 193 ASN ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS J 111 GLN J 163 GLN ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 ASN k 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.102183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.078252 restraints weight = 74602.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.080400 restraints weight = 52616.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.081983 restraints weight = 40553.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.083150 restraints weight = 33240.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.083975 restraints weight = 28528.833| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18834 Z= 0.185 Angle : 0.676 7.603 25587 Z= 0.356 Chirality : 0.046 0.280 2848 Planarity : 0.005 0.066 3345 Dihedral : 4.531 36.317 2500 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.17), residues: 2338 helix: 0.40 (0.13), residues: 1444 sheet: -1.53 (0.51), residues: 82 loop : -0.33 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 173 TYR 0.023 0.002 TYR e 130 PHE 0.019 0.002 PHE J 53 TRP 0.039 0.002 TRP D 184 HIS 0.007 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00398 (18824) covalent geometry : angle 0.67606 (25567) SS BOND : bond 0.00475 ( 10) SS BOND : angle 1.07529 ( 20) hydrogen bonds : bond 0.04396 ( 1037) hydrogen bonds : angle 4.59031 ( 3081) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 803 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.9604 (t80) cc_final: 0.8939 (t80) REVERT: A 41 SER cc_start: 0.9481 (m) cc_final: 0.9093 (t) REVERT: A 45 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7790 (mm-30) REVERT: A 52 LEU cc_start: 0.9809 (mm) cc_final: 0.9508 (mm) REVERT: A 55 MET cc_start: 0.9374 (ttt) cc_final: 0.9033 (tmm) REVERT: A 56 LEU cc_start: 0.9518 (mt) cc_final: 0.9235 (mt) REVERT: A 57 ASN cc_start: 0.9672 (m110) cc_final: 0.9429 (m110) REVERT: A 68 MET cc_start: 0.8799 (mtt) cc_final: 0.8485 (mtt) REVERT: A 71 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8830 (tm-30) REVERT: A 113 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8810 (mt-10) REVERT: B 21 ASN cc_start: 0.9541 (t0) cc_final: 0.9328 (t0) REVERT: B 30 LYS cc_start: 0.9086 (mmpt) cc_final: 0.8702 (mmmt) REVERT: B 50 GLN cc_start: 0.9273 (mt0) cc_final: 0.8796 (mt0) REVERT: B 68 MET cc_start: 0.9276 (mtt) cc_final: 0.8956 (mtt) REVERT: B 74 ASN cc_start: 0.9403 (m-40) cc_final: 0.8990 (m110) REVERT: B 104 ILE cc_start: 0.9243 (mt) cc_final: 0.8457 (tt) REVERT: B 111 LEU cc_start: 0.9213 (tp) cc_final: 0.8804 (tp) REVERT: B 114 GLN cc_start: 0.8899 (mt0) cc_final: 0.7542 (mt0) REVERT: B 144 MET cc_start: 0.9189 (ttt) cc_final: 0.8972 (ttt) REVERT: B 167 ARG cc_start: 0.9387 (ptm160) cc_final: 0.9126 (ptp-170) REVERT: C 25 LYS cc_start: 0.9321 (mttt) cc_final: 0.8999 (tptp) REVERT: C 53 ASN cc_start: 0.9495 (m-40) cc_final: 0.9224 (m110) REVERT: C 55 MET cc_start: 0.9170 (ttm) cc_final: 0.8515 (ttp) REVERT: C 74 ASN cc_start: 0.9414 (m110) cc_final: 0.9203 (m110) REVERT: C 79 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8895 (tp30) REVERT: C 128 GLU cc_start: 0.9145 (mp0) cc_final: 0.8853 (mp0) REVERT: C 131 LYS cc_start: 0.8695 (ttmt) cc_final: 0.8391 (mtpt) REVERT: C 187 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8934 (mm-30) REVERT: C 189 LEU cc_start: 0.9288 (mm) cc_final: 0.9053 (mp) REVERT: D 45 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7667 (mm-30) REVERT: D 56 LEU cc_start: 0.9719 (mt) cc_final: 0.9368 (mt) REVERT: D 130 TYR cc_start: 0.9262 (t80) cc_final: 0.8964 (t80) REVERT: D 131 LYS cc_start: 0.9238 (tttt) cc_final: 0.8942 (tttt) REVERT: D 193 ASN cc_start: 0.9199 (m-40) cc_final: 0.8623 (m-40) REVERT: D 215 MET cc_start: 0.7759 (ttt) cc_final: 0.7265 (ttm) REVERT: G 23 TRP cc_start: 0.9429 (t-100) cc_final: 0.9026 (t-100) REVERT: G 57 ASN cc_start: 0.9473 (m-40) cc_final: 0.9251 (m110) REVERT: G 96 MET cc_start: 0.1683 (mpp) cc_final: 0.0143 (mmm) REVERT: G 114 GLN cc_start: 0.8719 (mm110) cc_final: 0.8451 (mm110) REVERT: G 185 MET cc_start: 0.9104 (mtt) cc_final: 0.8468 (mtt) REVERT: G 211 LEU cc_start: 0.9034 (tp) cc_final: 0.8776 (tp) REVERT: G 214 MET cc_start: 0.9203 (mtm) cc_final: 0.8936 (ptp) REVERT: H 129 ILE cc_start: 0.8818 (tt) cc_final: 0.8266 (tt) REVERT: H 130 TYR cc_start: 0.5927 (t80) cc_final: 0.5548 (t80) REVERT: H 133 TRP cc_start: 0.8838 (m-10) cc_final: 0.7770 (m-10) REVERT: H 161 PHE cc_start: 0.8088 (t80) cc_final: 0.7129 (t80) REVERT: H 176 GLN cc_start: 0.7738 (pt0) cc_final: 0.7488 (pp30) REVERT: H 215 MET cc_start: 0.8972 (tpt) cc_final: 0.8449 (tpt) REVERT: J 6 VAL cc_start: 0.9133 (t) cc_final: 0.8493 (p) REVERT: J 10 ILE cc_start: 0.9367 (tp) cc_final: 0.9003 (tp) REVERT: J 24 LEU cc_start: 0.8937 (mp) cc_final: 0.8471 (mp) REVERT: J 25 PHE cc_start: 0.8515 (m-80) cc_final: 0.7855 (m-80) REVERT: J 31 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8357 (ttmt) REVERT: J 32 THR cc_start: 0.9119 (t) cc_final: 0.8738 (t) REVERT: J 43 GLU cc_start: 0.8518 (pp20) cc_final: 0.8223 (pp20) REVERT: J 46 PHE cc_start: 0.6481 (p90) cc_final: 0.5241 (p90) REVERT: J 76 LYS cc_start: 0.5901 (mttt) cc_final: 0.5595 (tppp) REVERT: J 100 MET cc_start: 0.6064 (mmm) cc_final: 0.5387 (tpp) REVERT: J 122 LEU cc_start: 0.8091 (mt) cc_final: 0.7887 (mp) REVERT: J 152 THR cc_start: 0.9077 (p) cc_final: 0.8805 (t) REVERT: N 179 GLN cc_start: 0.9120 (pp30) cc_final: 0.8323 (pm20) REVERT: Y 5 ASN cc_start: 0.7934 (t0) cc_final: 0.7653 (t0) REVERT: Y 20 LEU cc_start: 0.9657 (pp) cc_final: 0.9341 (pp) REVERT: Y 50 GLN cc_start: 0.8785 (mp10) cc_final: 0.8573 (mp10) REVERT: Y 56 LEU cc_start: 0.9436 (mt) cc_final: 0.9188 (mt) REVERT: Y 70 LYS cc_start: 0.9542 (mtmm) cc_final: 0.9291 (mttm) REVERT: Y 79 GLU cc_start: 0.8813 (tp30) cc_final: 0.8309 (tp30) REVERT: Y 117 TRP cc_start: 0.8386 (m-10) cc_final: 0.7772 (m-90) REVERT: Y 139 ASN cc_start: 0.9533 (m-40) cc_final: 0.9218 (m110) REVERT: d 23 TRP cc_start: 0.8533 (t-100) cc_final: 0.8324 (t-100) REVERT: d 39 MET cc_start: 0.7641 (tpp) cc_final: 0.7127 (tpt) REVERT: d 129 ILE cc_start: 0.9610 (tp) cc_final: 0.8862 (tp) REVERT: d 133 TRP cc_start: 0.8603 (m-10) cc_final: 0.7062 (m-10) REVERT: d 139 ASN cc_start: 0.9615 (m-40) cc_final: 0.9393 (m-40) REVERT: d 140 LYS cc_start: 0.9518 (mttt) cc_final: 0.9088 (tptp) REVERT: d 144 MET cc_start: 0.8540 (tmm) cc_final: 0.8269 (tmm) REVERT: d 167 ARG cc_start: 0.8529 (mmp-170) cc_final: 0.8072 (mmp80) REVERT: e 10 MET cc_start: 0.8306 (mmp) cc_final: 0.8036 (mmp) REVERT: e 13 GLN cc_start: 0.7768 (mp10) cc_final: 0.7541 (mp10) REVERT: e 39 MET cc_start: 0.9356 (tpp) cc_final: 0.9100 (tpp) REVERT: e 57 ASN cc_start: 0.9458 (m-40) cc_final: 0.9153 (m110) REVERT: e 66 MET cc_start: 0.8946 (mmm) cc_final: 0.8743 (mmm) REVERT: e 70 LYS cc_start: 0.9240 (ptpp) cc_final: 0.8976 (ptpt) REVERT: e 79 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8608 (pp20) REVERT: e 82 ARG cc_start: 0.9014 (tmm160) cc_final: 0.8768 (ttp80) REVERT: e 96 MET cc_start: 0.7061 (mtp) cc_final: 0.6672 (mmm) REVERT: e 117 TRP cc_start: 0.8525 (m-10) cc_final: 0.8301 (m-10) REVERT: e 118 MET cc_start: 0.8853 (mtt) cc_final: 0.8634 (mtt) REVERT: e 139 ASN cc_start: 0.9582 (m-40) cc_final: 0.9258 (m110) REVERT: e 215 MET cc_start: 0.8012 (ptm) cc_final: 0.7651 (ptt) REVERT: j 155 GLN cc_start: 0.6189 (mt0) cc_final: 0.5702 (pm20) REVERT: j 215 MET cc_start: 0.8180 (ppp) cc_final: 0.7785 (ppp) REVERT: k 21 ASN cc_start: 0.9408 (t0) cc_final: 0.9177 (t0) REVERT: k 57 ASN cc_start: 0.9579 (m-40) cc_final: 0.8876 (p0) REVERT: k 96 MET cc_start: 0.4999 (ttm) cc_final: 0.3848 (mpp) REVERT: k 100 ARG cc_start: 0.7839 (mmt180) cc_final: 0.7609 (tpm170) REVERT: k 104 ILE cc_start: 0.8632 (mm) cc_final: 0.8092 (mm) REVERT: k 118 MET cc_start: 0.8778 (mmm) cc_final: 0.7921 (ptp) REVERT: k 211 LEU cc_start: 0.9392 (tt) cc_final: 0.9076 (tt) outliers start: 1 outliers final: 0 residues processed: 804 average time/residue: 0.1422 time to fit residues: 167.2021 Evaluate side-chains 630 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 630 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 9 optimal weight: 0.0370 chunk 180 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 203 optimal weight: 40.0000 chunk 65 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 40.0000 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 139 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS J 108 ASN J 163 GLN Y 95 GLN ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.102310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.078530 restraints weight = 73882.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.080688 restraints weight = 52018.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.082298 restraints weight = 40036.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.083405 restraints weight = 32735.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.084292 restraints weight = 28270.571| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.6896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18834 Z= 0.149 Angle : 0.662 6.843 25587 Z= 0.345 Chirality : 0.046 0.217 2848 Planarity : 0.005 0.069 3345 Dihedral : 4.531 36.575 2500 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2338 helix: 0.53 (0.13), residues: 1437 sheet: -0.90 (0.67), residues: 57 loop : -0.28 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 143 TYR 0.035 0.002 TYR D 164 PHE 0.023 0.002 PHE G 161 TRP 0.035 0.002 TRP D 184 HIS 0.004 0.001 HIS J 54 Details of bonding type rmsd covalent geometry : bond 0.00330 (18824) covalent geometry : angle 0.66143 (25567) SS BOND : bond 0.00261 ( 10) SS BOND : angle 1.05190 ( 20) hydrogen bonds : bond 0.04217 ( 1037) hydrogen bonds : angle 4.54980 ( 3081) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 803 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.9575 (t80) cc_final: 0.8756 (t80) REVERT: A 41 SER cc_start: 0.9487 (m) cc_final: 0.9038 (t) REVERT: A 52 LEU cc_start: 0.9793 (mm) cc_final: 0.9469 (mm) REVERT: A 55 MET cc_start: 0.9414 (ttt) cc_final: 0.9094 (tmm) REVERT: A 56 LEU cc_start: 0.9507 (mt) cc_final: 0.9173 (mt) REVERT: A 57 ASN cc_start: 0.9676 (m110) cc_final: 0.9401 (m110) REVERT: A 70 LYS cc_start: 0.9438 (mtmm) cc_final: 0.9002 (mttt) REVERT: A 71 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8807 (tm-30) REVERT: A 76 GLU cc_start: 0.9263 (mt-10) cc_final: 0.9055 (pt0) REVERT: A 96 MET cc_start: -0.1132 (mpp) cc_final: -0.1344 (mmt) REVERT: A 113 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8764 (mt-10) REVERT: B 21 ASN cc_start: 0.9539 (t0) cc_final: 0.9280 (t0) REVERT: B 30 LYS cc_start: 0.8975 (mmpt) cc_final: 0.8592 (mmmt) REVERT: B 50 GLN cc_start: 0.9269 (mt0) cc_final: 0.8800 (mt0) REVERT: B 52 LEU cc_start: 0.9756 (mt) cc_final: 0.9546 (mm) REVERT: B 68 MET cc_start: 0.9291 (mtt) cc_final: 0.9023 (mtt) REVERT: B 70 LYS cc_start: 0.9697 (ptmm) cc_final: 0.9128 (ptmm) REVERT: B 74 ASN cc_start: 0.9375 (m-40) cc_final: 0.8803 (m110) REVERT: B 104 ILE cc_start: 0.9273 (mt) cc_final: 0.8699 (tt) REVERT: B 111 LEU cc_start: 0.9278 (tp) cc_final: 0.8828 (tp) REVERT: B 114 GLN cc_start: 0.8859 (mt0) cc_final: 0.7431 (mt0) REVERT: B 167 ARG cc_start: 0.9375 (ptm160) cc_final: 0.9071 (ptp-170) REVERT: C 25 LYS cc_start: 0.9334 (mttt) cc_final: 0.8963 (tptp) REVERT: C 53 ASN cc_start: 0.9448 (m-40) cc_final: 0.9195 (m110) REVERT: C 55 MET cc_start: 0.9133 (ttm) cc_final: 0.8519 (ttp) REVERT: C 74 ASN cc_start: 0.9405 (m110) cc_final: 0.9175 (m110) REVERT: C 128 GLU cc_start: 0.9116 (mp0) cc_final: 0.8874 (mp0) REVERT: C 170 LYS cc_start: 0.9640 (ptmm) cc_final: 0.9207 (ptpp) REVERT: C 187 GLU cc_start: 0.9257 (mt-10) cc_final: 0.9020 (mm-30) REVERT: C 189 LEU cc_start: 0.9278 (mm) cc_final: 0.9000 (mp) REVERT: D 41 SER cc_start: 0.9521 (t) cc_final: 0.8910 (p) REVERT: D 45 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7676 (mm-30) REVERT: D 56 LEU cc_start: 0.9729 (mt) cc_final: 0.9380 (mt) REVERT: D 57 ASN cc_start: 0.9619 (m110) cc_final: 0.9391 (m110) REVERT: D 130 TYR cc_start: 0.9242 (t80) cc_final: 0.9003 (t80) REVERT: D 131 LYS cc_start: 0.9192 (tttt) cc_final: 0.8810 (tttt) REVERT: D 141 ILE cc_start: 0.8915 (mt) cc_final: 0.8699 (mt) REVERT: D 163 ASP cc_start: 0.8575 (m-30) cc_final: 0.8365 (m-30) REVERT: D 169 TYR cc_start: 0.8566 (m-80) cc_final: 0.8323 (m-80) REVERT: D 215 MET cc_start: 0.7802 (ttt) cc_final: 0.7346 (ttm) REVERT: G 23 TRP cc_start: 0.9401 (t-100) cc_final: 0.8944 (t-100) REVERT: G 40 PHE cc_start: 0.9229 (t80) cc_final: 0.8850 (t80) REVERT: G 55 MET cc_start: 0.9275 (ttt) cc_final: 0.8981 (ttp) REVERT: G 57 ASN cc_start: 0.9483 (m-40) cc_final: 0.9253 (m110) REVERT: G 96 MET cc_start: 0.2173 (mpp) cc_final: 0.0718 (mmm) REVERT: G 114 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8301 (mm110) REVERT: G 139 ASN cc_start: 0.9638 (m110) cc_final: 0.9426 (m110) REVERT: G 181 VAL cc_start: 0.9226 (t) cc_final: 0.8881 (p) REVERT: G 185 MET cc_start: 0.9053 (mtt) cc_final: 0.8387 (mtt) REVERT: G 211 LEU cc_start: 0.9160 (tp) cc_final: 0.8740 (tp) REVERT: H 10 MET cc_start: 0.4585 (ttt) cc_final: 0.4318 (ttt) REVERT: H 161 PHE cc_start: 0.8130 (t80) cc_final: 0.7281 (t80) REVERT: H 167 ARG cc_start: 0.9080 (mmm160) cc_final: 0.8371 (mmm160) REVERT: H 176 GLN cc_start: 0.7767 (pt0) cc_final: 0.7524 (pp30) REVERT: H 215 MET cc_start: 0.9022 (tpt) cc_final: 0.8483 (tpt) REVERT: J 6 VAL cc_start: 0.9107 (t) cc_final: 0.8853 (m) REVERT: J 24 LEU cc_start: 0.8916 (mp) cc_final: 0.8212 (mm) REVERT: J 25 PHE cc_start: 0.8524 (m-80) cc_final: 0.7855 (m-80) REVERT: J 32 THR cc_start: 0.9016 (t) cc_final: 0.8750 (t) REVERT: J 35 ASN cc_start: 0.8900 (m-40) cc_final: 0.7541 (m-40) REVERT: J 43 GLU cc_start: 0.8510 (pp20) cc_final: 0.8277 (pp20) REVERT: J 76 LYS cc_start: 0.5882 (mttt) cc_final: 0.5669 (tppp) REVERT: J 100 MET cc_start: 0.5778 (mmm) cc_final: 0.5498 (tpp) REVERT: J 111 GLN cc_start: 0.9182 (mp-120) cc_final: 0.8718 (mm-40) REVERT: J 122 LEU cc_start: 0.8135 (mt) cc_final: 0.7888 (mp) REVERT: J 129 PHE cc_start: 0.7565 (p90) cc_final: 0.7349 (p90) REVERT: J 152 THR cc_start: 0.9015 (p) cc_final: 0.8729 (t) REVERT: N 153 ILE cc_start: 0.8632 (mt) cc_final: 0.8421 (mt) REVERT: N 185 MET cc_start: 0.8669 (ptp) cc_final: 0.8152 (ptp) REVERT: Y 5 ASN cc_start: 0.7875 (t0) cc_final: 0.7582 (t0) REVERT: Y 20 LEU cc_start: 0.9622 (pp) cc_final: 0.9322 (pp) REVERT: Y 56 LEU cc_start: 0.9463 (mt) cc_final: 0.9185 (mt) REVERT: Y 63 GLN cc_start: 0.9198 (mm110) cc_final: 0.8917 (mm-40) REVERT: Y 70 LYS cc_start: 0.9441 (mtmm) cc_final: 0.9197 (mttm) REVERT: Y 113 GLU cc_start: 0.8837 (pm20) cc_final: 0.8425 (pm20) REVERT: Y 114 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8831 (mm-40) REVERT: Y 117 TRP cc_start: 0.8357 (m-10) cc_final: 0.7508 (m-90) REVERT: Y 139 ASN cc_start: 0.9471 (m-40) cc_final: 0.9149 (m110) REVERT: d 39 MET cc_start: 0.7689 (tpp) cc_final: 0.7228 (tpt) REVERT: d 66 MET cc_start: 0.9186 (mtm) cc_final: 0.8968 (mtp) REVERT: d 68 MET cc_start: 0.7735 (mtp) cc_final: 0.7530 (mtp) REVERT: d 130 TYR cc_start: 0.7429 (t80) cc_final: 0.6855 (t80) REVERT: d 136 LEU cc_start: 0.9770 (tp) cc_final: 0.9526 (tp) REVERT: d 139 ASN cc_start: 0.9632 (m-40) cc_final: 0.9379 (m-40) REVERT: d 152 ASP cc_start: 0.8192 (m-30) cc_final: 0.7892 (m-30) REVERT: d 167 ARG cc_start: 0.8451 (mmp-170) cc_final: 0.7989 (mmp80) REVERT: e 10 MET cc_start: 0.8304 (mmp) cc_final: 0.8031 (mmp) REVERT: e 39 MET cc_start: 0.9337 (tpp) cc_final: 0.9094 (tpp) REVERT: e 57 ASN cc_start: 0.9375 (m-40) cc_final: 0.9143 (m110) REVERT: e 66 MET cc_start: 0.8946 (mmm) cc_final: 0.8679 (mmm) REVERT: e 70 LYS cc_start: 0.9243 (ptpp) cc_final: 0.8993 (ptpt) REVERT: e 79 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8645 (pp20) REVERT: e 82 ARG cc_start: 0.9033 (tmm160) cc_final: 0.8774 (ttp80) REVERT: e 96 MET cc_start: 0.7109 (mtp) cc_final: 0.6767 (mmm) REVERT: e 112 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8888 (tm-30) REVERT: e 117 TRP cc_start: 0.8553 (m-10) cc_final: 0.8290 (m-10) REVERT: e 118 MET cc_start: 0.8940 (mtt) cc_final: 0.8684 (mtt) REVERT: e 128 GLU cc_start: 0.8985 (pm20) cc_final: 0.8512 (pm20) REVERT: e 139 ASN cc_start: 0.9576 (m-40) cc_final: 0.9287 (m110) REVERT: e 145 TYR cc_start: 0.8674 (m-80) cc_final: 0.8443 (m-10) REVERT: e 215 MET cc_start: 0.8040 (ptm) cc_final: 0.7651 (ptt) REVERT: j 213 GLU cc_start: 0.9483 (mp0) cc_final: 0.9220 (pm20) REVERT: k 57 ASN cc_start: 0.9572 (m-40) cc_final: 0.8930 (p0) REVERT: k 76 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9136 (mm-30) REVERT: k 81 ASP cc_start: 0.9173 (m-30) cc_final: 0.8867 (m-30) REVERT: k 96 MET cc_start: 0.5043 (ttm) cc_final: 0.3993 (mpp) REVERT: k 100 ARG cc_start: 0.7864 (mmt180) cc_final: 0.7497 (tpm170) REVERT: k 104 ILE cc_start: 0.8509 (mm) cc_final: 0.8145 (mm) REVERT: k 128 GLU cc_start: 0.9011 (pm20) cc_final: 0.8806 (pm20) REVERT: k 132 ARG cc_start: 0.9377 (ttp-110) cc_final: 0.9052 (ptp-170) REVERT: k 173 ARG cc_start: 0.9123 (ttm-80) cc_final: 0.8846 (tmm-80) outliers start: 1 outliers final: 0 residues processed: 804 average time/residue: 0.1476 time to fit residues: 172.6288 Evaluate side-chains 639 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 21 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 138 optimal weight: 50.0000 chunk 74 optimal weight: 6.9990 chunk 131 optimal weight: 40.0000 chunk 84 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS J 163 GLN ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 ASN k 74 ASN ** k 120 ASN ** 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 = 0.3796 r_free = 0.3796 target = 0.100340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.076561 restraints weight = 74638.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.078670 restraints weight = 52508.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.080204 restraints weight = 40526.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.081334 restraints weight = 33336.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.082166 restraints weight = 28723.509| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.7275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18834 Z= 0.178 Angle : 0.674 9.157 25587 Z= 0.355 Chirality : 0.046 0.305 2848 Planarity : 0.005 0.069 3345 Dihedral : 4.570 38.474 2500 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2338 helix: 0.41 (0.13), residues: 1457 sheet: -0.92 (0.67), residues: 61 loop : -0.29 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 82 TYR 0.025 0.002 TYR e 130 PHE 0.015 0.002 PHE k 32 TRP 0.041 0.002 TRP D 184 HIS 0.007 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00386 (18824) covalent geometry : angle 0.67382 (25567) SS BOND : bond 0.00331 ( 10) SS BOND : angle 1.12616 ( 20) hydrogen bonds : bond 0.04246 ( 1037) hydrogen bonds : angle 4.69476 ( 3081) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 773 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8528 (t) cc_final: 0.8240 (p) REVERT: A 40 PHE cc_start: 0.9597 (t80) cc_final: 0.8788 (t80) REVERT: A 50 GLN cc_start: 0.9258 (tm-30) cc_final: 0.9050 (tm-30) REVERT: A 51 ASP cc_start: 0.9419 (m-30) cc_final: 0.9128 (m-30) REVERT: A 52 LEU cc_start: 0.9797 (mm) cc_final: 0.9513 (mm) REVERT: A 55 MET cc_start: 0.9433 (ttt) cc_final: 0.9054 (tmm) REVERT: A 56 LEU cc_start: 0.9516 (mt) cc_final: 0.9215 (mt) REVERT: A 57 ASN cc_start: 0.9662 (m110) cc_final: 0.9388 (m110) REVERT: A 71 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8843 (tm-30) REVERT: A 113 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8811 (mt-10) REVERT: B 21 ASN cc_start: 0.9499 (t0) cc_final: 0.9188 (t0) REVERT: B 30 LYS cc_start: 0.8991 (mmpt) cc_final: 0.8488 (mmmt) REVERT: B 32 PHE cc_start: 0.8641 (m-80) cc_final: 0.8300 (m-80) REVERT: B 66 MET cc_start: 0.8637 (mmm) cc_final: 0.8242 (mmm) REVERT: B 74 ASN cc_start: 0.9443 (m-40) cc_final: 0.9122 (m110) REVERT: B 167 ARG cc_start: 0.9411 (ptm160) cc_final: 0.9106 (ptp-170) REVERT: B 176 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8291 (tm-30) REVERT: C 25 LYS cc_start: 0.9351 (mttt) cc_final: 0.8971 (tptp) REVERT: C 53 ASN cc_start: 0.9467 (m-40) cc_final: 0.9168 (m110) REVERT: C 55 MET cc_start: 0.9208 (ttm) cc_final: 0.8617 (ttp) REVERT: C 128 GLU cc_start: 0.9157 (mp0) cc_final: 0.8875 (mp0) REVERT: C 131 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8571 (mtpt) REVERT: C 187 GLU cc_start: 0.9238 (mt-10) cc_final: 0.9028 (mm-30) REVERT: C 189 LEU cc_start: 0.9354 (mm) cc_final: 0.9121 (mp) REVERT: D 40 PHE cc_start: 0.9446 (t80) cc_final: 0.9236 (t80) REVERT: D 56 LEU cc_start: 0.9746 (mt) cc_final: 0.9414 (mt) REVERT: D 57 ASN cc_start: 0.9643 (m110) cc_final: 0.9397 (m110) REVERT: D 130 TYR cc_start: 0.9267 (t80) cc_final: 0.9044 (t80) REVERT: D 131 LYS cc_start: 0.9245 (tttt) cc_final: 0.8871 (tttt) REVERT: D 134 ILE cc_start: 0.9675 (mt) cc_final: 0.9442 (mt) REVERT: D 141 ILE cc_start: 0.8965 (mt) cc_final: 0.8744 (mt) REVERT: D 143 ARG cc_start: 0.8328 (mmm160) cc_final: 0.8068 (mmm160) REVERT: D 163 ASP cc_start: 0.8692 (m-30) cc_final: 0.8460 (m-30) REVERT: D 211 LEU cc_start: 0.8643 (tp) cc_final: 0.8417 (tp) REVERT: D 215 MET cc_start: 0.7949 (ttt) cc_final: 0.7407 (ttm) REVERT: G 23 TRP cc_start: 0.9413 (t-100) cc_final: 0.8996 (t-100) REVERT: G 40 PHE cc_start: 0.9290 (t80) cc_final: 0.8925 (t80) REVERT: G 55 MET cc_start: 0.9303 (ttt) cc_final: 0.9040 (ttp) REVERT: G 57 ASN cc_start: 0.9462 (m-40) cc_final: 0.9218 (m110) REVERT: G 96 MET cc_start: 0.2002 (mpp) cc_final: 0.0618 (mmm) REVERT: G 138 LEU cc_start: 0.9702 (mt) cc_final: 0.9496 (mt) REVERT: G 168 PHE cc_start: 0.9426 (t80) cc_final: 0.9214 (t80) REVERT: G 181 VAL cc_start: 0.9229 (t) cc_final: 0.8921 (p) REVERT: G 185 MET cc_start: 0.9119 (mtt) cc_final: 0.8442 (mtt) REVERT: G 193 ASN cc_start: 0.9264 (m-40) cc_final: 0.8950 (m-40) REVERT: G 211 LEU cc_start: 0.9224 (tp) cc_final: 0.8749 (tp) REVERT: G 214 MET cc_start: 0.9098 (mtm) cc_final: 0.8887 (mtm) REVERT: H 10 MET cc_start: 0.4716 (ttt) cc_final: 0.4357 (ttt) REVERT: H 161 PHE cc_start: 0.7989 (t80) cc_final: 0.7157 (t80) REVERT: H 215 MET cc_start: 0.9044 (tpt) cc_final: 0.8558 (tpt) REVERT: J 6 VAL cc_start: 0.9147 (t) cc_final: 0.8458 (p) REVERT: J 24 LEU cc_start: 0.9050 (mp) cc_final: 0.8463 (mm) REVERT: J 25 PHE cc_start: 0.8547 (m-80) cc_final: 0.7889 (m-80) REVERT: J 32 THR cc_start: 0.9017 (t) cc_final: 0.8763 (t) REVERT: J 35 ASN cc_start: 0.8908 (m-40) cc_final: 0.7500 (m-40) REVERT: J 43 GLU cc_start: 0.8523 (pp20) cc_final: 0.8266 (pp20) REVERT: J 76 LYS cc_start: 0.5866 (mttt) cc_final: 0.5515 (tppp) REVERT: J 88 PHE cc_start: 0.7683 (m-80) cc_final: 0.7037 (m-80) REVERT: J 100 MET cc_start: 0.5635 (mmm) cc_final: 0.5072 (tpt) REVERT: J 111 GLN cc_start: 0.9192 (mp-120) cc_final: 0.8770 (mm-40) REVERT: J 122 LEU cc_start: 0.8177 (mt) cc_final: 0.7914 (mp) REVERT: J 129 PHE cc_start: 0.7551 (p90) cc_final: 0.7219 (p90) REVERT: J 152 THR cc_start: 0.9025 (p) cc_final: 0.8741 (t) REVERT: N 185 MET cc_start: 0.8679 (ptp) cc_final: 0.8133 (ptp) REVERT: Y 5 ASN cc_start: 0.8061 (t0) cc_final: 0.7639 (t0) REVERT: Y 20 LEU cc_start: 0.9612 (pp) cc_final: 0.9296 (pp) REVERT: Y 56 LEU cc_start: 0.9446 (mt) cc_final: 0.9209 (mt) REVERT: Y 63 GLN cc_start: 0.9181 (mm110) cc_final: 0.8775 (mm-40) REVERT: Y 70 LYS cc_start: 0.9492 (mtmm) cc_final: 0.9237 (mttm) REVERT: Y 112 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8821 (tm-30) REVERT: Y 113 GLU cc_start: 0.8913 (pm20) cc_final: 0.8518 (pm20) REVERT: Y 139 ASN cc_start: 0.9499 (m-40) cc_final: 0.9173 (m110) REVERT: d 23 TRP cc_start: 0.8495 (t-100) cc_final: 0.8175 (t-100) REVERT: d 39 MET cc_start: 0.7761 (tpp) cc_final: 0.7560 (tpp) REVERT: d 129 ILE cc_start: 0.9604 (tp) cc_final: 0.9292 (tp) REVERT: d 130 TYR cc_start: 0.7371 (t80) cc_final: 0.6832 (t80) REVERT: d 139 ASN cc_start: 0.9665 (m-40) cc_final: 0.9195 (m-40) REVERT: d 140 LYS cc_start: 0.9285 (mtmm) cc_final: 0.9073 (mttp) REVERT: d 143 ARG cc_start: 0.9109 (mtt180) cc_final: 0.8781 (mtt90) REVERT: d 152 ASP cc_start: 0.8221 (m-30) cc_final: 0.7932 (m-30) REVERT: d 167 ARG cc_start: 0.8435 (mmp-170) cc_final: 0.7954 (mmp80) REVERT: e 10 MET cc_start: 0.8366 (mmp) cc_final: 0.8125 (mmp) REVERT: e 39 MET cc_start: 0.9309 (tpp) cc_final: 0.9106 (tpp) REVERT: e 55 MET cc_start: 0.9003 (ttt) cc_final: 0.8717 (ttt) REVERT: e 66 MET cc_start: 0.9120 (mmm) cc_final: 0.8763 (mmm) REVERT: e 70 LYS cc_start: 0.9314 (ptpp) cc_final: 0.9045 (ptpt) REVERT: e 79 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8745 (pp20) REVERT: e 82 ARG cc_start: 0.9072 (tmm160) cc_final: 0.8803 (ttp80) REVERT: e 96 MET cc_start: 0.7425 (mtp) cc_final: 0.7065 (tpp) REVERT: e 117 TRP cc_start: 0.8756 (m-10) cc_final: 0.8468 (m-10) REVERT: e 118 MET cc_start: 0.8911 (mtt) cc_final: 0.8702 (mtt) REVERT: e 215 MET cc_start: 0.7976 (ptm) cc_final: 0.7588 (ptt) REVERT: j 191 VAL cc_start: 0.9232 (m) cc_final: 0.8981 (p) REVERT: j 213 GLU cc_start: 0.9488 (mp0) cc_final: 0.9247 (pm20) REVERT: j 215 MET cc_start: 0.8459 (ppp) cc_final: 0.8202 (ppp) REVERT: k 44 SER cc_start: 0.9439 (p) cc_final: 0.8550 (p) REVERT: k 55 MET cc_start: 0.9514 (ttm) cc_final: 0.9269 (ttm) REVERT: k 57 ASN cc_start: 0.9575 (m-40) cc_final: 0.8932 (p0) REVERT: k 68 MET cc_start: 0.9440 (mtp) cc_final: 0.9163 (mtp) REVERT: k 70 LYS cc_start: 0.9140 (mtmt) cc_final: 0.8710 (mtmm) REVERT: k 81 ASP cc_start: 0.9198 (m-30) cc_final: 0.8827 (m-30) REVERT: k 96 MET cc_start: 0.5073 (ttm) cc_final: 0.4086 (mpp) REVERT: k 100 ARG cc_start: 0.7938 (mmt180) cc_final: 0.7618 (tpm170) REVERT: k 104 ILE cc_start: 0.8575 (mm) cc_final: 0.8224 (mm) REVERT: k 131 LYS cc_start: 0.9391 (ttmt) cc_final: 0.8944 (tttt) REVERT: k 132 ARG cc_start: 0.9389 (ttp-110) cc_final: 0.9022 (ttp-110) REVERT: k 173 ARG cc_start: 0.9142 (ttm-80) cc_final: 0.8891 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 773 average time/residue: 0.1451 time to fit residues: 163.6870 Evaluate side-chains 620 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 196 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 116 optimal weight: 30.0000 chunk 171 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 218 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN H 67 GLN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 GLN Y 95 GLN ** d 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 ASN k 9 GLN k 53 ASN k 74 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.099759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.076173 restraints weight = 75526.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.078308 restraints weight = 52579.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.079861 restraints weight = 40277.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.080997 restraints weight = 32942.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.081845 restraints weight = 28306.089| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.7604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18834 Z= 0.166 Angle : 0.687 11.993 25587 Z= 0.358 Chirality : 0.046 0.268 2848 Planarity : 0.005 0.073 3345 Dihedral : 4.577 38.092 2500 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.05 % Allowed : 1.70 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2338 helix: 0.48 (0.13), residues: 1457 sheet: -0.88 (0.70), residues: 56 loop : -0.35 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG N 162 TYR 0.018 0.002 TYR Y 145 PHE 0.022 0.002 PHE Y 40 TRP 0.041 0.002 TRP D 184 HIS 0.005 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00363 (18824) covalent geometry : angle 0.68599 (25567) SS BOND : bond 0.00401 ( 10) SS BOND : angle 1.42169 ( 20) hydrogen bonds : bond 0.04285 ( 1037) hydrogen bonds : angle 4.76175 ( 3081) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 758 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8647 (t) cc_final: 0.8353 (p) REVERT: A 40 PHE cc_start: 0.9598 (t80) cc_final: 0.8702 (t80) REVERT: A 41 SER cc_start: 0.9513 (m) cc_final: 0.9187 (m) REVERT: A 45 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7698 (mm-30) REVERT: A 50 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8932 (tm-30) REVERT: A 51 ASP cc_start: 0.9377 (m-30) cc_final: 0.9075 (m-30) REVERT: A 52 LEU cc_start: 0.9785 (mm) cc_final: 0.9530 (mm) REVERT: A 55 MET cc_start: 0.9447 (ttt) cc_final: 0.9120 (tmm) REVERT: A 56 LEU cc_start: 0.9503 (mt) cc_final: 0.9227 (mt) REVERT: A 57 ASN cc_start: 0.9653 (m110) cc_final: 0.9355 (m110) REVERT: A 71 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8828 (tm-30) REVERT: A 113 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8861 (mt-10) REVERT: B 21 ASN cc_start: 0.9466 (t0) cc_final: 0.9159 (t0) REVERT: B 30 LYS cc_start: 0.8985 (mmpt) cc_final: 0.8588 (mmmm) REVERT: B 32 PHE cc_start: 0.8693 (m-80) cc_final: 0.8349 (m-80) REVERT: B 52 LEU cc_start: 0.9730 (mt) cc_final: 0.9516 (mm) REVERT: B 66 MET cc_start: 0.8336 (mmm) cc_final: 0.7956 (mmm) REVERT: B 70 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8979 (mttm) REVERT: B 74 ASN cc_start: 0.9443 (m-40) cc_final: 0.9139 (m110) REVERT: B 82 ARG cc_start: 0.8976 (ttp80) cc_final: 0.8547 (ttp80) REVERT: B 111 LEU cc_start: 0.9528 (tp) cc_final: 0.9279 (tp) REVERT: B 114 GLN cc_start: 0.8836 (mt0) cc_final: 0.7836 (mt0) REVERT: B 131 LYS cc_start: 0.9597 (tttt) cc_final: 0.9360 (mmmt) REVERT: B 139 ASN cc_start: 0.9514 (m-40) cc_final: 0.9251 (m110) REVERT: B 167 ARG cc_start: 0.9412 (ptm160) cc_final: 0.8984 (ptt180) REVERT: B 176 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8345 (tm-30) REVERT: C 53 ASN cc_start: 0.9456 (m-40) cc_final: 0.9167 (m110) REVERT: C 55 MET cc_start: 0.9262 (ttm) cc_final: 0.8770 (ttp) REVERT: C 128 GLU cc_start: 0.9163 (mp0) cc_final: 0.8918 (mp0) REVERT: C 187 GLU cc_start: 0.9232 (mt-10) cc_final: 0.9013 (mm-30) REVERT: C 189 LEU cc_start: 0.9346 (mm) cc_final: 0.9139 (mp) REVERT: D 56 LEU cc_start: 0.9761 (mt) cc_final: 0.9427 (mt) REVERT: D 131 LYS cc_start: 0.9257 (tttt) cc_final: 0.8875 (mtpt) REVERT: D 134 ILE cc_start: 0.9698 (mt) cc_final: 0.9461 (mt) REVERT: D 141 ILE cc_start: 0.8961 (mt) cc_final: 0.8727 (mt) REVERT: D 143 ARG cc_start: 0.8454 (mmm160) cc_final: 0.8039 (mmm160) REVERT: D 144 MET cc_start: 0.7772 (ttt) cc_final: 0.7404 (ttm) REVERT: D 145 TYR cc_start: 0.8600 (t80) cc_final: 0.8346 (t80) REVERT: D 163 ASP cc_start: 0.8608 (m-30) cc_final: 0.8392 (m-30) REVERT: D 215 MET cc_start: 0.8064 (ttt) cc_final: 0.7559 (ttm) REVERT: G 23 TRP cc_start: 0.9393 (t-100) cc_final: 0.8976 (t-100) REVERT: G 39 MET cc_start: 0.9460 (ttp) cc_final: 0.8782 (tpt) REVERT: G 40 PHE cc_start: 0.9301 (t80) cc_final: 0.8907 (t80) REVERT: G 55 MET cc_start: 0.9326 (ttt) cc_final: 0.9075 (ttp) REVERT: G 57 ASN cc_start: 0.9435 (m-40) cc_final: 0.9183 (m110) REVERT: G 96 MET cc_start: 0.2217 (mpp) cc_final: 0.0645 (mmm) REVERT: G 131 LYS cc_start: 0.9426 (ttmt) cc_final: 0.9177 (mttt) REVERT: G 139 ASN cc_start: 0.9624 (m110) cc_final: 0.9378 (m110) REVERT: G 168 PHE cc_start: 0.9432 (t80) cc_final: 0.9212 (t80) REVERT: G 181 VAL cc_start: 0.9254 (t) cc_final: 0.8969 (p) REVERT: G 185 MET cc_start: 0.9057 (mtt) cc_final: 0.8420 (mtt) REVERT: G 211 LEU cc_start: 0.9206 (tp) cc_final: 0.8970 (tp) REVERT: H 10 MET cc_start: 0.4833 (ttt) cc_final: 0.4411 (ttt) REVERT: H 129 ILE cc_start: 0.8811 (tt) cc_final: 0.8319 (tt) REVERT: H 133 TRP cc_start: 0.8345 (m-10) cc_final: 0.7379 (m-10) REVERT: H 161 PHE cc_start: 0.8027 (t80) cc_final: 0.7126 (t80) REVERT: H 167 ARG cc_start: 0.9055 (mmm160) cc_final: 0.8386 (mmm160) REVERT: H 215 MET cc_start: 0.9079 (tpt) cc_final: 0.8563 (tpt) REVERT: J 6 VAL cc_start: 0.9168 (t) cc_final: 0.8492 (p) REVERT: J 24 LEU cc_start: 0.9089 (mp) cc_final: 0.8619 (mm) REVERT: J 25 PHE cc_start: 0.8520 (m-80) cc_final: 0.7840 (m-80) REVERT: J 32 THR cc_start: 0.8985 (t) cc_final: 0.8760 (t) REVERT: J 35 ASN cc_start: 0.8831 (m-40) cc_final: 0.7255 (m-40) REVERT: J 43 GLU cc_start: 0.8635 (pp20) cc_final: 0.8331 (pp20) REVERT: J 76 LYS cc_start: 0.6198 (mttt) cc_final: 0.5885 (tppp) REVERT: J 111 GLN cc_start: 0.9198 (mp-120) cc_final: 0.8820 (mm-40) REVERT: J 122 LEU cc_start: 0.8380 (mt) cc_final: 0.8096 (mt) REVERT: J 152 THR cc_start: 0.8990 (p) cc_final: 0.8726 (t) REVERT: N 172 LEU cc_start: 0.9073 (mt) cc_final: 0.8793 (mt) REVERT: N 179 GLN cc_start: 0.9154 (pp30) cc_final: 0.8367 (pm20) REVERT: Y 5 ASN cc_start: 0.8061 (t0) cc_final: 0.7666 (t0) REVERT: Y 20 LEU cc_start: 0.9678 (pp) cc_final: 0.9391 (pp) REVERT: Y 56 LEU cc_start: 0.9450 (mt) cc_final: 0.9216 (mt) REVERT: Y 63 GLN cc_start: 0.9075 (mm110) cc_final: 0.8664 (mm-40) REVERT: Y 70 LYS cc_start: 0.9503 (mtmm) cc_final: 0.9232 (mttm) REVERT: Y 79 GLU cc_start: 0.8840 (tp30) cc_final: 0.8584 (tp30) REVERT: Y 113 GLU cc_start: 0.8944 (pm20) cc_final: 0.8464 (pm20) REVERT: Y 139 ASN cc_start: 0.9439 (m-40) cc_final: 0.9099 (m110) REVERT: d 23 TRP cc_start: 0.8587 (t-100) cc_final: 0.8132 (t-100) REVERT: d 130 TYR cc_start: 0.7493 (t80) cc_final: 0.6975 (t80) REVERT: d 139 ASN cc_start: 0.9673 (m-40) cc_final: 0.9243 (m-40) REVERT: d 143 ARG cc_start: 0.9155 (mtt180) cc_final: 0.8828 (mtt90) REVERT: d 152 ASP cc_start: 0.8108 (m-30) cc_final: 0.7758 (m-30) REVERT: d 167 ARG cc_start: 0.8498 (mmp-170) cc_final: 0.8010 (mmp80) REVERT: e 25 LYS cc_start: 0.9638 (pttm) cc_final: 0.9301 (ptpp) REVERT: e 30 LYS cc_start: 0.8904 (mmpt) cc_final: 0.8695 (mmmt) REVERT: e 55 MET cc_start: 0.8997 (ttt) cc_final: 0.8739 (ttt) REVERT: e 66 MET cc_start: 0.9138 (mmm) cc_final: 0.8710 (mmm) REVERT: e 70 LYS cc_start: 0.9240 (ptpp) cc_final: 0.9000 (ptpt) REVERT: e 79 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8741 (pp20) REVERT: e 82 ARG cc_start: 0.9058 (tmm160) cc_final: 0.8753 (ttp80) REVERT: e 114 GLN cc_start: 0.8816 (mt0) cc_final: 0.8415 (tt0) REVERT: e 117 TRP cc_start: 0.8811 (m-10) cc_final: 0.8545 (m-10) REVERT: e 132 ARG cc_start: 0.9278 (ptp90) cc_final: 0.9050 (ptp-170) REVERT: e 139 ASN cc_start: 0.9552 (m-40) cc_final: 0.9244 (m110) REVERT: e 185 MET cc_start: 0.9095 (mtm) cc_final: 0.8860 (mtp) REVERT: j 213 GLU cc_start: 0.9464 (mp0) cc_final: 0.9236 (pm20) REVERT: j 215 MET cc_start: 0.8107 (ppp) cc_final: 0.7833 (ppp) REVERT: k 21 ASN cc_start: 0.9366 (t0) cc_final: 0.9100 (t0) REVERT: k 55 MET cc_start: 0.9518 (ttm) cc_final: 0.9276 (ttm) REVERT: k 70 LYS cc_start: 0.9231 (mtmt) cc_final: 0.8825 (mtmm) REVERT: k 81 ASP cc_start: 0.9190 (m-30) cc_final: 0.8781 (m-30) REVERT: k 96 MET cc_start: 0.5102 (ttm) cc_final: 0.4543 (ptp) REVERT: k 100 ARG cc_start: 0.7912 (mmt180) cc_final: 0.7582 (tpm170) REVERT: k 104 ILE cc_start: 0.8585 (mm) cc_final: 0.8212 (mm) REVERT: k 132 ARG cc_start: 0.9402 (ttp-110) cc_final: 0.9043 (ptp-170) REVERT: k 139 ASN cc_start: 0.9199 (m110) cc_final: 0.8994 (m110) REVERT: k 211 LEU cc_start: 0.9316 (tt) cc_final: 0.8967 (tt) outliers start: 1 outliers final: 0 residues processed: 758 average time/residue: 0.1487 time to fit residues: 163.3177 Evaluate side-chains 607 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 607 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 171 optimal weight: 20.0000 chunk 207 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 125 optimal weight: 0.0370 chunk 226 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 chunk 189 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 108 ASN J 163 GLN Y 95 GLN ** Y 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 155 GLN k 9 GLN k 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.100331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.076645 restraints weight = 74176.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.078786 restraints weight = 51838.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.080353 restraints weight = 39831.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.081524 restraints weight = 32613.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.082374 restraints weight = 27973.904| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.7812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18834 Z= 0.152 Angle : 0.697 11.695 25587 Z= 0.360 Chirality : 0.047 0.344 2848 Planarity : 0.005 0.074 3345 Dihedral : 4.600 38.253 2500 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.10 % Allowed : 0.95 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2338 helix: 0.50 (0.13), residues: 1446 sheet: -0.68 (0.69), residues: 56 loop : -0.40 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 162 TYR 0.029 0.002 TYR j 169 PHE 0.016 0.002 PHE N 161 TRP 0.042 0.002 TRP D 184 HIS 0.004 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00337 (18824) covalent geometry : angle 0.69682 (25567) SS BOND : bond 0.00198 ( 10) SS BOND : angle 1.22895 ( 20) hydrogen bonds : bond 0.04386 ( 1037) hydrogen bonds : angle 4.76590 ( 3081) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 759 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8475 (t) cc_final: 0.8184 (p) REVERT: A 40 PHE cc_start: 0.9603 (t80) cc_final: 0.9130 (t80) REVERT: A 41 SER cc_start: 0.9550 (m) cc_final: 0.9214 (p) REVERT: A 45 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 50 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8892 (tm-30) REVERT: A 51 ASP cc_start: 0.9378 (m-30) cc_final: 0.9085 (m-30) REVERT: A 52 LEU cc_start: 0.9797 (mm) cc_final: 0.9537 (mm) REVERT: A 56 LEU cc_start: 0.9502 (mt) cc_final: 0.9213 (mt) REVERT: A 57 ASN cc_start: 0.9630 (m110) cc_final: 0.9332 (m110) REVERT: A 71 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8870 (tm-30) REVERT: A 113 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8800 (mt-10) REVERT: B 10 MET cc_start: 0.8934 (mmp) cc_final: 0.8576 (mmp) REVERT: B 21 ASN cc_start: 0.9448 (t0) cc_final: 0.9076 (t0) REVERT: B 30 LYS cc_start: 0.8947 (mmpt) cc_final: 0.8543 (mmmm) REVERT: B 32 PHE cc_start: 0.8694 (m-80) cc_final: 0.8350 (m-80) REVERT: B 51 ASP cc_start: 0.9367 (m-30) cc_final: 0.9161 (m-30) REVERT: B 70 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8850 (mttm) REVERT: B 74 ASN cc_start: 0.9455 (m-40) cc_final: 0.9158 (m110) REVERT: B 82 ARG cc_start: 0.8983 (ttp80) cc_final: 0.8539 (ttp80) REVERT: B 139 ASN cc_start: 0.9511 (m-40) cc_final: 0.9260 (m-40) REVERT: C 53 ASN cc_start: 0.9454 (m-40) cc_final: 0.9169 (m110) REVERT: C 55 MET cc_start: 0.9268 (ttm) cc_final: 0.8788 (ttp) REVERT: C 128 GLU cc_start: 0.9159 (mp0) cc_final: 0.8915 (mp0) REVERT: C 139 ASN cc_start: 0.9140 (t0) cc_final: 0.8078 (t0) REVERT: C 143 ARG cc_start: 0.9485 (mtt180) cc_final: 0.9211 (mtt180) REVERT: C 182 LYS cc_start: 0.9512 (mttp) cc_final: 0.8870 (mttm) REVERT: C 189 LEU cc_start: 0.9338 (mm) cc_final: 0.9083 (mp) REVERT: D 56 LEU cc_start: 0.9761 (mt) cc_final: 0.9476 (mt) REVERT: D 57 ASN cc_start: 0.9659 (m110) cc_final: 0.9411 (m-40) REVERT: D 130 TYR cc_start: 0.9364 (t80) cc_final: 0.8927 (t80) REVERT: D 131 LYS cc_start: 0.9319 (tttt) cc_final: 0.8883 (mtpt) REVERT: D 134 ILE cc_start: 0.9713 (mt) cc_final: 0.9486 (mt) REVERT: D 141 ILE cc_start: 0.8941 (mt) cc_final: 0.8735 (mt) REVERT: D 143 ARG cc_start: 0.8498 (mmm160) cc_final: 0.8007 (mmm160) REVERT: D 163 ASP cc_start: 0.8634 (m-30) cc_final: 0.8419 (m-30) REVERT: D 215 MET cc_start: 0.8180 (ttt) cc_final: 0.7616 (ttm) REVERT: G 23 TRP cc_start: 0.9398 (t-100) cc_final: 0.9028 (t-100) REVERT: G 39 MET cc_start: 0.9459 (ttp) cc_final: 0.8856 (tpt) REVERT: G 40 PHE cc_start: 0.9283 (t80) cc_final: 0.8884 (t80) REVERT: G 57 ASN cc_start: 0.9420 (m-40) cc_final: 0.9184 (m110) REVERT: G 96 MET cc_start: 0.1856 (mpp) cc_final: 0.0394 (mmm) REVERT: G 111 LEU cc_start: 0.8952 (mt) cc_final: 0.8653 (mt) REVERT: G 112 GLN cc_start: 0.9504 (mp10) cc_final: 0.9277 (mp10) REVERT: G 131 LYS cc_start: 0.9417 (ttmt) cc_final: 0.9159 (mttt) REVERT: G 139 ASN cc_start: 0.9585 (m110) cc_final: 0.9371 (m110) REVERT: G 168 PHE cc_start: 0.9448 (t80) cc_final: 0.9178 (t80) REVERT: G 181 VAL cc_start: 0.9260 (t) cc_final: 0.8988 (p) REVERT: G 185 MET cc_start: 0.9028 (mtt) cc_final: 0.8411 (mtt) REVERT: G 203 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8616 (mmmm) REVERT: G 211 LEU cc_start: 0.9176 (tp) cc_final: 0.8825 (tp) REVERT: H 10 MET cc_start: 0.4777 (ttt) cc_final: 0.4377 (ttt) REVERT: H 13 GLN cc_start: 0.6582 (tm-30) cc_final: 0.6368 (tm-30) REVERT: H 129 ILE cc_start: 0.8807 (tt) cc_final: 0.8311 (tt) REVERT: H 130 TYR cc_start: 0.5876 (t80) cc_final: 0.5458 (t80) REVERT: H 133 TRP cc_start: 0.8366 (m-10) cc_final: 0.7390 (m-10) REVERT: H 161 PHE cc_start: 0.7999 (t80) cc_final: 0.7098 (t80) REVERT: H 167 ARG cc_start: 0.9062 (mmm160) cc_final: 0.8404 (mmm160) REVERT: H 215 MET cc_start: 0.9050 (tpt) cc_final: 0.8522 (tpt) REVERT: J 6 VAL cc_start: 0.9105 (t) cc_final: 0.8363 (p) REVERT: J 24 LEU cc_start: 0.9074 (mp) cc_final: 0.8603 (mm) REVERT: J 25 PHE cc_start: 0.8462 (m-80) cc_final: 0.7799 (m-80) REVERT: J 32 THR cc_start: 0.8878 (t) cc_final: 0.8660 (t) REVERT: J 35 ASN cc_start: 0.8785 (m-40) cc_final: 0.7123 (m-40) REVERT: J 43 GLU cc_start: 0.8604 (pp20) cc_final: 0.8308 (pp20) REVERT: J 76 LYS cc_start: 0.6592 (mttt) cc_final: 0.6122 (tppp) REVERT: J 78 ILE cc_start: 0.8755 (pt) cc_final: 0.8530 (pt) REVERT: J 111 GLN cc_start: 0.9199 (mp-120) cc_final: 0.8797 (mm-40) REVERT: J 122 LEU cc_start: 0.8416 (mt) cc_final: 0.8118 (mt) REVERT: J 152 THR cc_start: 0.8948 (p) cc_final: 0.8695 (t) REVERT: N 179 GLN cc_start: 0.9007 (pp30) cc_final: 0.8392 (pm20) REVERT: N 185 MET cc_start: 0.9080 (ppp) cc_final: 0.8826 (ppp) REVERT: Y 20 LEU cc_start: 0.9630 (pp) cc_final: 0.9399 (pp) REVERT: Y 55 MET cc_start: 0.9250 (tmm) cc_final: 0.8969 (tmm) REVERT: Y 56 LEU cc_start: 0.9465 (mt) cc_final: 0.9151 (mt) REVERT: Y 63 GLN cc_start: 0.9009 (mm110) cc_final: 0.8638 (mm-40) REVERT: Y 113 GLU cc_start: 0.8669 (pm20) cc_final: 0.8304 (pm20) REVERT: Y 139 ASN cc_start: 0.9435 (m-40) cc_final: 0.9096 (m110) REVERT: d 23 TRP cc_start: 0.8494 (t-100) cc_final: 0.8204 (t-100) REVERT: d 39 MET cc_start: 0.7535 (tpp) cc_final: 0.7173 (tpt) REVERT: d 112 GLN cc_start: 0.9518 (mp10) cc_final: 0.9092 (tm-30) REVERT: d 129 ILE cc_start: 0.9582 (tp) cc_final: 0.9266 (tp) REVERT: d 130 TYR cc_start: 0.7433 (t80) cc_final: 0.6980 (t80) REVERT: d 132 ARG cc_start: 0.9534 (ttp-110) cc_final: 0.9324 (ttp80) REVERT: d 139 ASN cc_start: 0.9678 (m-40) cc_final: 0.9210 (m110) REVERT: d 140 LYS cc_start: 0.9293 (mtmm) cc_final: 0.9073 (mtmm) REVERT: d 143 ARG cc_start: 0.9168 (mtt180) cc_final: 0.8822 (mtt90) REVERT: d 152 ASP cc_start: 0.8146 (m-30) cc_final: 0.7789 (m-30) REVERT: d 167 ARG cc_start: 0.8429 (mmp-170) cc_final: 0.7937 (mmp80) REVERT: e 25 LYS cc_start: 0.9620 (pttm) cc_final: 0.8880 (ptpp) REVERT: e 66 MET cc_start: 0.9118 (mmm) cc_final: 0.8534 (mmm) REVERT: e 70 LYS cc_start: 0.9240 (ptpp) cc_final: 0.8874 (ptpt) REVERT: e 79 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8736 (pp20) REVERT: e 82 ARG cc_start: 0.9077 (tmm160) cc_final: 0.8776 (ttp80) REVERT: e 117 TRP cc_start: 0.8811 (m-10) cc_final: 0.8610 (m-10) REVERT: e 118 MET cc_start: 0.8830 (mtt) cc_final: 0.8152 (mmp) REVERT: e 132 ARG cc_start: 0.9312 (ptp90) cc_final: 0.8994 (ptp-170) REVERT: e 139 ASN cc_start: 0.9603 (m-40) cc_final: 0.9284 (m110) REVERT: e 185 MET cc_start: 0.9063 (mtm) cc_final: 0.8859 (mtp) REVERT: k 44 SER cc_start: 0.9357 (p) cc_final: 0.8845 (p) REVERT: k 76 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9127 (mm-30) REVERT: k 81 ASP cc_start: 0.9183 (m-30) cc_final: 0.8763 (m-30) REVERT: k 96 MET cc_start: 0.5076 (ttm) cc_final: 0.4539 (ptp) REVERT: k 100 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7584 (tpm170) REVERT: k 104 ILE cc_start: 0.8593 (mm) cc_final: 0.8229 (mm) REVERT: k 131 LYS cc_start: 0.9290 (ttmt) cc_final: 0.8959 (tttt) REVERT: k 132 ARG cc_start: 0.9444 (ttp-110) cc_final: 0.9065 (ptp-170) REVERT: k 211 LEU cc_start: 0.9345 (tt) cc_final: 0.8911 (tt) outliers start: 2 outliers final: 0 residues processed: 760 average time/residue: 0.1466 time to fit residues: 162.1283 Evaluate side-chains 611 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 611 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 108 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 133 optimal weight: 40.0000 chunk 209 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 230 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 108 ASN J 163 GLN Y 95 GLN ** Y 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 HIS ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 12 HIS k 9 GLN k 53 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.099302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.076192 restraints weight = 74959.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.078358 restraints weight = 51686.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.079914 restraints weight = 39354.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.081006 restraints weight = 32047.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.081874 restraints weight = 27521.755| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.8078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18834 Z= 0.165 Angle : 0.724 10.208 25587 Z= 0.377 Chirality : 0.047 0.301 2848 Planarity : 0.005 0.075 3345 Dihedral : 4.717 38.120 2500 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.05 % Allowed : 0.85 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2338 helix: 0.50 (0.14), residues: 1441 sheet: -0.62 (0.69), residues: 52 loop : -0.32 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 82 TYR 0.026 0.002 TYR e 130 PHE 0.022 0.002 PHE Y 40 TRP 0.043 0.002 TRP D 184 HIS 0.006 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00364 (18824) covalent geometry : angle 0.72278 (25567) SS BOND : bond 0.00243 ( 10) SS BOND : angle 1.53050 ( 20) hydrogen bonds : bond 0.04410 ( 1037) hydrogen bonds : angle 4.85104 ( 3081) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 754 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8499 (t) cc_final: 0.8220 (p) REVERT: A 41 SER cc_start: 0.9534 (m) cc_final: 0.9133 (m) REVERT: A 50 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8895 (tm-30) REVERT: A 51 ASP cc_start: 0.9342 (m-30) cc_final: 0.9024 (m-30) REVERT: A 52 LEU cc_start: 0.9785 (mm) cc_final: 0.9578 (mm) REVERT: A 56 LEU cc_start: 0.9427 (mt) cc_final: 0.9224 (mt) REVERT: A 57 ASN cc_start: 0.9641 (m110) cc_final: 0.9412 (m-40) REVERT: A 71 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8795 (tm-30) REVERT: A 113 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8784 (mt-10) REVERT: A 128 GLU cc_start: 0.9519 (mp0) cc_final: 0.9223 (pm20) REVERT: B 10 MET cc_start: 0.8926 (mmp) cc_final: 0.8587 (mmp) REVERT: B 30 LYS cc_start: 0.8875 (mmpt) cc_final: 0.8554 (mmmm) REVERT: B 32 PHE cc_start: 0.8654 (m-80) cc_final: 0.8309 (m-80) REVERT: B 43 LEU cc_start: 0.9704 (tp) cc_final: 0.9451 (tp) REVERT: B 51 ASP cc_start: 0.9328 (m-30) cc_final: 0.9113 (m-30) REVERT: B 66 MET cc_start: 0.8348 (mmm) cc_final: 0.8083 (mmm) REVERT: B 70 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8875 (mttm) REVERT: B 74 ASN cc_start: 0.9456 (m-40) cc_final: 0.9169 (m110) REVERT: B 82 ARG cc_start: 0.9021 (ttp80) cc_final: 0.8574 (ttp80) REVERT: B 86 VAL cc_start: 0.7994 (t) cc_final: 0.7177 (p) REVERT: B 131 LYS cc_start: 0.9627 (mttt) cc_final: 0.9370 (mmtt) REVERT: B 139 ASN cc_start: 0.9527 (m-40) cc_final: 0.9232 (m-40) REVERT: C 48 THR cc_start: 0.9350 (p) cc_final: 0.9110 (p) REVERT: C 53 ASN cc_start: 0.9449 (m-40) cc_final: 0.9132 (m110) REVERT: C 55 MET cc_start: 0.9261 (ttm) cc_final: 0.8829 (ttp) REVERT: C 67 GLN cc_start: 0.8420 (pm20) cc_final: 0.8015 (pm20) REVERT: C 79 GLU cc_start: 0.8787 (mp0) cc_final: 0.8544 (mp0) REVERT: C 128 GLU cc_start: 0.9167 (mp0) cc_final: 0.8918 (mp0) REVERT: C 139 ASN cc_start: 0.9152 (t0) cc_final: 0.8010 (t0) REVERT: C 143 ARG cc_start: 0.9503 (mtt180) cc_final: 0.9077 (mtt180) REVERT: C 187 GLU cc_start: 0.9305 (mp0) cc_final: 0.9025 (mp0) REVERT: C 189 LEU cc_start: 0.9348 (mm) cc_final: 0.9025 (mp) REVERT: D 56 LEU cc_start: 0.9756 (mt) cc_final: 0.9467 (mt) REVERT: D 70 LYS cc_start: 0.9466 (pttm) cc_final: 0.9235 (pttm) REVERT: D 130 TYR cc_start: 0.9273 (t80) cc_final: 0.8853 (t80) REVERT: D 131 LYS cc_start: 0.9308 (tttt) cc_final: 0.8912 (mtpt) REVERT: D 141 ILE cc_start: 0.8899 (mt) cc_final: 0.8673 (mt) REVERT: D 143 ARG cc_start: 0.8630 (mmm160) cc_final: 0.8025 (mmm160) REVERT: D 145 TYR cc_start: 0.8494 (t80) cc_final: 0.8110 (t80) REVERT: D 163 ASP cc_start: 0.8587 (m-30) cc_final: 0.8372 (m-30) REVERT: D 215 MET cc_start: 0.8161 (ttt) cc_final: 0.7557 (ttm) REVERT: G 23 TRP cc_start: 0.9335 (t-100) cc_final: 0.8832 (t-100) REVERT: G 39 MET cc_start: 0.9438 (ttp) cc_final: 0.8930 (tpt) REVERT: G 57 ASN cc_start: 0.9357 (m-40) cc_final: 0.9104 (m110) REVERT: G 68 MET cc_start: 0.7132 (mtt) cc_final: 0.6927 (mtp) REVERT: G 96 MET cc_start: 0.1784 (mpp) cc_final: 0.0766 (mmm) REVERT: G 131 LYS cc_start: 0.9416 (ttmt) cc_final: 0.9165 (tttt) REVERT: G 139 ASN cc_start: 0.9587 (m110) cc_final: 0.9382 (m110) REVERT: G 168 PHE cc_start: 0.9434 (t80) cc_final: 0.9130 (t80) REVERT: G 181 VAL cc_start: 0.9269 (t) cc_final: 0.8995 (p) REVERT: G 185 MET cc_start: 0.9004 (mtt) cc_final: 0.8373 (mtt) REVERT: G 211 LEU cc_start: 0.9148 (tp) cc_final: 0.8785 (tp) REVERT: H 129 ILE cc_start: 0.8820 (tt) cc_final: 0.8304 (tt) REVERT: H 130 TYR cc_start: 0.5926 (t80) cc_final: 0.5545 (t80) REVERT: H 133 TRP cc_start: 0.8374 (m-10) cc_final: 0.7393 (m-10) REVERT: H 152 ASP cc_start: 0.8266 (m-30) cc_final: 0.8039 (m-30) REVERT: H 161 PHE cc_start: 0.7980 (t80) cc_final: 0.7003 (t80) REVERT: H 167 ARG cc_start: 0.9047 (mmm160) cc_final: 0.8399 (mmm160) REVERT: H 215 MET cc_start: 0.9058 (tpt) cc_final: 0.8542 (tpt) REVERT: J 6 VAL cc_start: 0.9184 (t) cc_final: 0.8485 (p) REVERT: J 24 LEU cc_start: 0.9138 (mp) cc_final: 0.8614 (mm) REVERT: J 25 PHE cc_start: 0.8464 (m-80) cc_final: 0.7768 (m-80) REVERT: J 32 THR cc_start: 0.8866 (t) cc_final: 0.8637 (t) REVERT: J 35 ASN cc_start: 0.8750 (m-40) cc_final: 0.7020 (m-40) REVERT: J 43 GLU cc_start: 0.8587 (pp20) cc_final: 0.8282 (pp20) REVERT: J 76 LYS cc_start: 0.6561 (mttt) cc_final: 0.6177 (tppp) REVERT: J 78 ILE cc_start: 0.8805 (pt) cc_final: 0.8594 (pt) REVERT: J 97 ILE cc_start: 0.8190 (mm) cc_final: 0.7417 (tp) REVERT: J 111 GLN cc_start: 0.9138 (mp-120) cc_final: 0.8728 (mm-40) REVERT: J 122 LEU cc_start: 0.8460 (mt) cc_final: 0.8152 (mt) REVERT: J 152 THR cc_start: 0.8946 (p) cc_final: 0.8699 (t) REVERT: N 172 LEU cc_start: 0.8980 (mt) cc_final: 0.8466 (mt) REVERT: N 179 GLN cc_start: 0.9146 (pp30) cc_final: 0.8432 (pm20) REVERT: N 182 LYS cc_start: 0.9154 (mttt) cc_final: 0.8665 (mmmt) REVERT: Y 5 ASN cc_start: 0.8379 (t0) cc_final: 0.8083 (t0) REVERT: Y 20 LEU cc_start: 0.9711 (pp) cc_final: 0.9433 (pp) REVERT: Y 56 LEU cc_start: 0.9475 (mt) cc_final: 0.9216 (mt) REVERT: Y 63 GLN cc_start: 0.8988 (mm110) cc_final: 0.8587 (mm-40) REVERT: Y 139 ASN cc_start: 0.9473 (m-40) cc_final: 0.9124 (m110) REVERT: d 66 MET cc_start: 0.9274 (mtm) cc_final: 0.8921 (mtp) REVERT: d 67 GLN cc_start: 0.8813 (mt0) cc_final: 0.8424 (pp30) REVERT: d 112 GLN cc_start: 0.9499 (mp10) cc_final: 0.9048 (tm-30) REVERT: d 130 TYR cc_start: 0.7523 (t80) cc_final: 0.6978 (t80) REVERT: d 139 ASN cc_start: 0.9689 (m-40) cc_final: 0.9281 (m110) REVERT: d 143 ARG cc_start: 0.9156 (mtt180) cc_final: 0.8799 (mtm-85) REVERT: d 152 ASP cc_start: 0.8201 (m-30) cc_final: 0.7813 (m-30) REVERT: e 39 MET cc_start: 0.9431 (tpp) cc_final: 0.9163 (tpp) REVERT: e 57 ASN cc_start: 0.9362 (m110) cc_final: 0.9113 (m110) REVERT: e 79 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8762 (pp20) REVERT: e 82 ARG cc_start: 0.9093 (tmm160) cc_final: 0.8781 (ttp80) REVERT: e 118 MET cc_start: 0.8759 (mtt) cc_final: 0.8036 (mmp) REVERT: e 132 ARG cc_start: 0.9343 (ptp90) cc_final: 0.9028 (ptp-170) REVERT: j 215 MET cc_start: 0.8552 (ppp) cc_final: 0.8328 (ppp) REVERT: k 25 LYS cc_start: 0.9539 (ptmm) cc_final: 0.9325 (ptmm) REVERT: k 55 MET cc_start: 0.9503 (ttm) cc_final: 0.9235 (ttm) REVERT: k 96 MET cc_start: 0.5126 (ttm) cc_final: 0.4568 (ptp) REVERT: k 104 ILE cc_start: 0.8650 (mm) cc_final: 0.8362 (mm) REVERT: k 131 LYS cc_start: 0.9291 (ttmt) cc_final: 0.9045 (mtpt) REVERT: k 132 ARG cc_start: 0.9437 (ttp-110) cc_final: 0.9057 (ptp-170) REVERT: k 173 ARG cc_start: 0.8974 (ttt180) cc_final: 0.8591 (tmm-80) REVERT: k 211 LEU cc_start: 0.9373 (tt) cc_final: 0.8934 (tt) outliers start: 1 outliers final: 0 residues processed: 754 average time/residue: 0.1470 time to fit residues: 161.8322 Evaluate side-chains 606 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 606 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 225 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 193 optimal weight: 0.5980 chunk 208 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 202 optimal weight: 30.0000 chunk 228 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS J 108 ASN J 163 GLN ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 GLN ** Y 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 9 GLN k 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.100274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.077016 restraints weight = 74670.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.079198 restraints weight = 51540.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.080762 restraints weight = 39322.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.081886 restraints weight = 32044.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.082740 restraints weight = 27501.176| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.8274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18834 Z= 0.157 Angle : 0.739 10.742 25587 Z= 0.387 Chirality : 0.048 0.294 2848 Planarity : 0.005 0.073 3345 Dihedral : 4.726 37.842 2500 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.05 % Allowed : 0.60 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.17), residues: 2338 helix: 0.54 (0.14), residues: 1435 sheet: 0.34 (0.89), residues: 34 loop : -0.31 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG j 167 TYR 0.031 0.002 TYR j 169 PHE 0.023 0.002 PHE A 40 TRP 0.043 0.002 TRP D 184 HIS 0.006 0.001 HIS d 84 Details of bonding type rmsd covalent geometry : bond 0.00350 (18824) covalent geometry : angle 0.73833 (25567) SS BOND : bond 0.00171 ( 10) SS BOND : angle 1.37735 ( 20) hydrogen bonds : bond 0.04412 ( 1037) hydrogen bonds : angle 4.96162 ( 3081) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 759 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8383 (t) cc_final: 0.8161 (p) REVERT: A 41 SER cc_start: 0.9526 (m) cc_final: 0.9211 (m) REVERT: A 50 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8851 (tm-30) REVERT: A 51 ASP cc_start: 0.9328 (m-30) cc_final: 0.8993 (m-30) REVERT: A 52 LEU cc_start: 0.9799 (mm) cc_final: 0.9538 (mm) REVERT: A 57 ASN cc_start: 0.9630 (m110) cc_final: 0.9397 (m-40) REVERT: A 63 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8135 (mp10) REVERT: A 71 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8843 (tm-30) REVERT: A 113 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8839 (mt-10) REVERT: A 144 MET cc_start: 0.8981 (ttt) cc_final: 0.8752 (ttt) REVERT: B 10 MET cc_start: 0.8935 (mmp) cc_final: 0.8575 (mmp) REVERT: B 30 LYS cc_start: 0.8905 (mmpt) cc_final: 0.8559 (mmmm) REVERT: B 32 PHE cc_start: 0.8653 (m-80) cc_final: 0.8338 (m-80) REVERT: B 51 ASP cc_start: 0.9317 (m-30) cc_final: 0.9113 (m-30) REVERT: B 70 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8842 (mttm) REVERT: B 74 ASN cc_start: 0.9454 (m-40) cc_final: 0.9166 (m110) REVERT: B 82 ARG cc_start: 0.9027 (ttp80) cc_final: 0.8580 (ttp80) REVERT: B 86 VAL cc_start: 0.8028 (t) cc_final: 0.7266 (p) REVERT: B 139 ASN cc_start: 0.9529 (m-40) cc_final: 0.9238 (m-40) REVERT: C 48 THR cc_start: 0.9377 (p) cc_final: 0.9143 (p) REVERT: C 53 ASN cc_start: 0.9461 (m-40) cc_final: 0.9140 (m110) REVERT: C 55 MET cc_start: 0.9259 (ttm) cc_final: 0.8870 (ttp) REVERT: C 67 GLN cc_start: 0.8244 (pm20) cc_final: 0.8014 (pm20) REVERT: C 128 GLU cc_start: 0.9157 (mp0) cc_final: 0.8927 (mp0) REVERT: C 129 ILE cc_start: 0.9063 (mt) cc_final: 0.8775 (mt) REVERT: C 139 ASN cc_start: 0.9152 (t0) cc_final: 0.8056 (t0) REVERT: C 143 ARG cc_start: 0.9483 (mtt180) cc_final: 0.9082 (mtt180) REVERT: C 182 LYS cc_start: 0.9465 (mttm) cc_final: 0.9234 (mttt) REVERT: C 187 GLU cc_start: 0.9268 (mp0) cc_final: 0.9044 (mp0) REVERT: C 189 LEU cc_start: 0.9314 (mm) cc_final: 0.8962 (mp) REVERT: D 56 LEU cc_start: 0.9778 (mt) cc_final: 0.9478 (mt) REVERT: D 57 ASN cc_start: 0.9653 (m110) cc_final: 0.9403 (m110) REVERT: D 70 LYS cc_start: 0.9445 (pttm) cc_final: 0.9216 (pttm) REVERT: D 130 TYR cc_start: 0.9254 (t80) cc_final: 0.8847 (t80) REVERT: D 131 LYS cc_start: 0.9339 (tttt) cc_final: 0.8931 (mtpt) REVERT: D 134 ILE cc_start: 0.9748 (mt) cc_final: 0.9521 (mt) REVERT: D 141 ILE cc_start: 0.8892 (mt) cc_final: 0.8650 (mt) REVERT: D 143 ARG cc_start: 0.8669 (mmm160) cc_final: 0.8026 (mmm160) REVERT: D 145 TYR cc_start: 0.8478 (t80) cc_final: 0.8116 (t80) REVERT: D 163 ASP cc_start: 0.8558 (m-30) cc_final: 0.8345 (m-30) REVERT: D 215 MET cc_start: 0.8100 (ttt) cc_final: 0.7501 (ttm) REVERT: G 23 TRP cc_start: 0.9241 (t-100) cc_final: 0.8807 (t-100) REVERT: G 39 MET cc_start: 0.9430 (ttp) cc_final: 0.9089 (tpt) REVERT: G 55 MET cc_start: 0.9571 (tmm) cc_final: 0.9306 (tmm) REVERT: G 57 ASN cc_start: 0.9317 (m-40) cc_final: 0.9020 (m110) REVERT: G 68 MET cc_start: 0.7024 (mtt) cc_final: 0.6786 (mtp) REVERT: G 96 MET cc_start: 0.1749 (mpp) cc_final: 0.0945 (mmm) REVERT: G 131 LYS cc_start: 0.9406 (ttmt) cc_final: 0.9142 (tttt) REVERT: G 139 ASN cc_start: 0.9565 (m110) cc_final: 0.9337 (m110) REVERT: G 168 PHE cc_start: 0.9432 (t80) cc_final: 0.9101 (t80) REVERT: G 181 VAL cc_start: 0.9275 (t) cc_final: 0.9019 (p) REVERT: G 185 MET cc_start: 0.8990 (mtt) cc_final: 0.8368 (mtt) REVERT: H 55 MET cc_start: 0.9137 (mmp) cc_final: 0.8891 (mmt) REVERT: H 129 ILE cc_start: 0.8816 (tt) cc_final: 0.8296 (tt) REVERT: H 130 TYR cc_start: 0.5978 (t80) cc_final: 0.5556 (t80) REVERT: H 131 LYS cc_start: 0.8788 (mttp) cc_final: 0.8452 (mptt) REVERT: H 133 TRP cc_start: 0.8369 (m-10) cc_final: 0.7393 (m-10) REVERT: H 152 ASP cc_start: 0.8213 (m-30) cc_final: 0.7955 (m-30) REVERT: H 161 PHE cc_start: 0.7998 (t80) cc_final: 0.7075 (t80) REVERT: H 167 ARG cc_start: 0.9037 (mmm160) cc_final: 0.8398 (mmm160) REVERT: H 215 MET cc_start: 0.9052 (tpt) cc_final: 0.8534 (tpt) REVERT: J 6 VAL cc_start: 0.9110 (t) cc_final: 0.8446 (p) REVERT: J 24 LEU cc_start: 0.9152 (mp) cc_final: 0.8621 (mm) REVERT: J 25 PHE cc_start: 0.8393 (m-80) cc_final: 0.7698 (m-80) REVERT: J 35 ASN cc_start: 0.8701 (m-40) cc_final: 0.7233 (m-40) REVERT: J 43 GLU cc_start: 0.8556 (pp20) cc_final: 0.8194 (pp20) REVERT: J 76 LYS cc_start: 0.6520 (mttt) cc_final: 0.5966 (tppp) REVERT: J 97 ILE cc_start: 0.8277 (mm) cc_final: 0.7618 (tp) REVERT: J 111 GLN cc_start: 0.9121 (mp-120) cc_final: 0.8734 (mm-40) REVERT: J 122 LEU cc_start: 0.8418 (mt) cc_final: 0.8166 (mt) REVERT: J 152 THR cc_start: 0.8887 (p) cc_final: 0.8631 (t) REVERT: N 179 GLN cc_start: 0.9190 (pp30) cc_final: 0.7955 (pm20) REVERT: N 182 LYS cc_start: 0.9193 (mttt) cc_final: 0.8750 (mttt) REVERT: N 213 GLU cc_start: 0.8890 (pm20) cc_final: 0.8676 (pm20) REVERT: Y 5 ASN cc_start: 0.8400 (t0) cc_final: 0.8108 (t0) REVERT: Y 20 LEU cc_start: 0.9693 (pp) cc_final: 0.9418 (pp) REVERT: Y 55 MET cc_start: 0.9310 (tmm) cc_final: 0.9030 (tmm) REVERT: Y 56 LEU cc_start: 0.9465 (mt) cc_final: 0.9159 (mt) REVERT: Y 63 GLN cc_start: 0.8946 (mm110) cc_final: 0.8534 (mm-40) REVERT: Y 144 MET cc_start: 0.8818 (ppp) cc_final: 0.8587 (ppp) REVERT: d 23 TRP cc_start: 0.8315 (t-100) cc_final: 0.8033 (t-100) REVERT: d 66 MET cc_start: 0.9255 (mtm) cc_final: 0.8967 (mtp) REVERT: d 67 GLN cc_start: 0.8767 (mt0) cc_final: 0.8513 (pp30) REVERT: d 112 GLN cc_start: 0.9512 (mp10) cc_final: 0.9080 (tm-30) REVERT: d 129 ILE cc_start: 0.9615 (tp) cc_final: 0.9256 (tp) REVERT: d 139 ASN cc_start: 0.9672 (m-40) cc_final: 0.9265 (m110) REVERT: d 143 ARG cc_start: 0.9201 (mtt180) cc_final: 0.8822 (mtm-85) REVERT: d 152 ASP cc_start: 0.8189 (m-30) cc_final: 0.7803 (m-30) REVERT: d 167 ARG cc_start: 0.8403 (mmp-170) cc_final: 0.7962 (mmp80) REVERT: d 214 MET cc_start: 0.8666 (mpp) cc_final: 0.8345 (mpp) REVERT: e 23 TRP cc_start: 0.9311 (t-100) cc_final: 0.9016 (t-100) REVERT: e 25 LYS cc_start: 0.9448 (ptpp) cc_final: 0.8640 (ptpp) REVERT: e 39 MET cc_start: 0.9373 (tpp) cc_final: 0.9149 (tpp) REVERT: e 40 PHE cc_start: 0.9308 (t80) cc_final: 0.8973 (t80) REVERT: e 55 MET cc_start: 0.9010 (ttt) cc_final: 0.8293 (ttm) REVERT: e 57 ASN cc_start: 0.9346 (m110) cc_final: 0.9080 (m110) REVERT: e 79 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8781 (pp20) REVERT: e 82 ARG cc_start: 0.9116 (tmm160) cc_final: 0.8793 (ttp80) REVERT: e 118 MET cc_start: 0.8756 (mtt) cc_final: 0.8074 (mmp) REVERT: e 132 ARG cc_start: 0.9344 (ptp90) cc_final: 0.9074 (ptp-170) REVERT: e 139 ASN cc_start: 0.9566 (m-40) cc_final: 0.9242 (m110) REVERT: e 215 MET cc_start: 0.8227 (ptm) cc_final: 0.7821 (ptp) REVERT: k 55 MET cc_start: 0.9499 (ttm) cc_final: 0.9233 (ttm) REVERT: k 96 MET cc_start: 0.5032 (ttm) cc_final: 0.4530 (ptp) REVERT: k 104 ILE cc_start: 0.8496 (mm) cc_final: 0.8248 (mm) REVERT: k 131 LYS cc_start: 0.9326 (ttmt) cc_final: 0.9050 (mtpt) REVERT: k 132 ARG cc_start: 0.9427 (ttp-110) cc_final: 0.9060 (ptp-170) REVERT: k 173 ARG cc_start: 0.8989 (ttt180) cc_final: 0.8588 (tmm-80) REVERT: k 211 LEU cc_start: 0.9373 (tt) cc_final: 0.8960 (tt) outliers start: 1 outliers final: 0 residues processed: 759 average time/residue: 0.1473 time to fit residues: 162.8062 Evaluate side-chains 612 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 62 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 145 optimal weight: 40.0000 chunk 184 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN J 92 HIS J 108 ASN J 163 GLN ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 ASN ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 GLN ** Y 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 9 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.098425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.075457 restraints weight = 76913.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.077637 restraints weight = 52698.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.079202 restraints weight = 39840.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.080258 restraints weight = 32351.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.081122 restraints weight = 27803.438| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.8566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18834 Z= 0.185 Angle : 0.770 11.076 25587 Z= 0.405 Chirality : 0.049 0.278 2848 Planarity : 0.006 0.072 3345 Dihedral : 4.911 38.475 2500 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.05 % Allowed : 0.55 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2338 helix: 0.32 (0.13), residues: 1435 sheet: 0.40 (0.89), residues: 34 loop : -0.41 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG j 167 TYR 0.031 0.002 TYR e 130 PHE 0.020 0.002 PHE Y 40 TRP 0.076 0.003 TRP Y 117 HIS 0.006 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00411 (18824) covalent geometry : angle 0.76928 (25567) SS BOND : bond 0.00205 ( 10) SS BOND : angle 1.38592 ( 20) hydrogen bonds : bond 0.04565 ( 1037) hydrogen bonds : angle 5.12029 ( 3081) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.55 seconds wall clock time: 65 minutes 58.57 seconds (3958.57 seconds total)