Starting phenix.real_space_refine on Thu Mar 5 01:11:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y9z_10742/03_2026/6y9z_10742.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y9z_10742/03_2026/6y9z_10742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y9z_10742/03_2026/6y9z_10742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y9z_10742/03_2026/6y9z_10742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y9z_10742/03_2026/6y9z_10742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y9z_10742/03_2026/6y9z_10742.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 4.19, per 1000 atoms: 0.23 Number of scatterers: 18418 At special positions: 0 Unit cell: (139.92, 182.32, 104.94, 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: 1.59 Conformation dependent library (CDL) restraints added in 797.6 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: 0.53 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: 3.526A 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: 3.792A 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: 3.595A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.805A 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: 4.008A 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: 3.536A pdb=" N GLU C 187 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.961A 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: 3.872A 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: 4.766A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.878A 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: 3.896A pdb=" N TRP G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.893A 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: 4.893A 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: 4.121A 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: 3.789A 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: 3.592A 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: 3.676A 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: 3.700A pdb=" N GLN Y 114 " --> pdb=" O THR Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 126 through 146 removed outlier: 3.602A pdb=" N ARG Y 132 " --> pdb=" O GLU Y 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 30 removed outlier: 3.672A 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: 4.876A 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: 3.905A 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: 3.905A 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: 3.523A 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: 3.581A 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: 3.922A 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: 4.394A 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: 6.543A pdb=" N VAL J 128 " --> pdb=" O MET J 100 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER J 21 " --> pdb=" O LYS J 133 " (cutoff:3.500A) removed outlier: 6.101A 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: 3.511A pdb=" N ASP J 160 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA J 11 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 5.523A 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: 3.766A 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: 3.539A 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: 2.90 Time building geometry restraints manager: 2.12 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: 7779 1.44 - 1.67: 10790 1.67 - 1.90: 252 1.90 - 2.13: 0 2.13 - 2.36: 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 -0.907 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 2.365 -0.843 1.37e-02 5.33e+03 3.79e+03 bond pdb=" N ARG C 18 " pdb=" CA ARG C 18 " ideal model delta sigma weight residual 1.456 2.273 -0.816 1.33e-02 5.65e+03 3.77e+03 bond pdb=" C HIS e 84 " pdb=" N PRO e 85 " ideal model delta sigma weight residual 1.330 1.513 -0.183 1.22e-02 6.72e+03 2.25e+02 bond pdb=" CD2 HIS J 54 " pdb=" NE2 HIS J 54 " ideal model delta sigma weight residual 1.374 1.292 0.082 1.10e-02 8.26e+03 5.51e+01 ... (remaining 18819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.82: 25549 9.82 - 19.64: 14 19.64 - 29.45: 3 29.45 - 39.27: 0 39.27 - 49.09: 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 64.14 49.09 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 118.21 145.62 -27.41 1.36e+00 5.41e-01 4.06e+02 angle pdb=" O PRO C 147 " pdb=" C PRO C 147 " pdb=" N THR C 148 " ideal model delta sigma weight residual 122.30 108.72 13.58 1.36e+00 5.41e-01 9.97e+01 angle pdb=" C HIS e 84 " pdb=" N PRO e 85 " pdb=" CA PRO e 85 " ideal model delta sigma weight residual 120.03 129.81 -9.78 9.90e-01 1.02e+00 9.76e+01 ... (remaining 25562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10634 17.97 - 35.93: 712 35.93 - 53.90: 179 53.90 - 71.86: 19 71.86 - 89.83: 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 -163.17 40.57 0 2.50e+00 1.60e-01 2.63e+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 122.80 158.73 -35.93 0 2.50e+00 1.60e-01 2.06e+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 -134.83 48.83 1 1.00e+01 1.00e-02 3.28e+01 ... (remaining 11554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.945: 2846 0.945 - 1.889: 1 1.889 - 2.834: 0 2.834 - 3.778: 0 3.778 - 4.723: 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 7.23 -4.72 2.00e-01 2.50e+01 5.58e+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 6.58e+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 0.43 2.00e-01 2.50e+01 4.53e+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 7.91e-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 " -0.065 2.00e-02 2.50e+03 9.96e-02 9.93e+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 7.85e-02 6.16e+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: 1.63 - 2.29: 6 2.29 - 2.94: 7722 2.94 - 3.59: 27516 3.59 - 4.25: 40149 4.25 - 4.90: 65743 Nonbonded interactions: 141136 Sorted by model distance: nonbonded pdb=" CG2 VAL G 181 " pdb=" OE1 GLU d 180 " model vdw 1.631 3.460 nonbonded pdb=" OE1 GLN G 7 " pdb=" NE2 GLN k 9 " model vdw 1.829 3.120 nonbonded pdb=" OE1 GLU D 180 " pdb=" CG2 VAL H 181 " model vdw 1.926 3.460 nonbonded pdb=" CD2 LEU C 151 " pdb=" OE1 GLN k 192 " model vdw 2.058 3.460 nonbonded pdb=" NH2 ARG C 143 " pdb=" O GLN C 176 " model vdw 2.124 3.120 ... (remaining 141131 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: 0.170 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.690 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 0.907 18834 Z= 0.922 Angle : 1.068 49.088 25587 Z= 0.726 Chirality : 0.108 4.723 2848 Planarity : 0.007 0.100 3345 Dihedral : 13.054 89.825 7127 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.93 % Favored : 98.03 % 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 0.099 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 0.01240 (18824) covalent geometry : angle 1.06846 (25567) SS BOND : bond 0.00321 ( 10) SS BOND : angle 0.97908 ( 20) hydrogen bonds : bond 0.13585 ( 1037) hydrogen bonds : angle 5.13690 ( 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 1194 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1185 time to evaluate : 0.678 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 9 GLN cc_start: 0.9334 (mp10) cc_final: 0.9089 (pp30) REVERT: A 27 VAL cc_start: 0.9711 (t) cc_final: 0.9259 (t) REVERT: A 49 PRO cc_start: 0.9711 (Cg_exo) cc_final: 0.9399 (Cg_endo) REVERT: A 55 MET cc_start: 0.9348 (mtp) cc_final: 0.9137 (mtp) REVERT: A 67 GLN cc_start: 0.9635 (tp40) cc_final: 0.9397 (tm-30) REVERT: A 72 THR cc_start: 0.9752 (m) cc_final: 0.9389 (p) REVERT: A 79 GLU cc_start: 0.9671 (tm-30) cc_final: 0.9457 (pp20) REVERT: A 114 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8352 (pt0) REVERT: A 125 PRO cc_start: 0.9091 (Cg_exo) cc_final: 0.8768 (Cg_endo) REVERT: A 135 ILE cc_start: 0.9473 (mt) cc_final: 0.9151 (mt) REVERT: B 5 ASN cc_start: 0.9137 (t0) cc_final: 0.8863 (m110) REVERT: B 28 GLU cc_start: 0.9350 (tt0) cc_final: 0.9134 (mt-10) REVERT: B 30 LYS cc_start: 0.8752 (mmtp) cc_final: 0.7826 (mmtm) REVERT: B 35 GLU cc_start: 0.9335 (pm20) cc_final: 0.8956 (pp20) REVERT: B 39 MET cc_start: 0.9497 (tpp) cc_final: 0.8999 (tpp) REVERT: B 51 ASP cc_start: 0.9007 (m-30) cc_final: 0.8782 (m-30) REVERT: B 59 VAL cc_start: 0.9548 (t) cc_final: 0.9293 (t) REVERT: B 75 GLU cc_start: 0.9567 (tt0) cc_final: 0.9354 (pt0) REVERT: B 114 GLN cc_start: 0.9224 (mt0) cc_final: 0.8554 (mt0) REVERT: B 118 MET cc_start: 0.9530 (mtm) cc_final: 0.9172 (mmm) REVERT: B 165 VAL cc_start: 0.9714 (p) cc_final: 0.8913 (m) REVERT: B 169 TYR cc_start: 0.9134 (m-10) cc_final: 0.8838 (m-10) REVERT: B 181 VAL cc_start: 0.9521 (t) cc_final: 0.9205 (t) REVERT: B 187 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9191 (pp20) REVERT: B 193 ASN cc_start: 0.9108 (m110) cc_final: 0.8901 (m-40) REVERT: B 203 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7696 (mtmt) REVERT: B 213 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9128 (pt0) REVERT: C 23 TRP cc_start: 0.9387 (t-100) cc_final: 0.9006 (t-100) REVERT: C 26 VAL cc_start: 0.9508 (p) cc_final: 0.9241 (p) REVERT: C 32 PHE cc_start: 0.8316 (m-80) cc_final: 0.7847 (m-80) REVERT: C 43 LEU cc_start: 0.9433 (mt) cc_final: 0.8606 (mm) REVERT: C 51 ASP cc_start: 0.9568 (m-30) cc_final: 0.9156 (m-30) REVERT: C 53 ASN cc_start: 0.9492 (m-40) cc_final: 0.9238 (m110) REVERT: C 55 MET cc_start: 0.8965 (mtp) cc_final: 0.8753 (ttp) REVERT: C 72 THR cc_start: 0.9049 (m) cc_final: 0.8503 (p) REVERT: C 75 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9094 (pt0) REVERT: C 76 GLU cc_start: 0.9521 (mm-30) cc_final: 0.8962 (mm-30) REVERT: C 96 MET cc_start: -0.4731 (mmt) cc_final: -0.5321 (mtm) REVERT: C 103 ASP cc_start: 0.8946 (m-30) cc_final: 0.8516 (m-30) REVERT: C 104 ILE cc_start: 0.8580 (mm) cc_final: 0.8349 (tt) REVERT: C 118 MET cc_start: 0.8987 (ttm) cc_final: 0.8585 (ttm) REVERT: C 129 ILE cc_start: 0.9540 (mt) cc_final: 0.9322 (mt) REVERT: C 140 LYS cc_start: 0.9260 (mttt) cc_final: 0.8803 (tptp) REVERT: C 159 GLU cc_start: 0.9345 (tt0) cc_final: 0.9053 (mp0) REVERT: C 179 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8560 (tm-30) REVERT: C 199 LYS cc_start: 0.9505 (tttt) cc_final: 0.9165 (tptp) REVERT: D 23 TRP cc_start: 0.9605 (t-100) cc_final: 0.8949 (t60) REVERT: D 24 VAL cc_start: 0.9609 (m) cc_final: 0.9398 (p) REVERT: D 49 PRO cc_start: 0.9559 (Cg_exo) cc_final: 0.9320 (Cg_endo) REVERT: D 52 LEU cc_start: 0.9738 (mt) cc_final: 0.9508 (mt) REVERT: D 55 MET cc_start: 0.9466 (mtp) cc_final: 0.8961 (ttp) REVERT: D 104 ILE cc_start: 0.9006 (tt) cc_final: 0.8618 (tt) REVERT: D 111 LEU cc_start: 0.9178 (tp) cc_final: 0.8836 (pp) REVERT: D 129 ILE cc_start: 0.9582 (mt) cc_final: 0.9239 (tp) REVERT: D 130 TYR cc_start: 0.8768 (t80) cc_final: 0.8501 (t80) REVERT: D 131 LYS cc_start: 0.9488 (ttmt) cc_final: 0.9116 (ptpt) REVERT: D 140 LYS cc_start: 0.9600 (mttt) cc_final: 0.9354 (tptp) REVERT: D 151 LEU cc_start: 0.8291 (mt) cc_final: 0.7994 (mt) REVERT: D 170 LYS cc_start: 0.9347 (tttt) cc_final: 0.9127 (ptmm) REVERT: D 172 LEU cc_start: 0.9649 (tp) cc_final: 0.9424 (tp) REVERT: D 215 MET cc_start: 0.8722 (mtm) cc_final: 0.7947 (mtm) REVERT: G 55 MET cc_start: 0.9630 (mtp) cc_final: 0.9339 (mtp) REVERT: G 66 MET cc_start: 0.9668 (mmm) cc_final: 0.9388 (ptp) REVERT: G 104 ILE cc_start: 0.9380 (tt) cc_final: 0.9122 (pt) REVERT: G 130 TYR cc_start: 0.9475 (t80) cc_final: 0.8954 (t80) REVERT: G 141 ILE cc_start: 0.9054 (mt) cc_final: 0.8597 (mt) REVERT: G 151 LEU cc_start: 0.9118 (mt) cc_final: 0.8690 (mt) REVERT: G 153 ILE cc_start: 0.7593 (mt) cc_final: 0.7150 (tp) REVERT: G 187 GLU cc_start: 0.9785 (mt-10) cc_final: 0.9381 (mm-30) REVERT: G 205 LEU cc_start: 0.8576 (tt) cc_final: 0.8355 (tt) REVERT: G 215 MET cc_start: 0.9380 (mtm) cc_final: 0.9143 (ppp) REVERT: H 10 MET cc_start: 0.6095 (ptt) cc_final: 0.5459 (ttm) REVERT: H 23 TRP cc_start: 0.9547 (t-100) cc_final: 0.8571 (t60) REVERT: H 33 SER cc_start: 0.8507 (m) cc_final: 0.8299 (p) REVERT: H 55 MET cc_start: 0.9006 (mtp) cc_final: 0.8589 (mmt) REVERT: H 66 MET cc_start: 0.9380 (mmm) cc_final: 0.9002 (mmm) REVERT: H 67 GLN cc_start: 0.9322 (tp40) cc_final: 0.8766 (mt0) REVERT: H 68 MET cc_start: 0.9352 (mtp) cc_final: 0.8946 (mmm) REVERT: H 114 GLN cc_start: 0.9407 (mm-40) cc_final: 0.9109 (pt0) REVERT: H 128 GLU cc_start: 0.9592 (mm-30) cc_final: 0.9222 (mp0) REVERT: H 131 LYS cc_start: 0.9367 (ttmt) cc_final: 0.9153 (tttp) REVERT: H 143 ARG cc_start: 0.9493 (mtt180) cc_final: 0.9253 (mtm180) REVERT: H 144 MET cc_start: 0.9442 (ttp) cc_final: 0.9106 (tmm) REVERT: H 152 ASP cc_start: 0.9448 (m-30) cc_final: 0.9016 (p0) REVERT: H 168 PHE cc_start: 0.9405 (t80) cc_final: 0.9059 (t80) REVERT: H 193 ASN cc_start: 0.8118 (m-40) cc_final: 0.7759 (m-40) REVERT: J 29 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8054 (p) REVERT: J 40 SER cc_start: 0.8505 (m) cc_final: 0.8063 (p) REVERT: J 44 LYS cc_start: 0.9216 (mmtm) cc_final: 0.8973 (mmtp) REVERT: J 113 PHE cc_start: 0.9130 (p90) cc_final: 0.8875 (p90) REVERT: J 138 ILE cc_start: 0.4674 (mm) cc_final: 0.4311 (mm) REVERT: J 152 THR cc_start: 0.7922 (p) cc_final: 0.7528 (t) REVERT: J 158 ILE cc_start: 0.8915 (mt) cc_final: 0.8612 (mt) REVERT: N 153 ILE cc_start: 0.8547 (mm) cc_final: 0.8316 (tp) REVERT: Y 49 PRO cc_start: 0.9614 (Cg_exo) cc_final: 0.9311 (Cg_endo) REVERT: Y 57 ASN cc_start: 0.9448 (m-40) cc_final: 0.9008 (p0) REVERT: Y 63 GLN cc_start: 0.9351 (mm-40) cc_final: 0.8392 (mp10) REVERT: Y 103 ASP cc_start: 0.9133 (t0) cc_final: 0.8930 (t70) REVERT: Y 120 ASN cc_start: 0.9126 (t0) cc_final: 0.8484 (p0) REVERT: Y 121 ASN cc_start: 0.9137 (m-40) cc_final: 0.8910 (m110) REVERT: Y 131 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8832 (ptpt) REVERT: Y 136 LEU cc_start: 0.9789 (mt) cc_final: 0.9524 (mt) REVERT: d 15 ILE cc_start: 0.8154 (pt) cc_final: 0.7730 (mt) REVERT: d 23 TRP cc_start: 0.9523 (t-100) cc_final: 0.8908 (t60) REVERT: d 25 LYS cc_start: 0.9282 (tttt) cc_final: 0.8991 (tptp) REVERT: d 30 LYS cc_start: 0.7751 (mttm) cc_final: 0.7452 (mtpt) REVERT: d 55 MET cc_start: 0.9396 (mtp) cc_final: 0.8923 (ptm) REVERT: d 67 GLN cc_start: 0.9217 (tp-100) cc_final: 0.8934 (mt0) REVERT: d 76 GLU cc_start: 0.9752 (mm-30) cc_final: 0.9350 (mt-10) REVERT: d 168 PHE cc_start: 0.9454 (t80) cc_final: 0.8924 (t80) REVERT: e 25 LYS cc_start: 0.9754 (mttt) cc_final: 0.9510 (ptpp) REVERT: e 43 LEU cc_start: 0.8892 (mt) cc_final: 0.8579 (mp) REVERT: e 113 GLU cc_start: 0.9285 (mt-10) cc_final: 0.9035 (mt-10) REVERT: e 139 ASN cc_start: 0.9751 (m-40) cc_final: 0.9465 (t0) REVERT: e 140 LYS cc_start: 0.9651 (mttt) cc_final: 0.9196 (mttp) REVERT: e 145 TYR cc_start: 0.7325 (m-80) cc_final: 0.7021 (m-80) REVERT: e 169 TYR cc_start: 0.9261 (m-10) cc_final: 0.9055 (m-10) REVERT: e 214 MET cc_start: 0.8849 (mtt) cc_final: 0.8555 (mmt) REVERT: j 181 VAL cc_start: 0.9608 (t) cc_final: 0.9346 (t) REVERT: j 191 VAL cc_start: 0.8699 (t) cc_final: 0.8016 (p) REVERT: k 52 LEU cc_start: 0.9686 (mt) cc_final: 0.9265 (mt) REVERT: k 72 THR cc_start: 0.9407 (m) cc_final: 0.9112 (p) REVERT: k 79 GLU cc_start: 0.9658 (mt-10) cc_final: 0.9216 (tp30) REVERT: k 80 TRP cc_start: 0.9614 (t-100) cc_final: 0.9334 (t-100) REVERT: k 81 ASP cc_start: 0.9524 (t70) cc_final: 0.9284 (m-30) REVERT: k 82 ARG cc_start: 0.9187 (ttp80) cc_final: 0.8631 (ttp80) REVERT: k 83 VAL cc_start: 0.9737 (p) cc_final: 0.8947 (p) REVERT: k 104 ILE cc_start: 0.8484 (mm) cc_final: 0.7994 (mm) REVERT: k 130 TYR cc_start: 0.9377 (t80) cc_final: 0.9097 (t80) REVERT: k 140 LYS cc_start: 0.9476 (mttt) cc_final: 0.8932 (tmtt) REVERT: k 168 PHE cc_start: 0.9588 (t80) cc_final: 0.9058 (t80) REVERT: k 179 GLN cc_start: 0.9390 (tp-100) cc_final: 0.8946 (tp-100) REVERT: k 180 GLU cc_start: 0.9338 (mp0) cc_final: 0.9128 (mp0) REVERT: k 182 LYS cc_start: 0.9460 (ttmm) cc_final: 0.9089 (ptpt) REVERT: k 185 MET cc_start: 0.9501 (mtm) cc_final: 0.9074 (mtm) REVERT: k 187 GLU cc_start: 0.9561 (mt-10) cc_final: 0.9318 (pt0) REVERT: k 191 VAL cc_start: 0.9036 (m) cc_final: 0.8609 (m) REVERT: k 193 ASN cc_start: 0.8937 (m110) cc_final: 0.8309 (m-40) REVERT: k 212 GLU cc_start: 0.9486 (tt0) cc_final: 0.9220 (pm20) outliers start: 9 outliers final: 2 residues processed: 1187 average time/residue: 0.1647 time to fit residues: 277.2159 Evaluate side-chains 760 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 757 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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: 10.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN B 7 GLN B 9 GLN B 87 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 183 ASN B 219 GLN C 57 ASN C 62 HIS C 192 GLN C 219 GLN D 4 GLN D 95 GLN D 114 GLN G 4 GLN G 84 HIS G 179 GLN G 183 ASN H 4 GLN H 183 ASN H 193 ASN N 219 GLN Y 4 GLN Y 21 ASN Y 95 GLN d 4 GLN d 95 GLN e 4 GLN ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 219 GLN ** j 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 219 GLN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 95 GLN k 112 GLN ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.086183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.061289 restraints weight = 72621.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063430 restraints weight = 49726.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.065033 restraints weight = 37723.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066233 restraints weight = 30521.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067150 restraints weight = 25933.028| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4784 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= 0.182 Angle : 0.693 7.542 25587 Z= 0.364 Chirality : 0.046 0.268 2848 Planarity : 0.005 0.058 3345 Dihedral : 4.150 27.409 2500 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.35 % Allowed : 4.20 % Favored : 95.45 % 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: -0.14 (0.17), residues: 2338 helix: 0.27 (0.13), residues: 1439 sheet: -1.56 (0.62), residues: 67 loop : -0.39 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 143 TYR 0.016 0.002 TYR D 169 PHE 0.034 0.003 PHE J 60 TRP 0.026 0.002 TRP B 23 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00403 (18824) covalent geometry : angle 0.69259 (25567) SS BOND : bond 0.00873 ( 10) SS BOND : angle 1.27288 ( 20) hydrogen bonds : bond 0.04854 ( 1037) hydrogen bonds : angle 4.55204 ( 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 938 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 931 time to evaluate : 0.738 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 9 GLN cc_start: 0.9418 (mp10) cc_final: 0.9027 (pp30) REVERT: A 27 VAL cc_start: 0.9702 (t) cc_final: 0.9398 (t) REVERT: A 28 GLU cc_start: 0.9576 (mm-30) cc_final: 0.9242 (mm-30) REVERT: A 50 GLN cc_start: 0.9407 (tm-30) cc_final: 0.9190 (tm-30) REVERT: A 52 LEU cc_start: 0.9782 (mt) cc_final: 0.9310 (mt) REVERT: A 56 LEU cc_start: 0.9845 (mt) cc_final: 0.9375 (mt) REVERT: A 67 GLN cc_start: 0.9615 (tp40) cc_final: 0.9295 (tm-30) REVERT: A 68 MET cc_start: 0.9334 (mtm) cc_final: 0.8984 (ptp) REVERT: A 72 THR cc_start: 0.9787 (m) cc_final: 0.9314 (p) REVERT: A 125 PRO cc_start: 0.9013 (Cg_exo) cc_final: 0.8762 (Cg_endo) REVERT: A 135 ILE cc_start: 0.9349 (mt) cc_final: 0.9122 (mt) REVERT: B 5 ASN cc_start: 0.9212 (t0) cc_final: 0.8760 (m110) REVERT: B 7 GLN cc_start: 0.7887 (tp40) cc_final: 0.7686 (tp-100) REVERT: B 20 LEU cc_start: 0.9619 (mt) cc_final: 0.9416 (mt) REVERT: B 25 LYS cc_start: 0.9595 (ptpp) cc_final: 0.9379 (pttm) REVERT: B 30 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8399 (mppt) REVERT: B 39 MET cc_start: 0.9614 (tpp) cc_final: 0.9174 (tpt) REVERT: B 45 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8355 (mm-30) REVERT: B 68 MET cc_start: 0.9514 (mtm) cc_final: 0.9275 (mtt) REVERT: B 75 GLU cc_start: 0.9714 (tt0) cc_final: 0.9409 (pp20) REVERT: B 79 GLU cc_start: 0.9366 (pt0) cc_final: 0.9120 (pt0) REVERT: B 118 MET cc_start: 0.9552 (mtm) cc_final: 0.9255 (mmm) REVERT: B 128 GLU cc_start: 0.9403 (mp0) cc_final: 0.9135 (mp0) REVERT: B 169 TYR cc_start: 0.9488 (m-10) cc_final: 0.8870 (m-10) REVERT: B 181 VAL cc_start: 0.9614 (t) cc_final: 0.9137 (t) REVERT: B 185 MET cc_start: 0.9662 (ptp) cc_final: 0.9345 (ptp) REVERT: B 187 GLU cc_start: 0.9492 (mt-10) cc_final: 0.9214 (pp20) REVERT: B 213 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9047 (pt0) REVERT: B 214 MET cc_start: 0.9117 (mtt) cc_final: 0.8881 (mtt) REVERT: C 10 MET cc_start: 0.8551 (mtt) cc_final: 0.8338 (ttm) REVERT: C 15 ILE cc_start: 0.8801 (tp) cc_final: 0.8549 (tp) REVERT: C 23 TRP cc_start: 0.9448 (t-100) cc_final: 0.8965 (t-100) REVERT: C 43 LEU cc_start: 0.9497 (mt) cc_final: 0.8729 (mm) REVERT: C 55 MET cc_start: 0.9101 (mtp) cc_final: 0.8844 (mtt) REVERT: C 76 GLU cc_start: 0.9504 (mm-30) cc_final: 0.8981 (mm-30) REVERT: C 96 MET cc_start: -0.5262 (mmt) cc_final: -0.5758 (mtm) REVERT: C 103 ASP cc_start: 0.8854 (m-30) cc_final: 0.8517 (m-30) REVERT: C 104 ILE cc_start: 0.8481 (mm) cc_final: 0.7826 (mm) REVERT: C 114 GLN cc_start: 0.9607 (mt0) cc_final: 0.9334 (mt0) REVERT: C 129 ILE cc_start: 0.9676 (mt) cc_final: 0.9472 (mt) REVERT: C 133 TRP cc_start: 0.8951 (m-10) cc_final: 0.8591 (m100) REVERT: C 140 LYS cc_start: 0.9342 (mttt) cc_final: 0.8887 (tptp) REVERT: C 144 MET cc_start: 0.8662 (tmm) cc_final: 0.8411 (tmm) REVERT: C 166 ASP cc_start: 0.8881 (t0) cc_final: 0.7742 (t70) REVERT: D 23 TRP cc_start: 0.9523 (t-100) cc_final: 0.8950 (t60) REVERT: D 39 MET cc_start: 0.9692 (mmp) cc_final: 0.9289 (mmm) REVERT: D 49 PRO cc_start: 0.9568 (Cg_exo) cc_final: 0.9344 (Cg_endo) REVERT: D 52 LEU cc_start: 0.9709 (mt) cc_final: 0.9369 (mt) REVERT: D 53 ASN cc_start: 0.9232 (m-40) cc_final: 0.8948 (m110) REVERT: D 55 MET cc_start: 0.9507 (mtp) cc_final: 0.9081 (ttp) REVERT: D 129 ILE cc_start: 0.9572 (mt) cc_final: 0.9308 (tp) REVERT: D 130 TYR cc_start: 0.8732 (t80) cc_final: 0.8359 (t80) REVERT: D 131 LYS cc_start: 0.9493 (ttmt) cc_final: 0.8966 (mttp) REVERT: D 140 LYS cc_start: 0.9615 (mttt) cc_final: 0.9341 (tptp) REVERT: D 215 MET cc_start: 0.8243 (mtm) cc_final: 0.7410 (mtm) REVERT: G 23 TRP cc_start: 0.9591 (t-100) cc_final: 0.9168 (t60) REVERT: G 25 LYS cc_start: 0.9369 (ptpp) cc_final: 0.9151 (ptpp) REVERT: G 40 PHE cc_start: 0.9629 (t80) cc_final: 0.9382 (t80) REVERT: G 55 MET cc_start: 0.9635 (mtp) cc_final: 0.9328 (mtp) REVERT: G 58 THR cc_start: 0.9227 (p) cc_final: 0.8752 (p) REVERT: G 112 GLN cc_start: 0.9625 (mp10) cc_final: 0.9420 (mp10) REVERT: G 140 LYS cc_start: 0.9704 (mtpp) cc_final: 0.9431 (mtpp) REVERT: G 168 PHE cc_start: 0.9278 (t80) cc_final: 0.8967 (t80) REVERT: G 188 THR cc_start: 0.9249 (p) cc_final: 0.8988 (p) REVERT: H 25 LYS cc_start: 0.9738 (tttt) cc_final: 0.9478 (tppt) REVERT: H 30 LYS cc_start: 0.8106 (ptpt) cc_final: 0.7271 (ptpt) REVERT: H 33 SER cc_start: 0.8612 (m) cc_final: 0.8326 (t) REVERT: H 39 MET cc_start: 0.9144 (mtt) cc_final: 0.8921 (mtt) REVERT: H 66 MET cc_start: 0.9465 (mmm) cc_final: 0.9021 (mmm) REVERT: H 67 GLN cc_start: 0.9411 (tp40) cc_final: 0.9038 (mt0) REVERT: H 100 ARG cc_start: 0.9229 (ttt-90) cc_final: 0.8594 (mmp-170) REVERT: H 118 MET cc_start: 0.8558 (mmm) cc_final: 0.7940 (mmm) REVERT: H 128 GLU cc_start: 0.9637 (mm-30) cc_final: 0.9267 (mp0) REVERT: H 143 ARG cc_start: 0.9509 (mtt180) cc_final: 0.9279 (mtm180) REVERT: H 145 TYR cc_start: 0.9129 (m-80) cc_final: 0.8732 (m-10) REVERT: H 152 ASP cc_start: 0.9506 (m-30) cc_final: 0.8968 (p0) REVERT: H 161 PHE cc_start: 0.8628 (t80) cc_final: 0.8214 (t80) REVERT: H 182 LYS cc_start: 0.9773 (pttp) cc_final: 0.9491 (pttp) REVERT: H 215 MET cc_start: 0.5591 (mtp) cc_final: 0.5362 (mtp) REVERT: J 9 ASP cc_start: 0.8321 (m-30) cc_final: 0.8119 (m-30) REVERT: J 29 VAL cc_start: 0.8892 (t) cc_final: 0.8610 (p) REVERT: J 36 PHE cc_start: 0.9652 (t80) cc_final: 0.9446 (t80) REVERT: J 40 SER cc_start: 0.9068 (m) cc_final: 0.8090 (p) REVERT: J 48 TYR cc_start: 0.8482 (m-10) cc_final: 0.8120 (m-80) REVERT: J 60 PHE cc_start: 0.7709 (t80) cc_final: 0.7139 (t80) REVERT: J 83 PHE cc_start: 0.8447 (p90) cc_final: 0.7946 (p90) REVERT: J 84 GLU cc_start: 0.7908 (pm20) cc_final: 0.7462 (pp20) REVERT: J 113 PHE cc_start: 0.9172 (p90) cc_final: 0.8697 (p90) REVERT: J 119 THR cc_start: 0.7741 (p) cc_final: 0.6829 (m) REVERT: J 127 VAL cc_start: 0.9543 (p) cc_final: 0.9328 (p) REVERT: N 178 SER cc_start: 0.8601 (p) cc_final: 0.8212 (t) REVERT: N 203 LYS cc_start: 0.7781 (pttt) cc_final: 0.7497 (pttt) REVERT: N 213 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9215 (pt0) REVERT: Y 10 MET cc_start: 0.9100 (pmm) cc_final: 0.8683 (mmp) REVERT: Y 28 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9084 (mm-30) REVERT: Y 32 PHE cc_start: 0.7968 (m-80) cc_final: 0.7665 (m-10) REVERT: Y 39 MET cc_start: 0.9136 (mpp) cc_final: 0.8848 (mmt) REVERT: Y 63 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8802 (mp10) REVERT: Y 67 GLN cc_start: 0.9769 (mm-40) cc_final: 0.9421 (mm-40) REVERT: Y 68 MET cc_start: 0.9463 (mtm) cc_final: 0.8963 (mtp) REVERT: Y 71 GLU cc_start: 0.9565 (mt-10) cc_final: 0.9275 (mt-10) REVERT: Y 75 GLU cc_start: 0.9494 (OUTLIER) cc_final: 0.9069 (mp0) REVERT: Y 79 GLU cc_start: 0.9482 (tp30) cc_final: 0.9228 (pp20) REVERT: Y 100 ARG cc_start: 0.9172 (ttm-80) cc_final: 0.8761 (tpp80) REVERT: Y 103 ASP cc_start: 0.9229 (t0) cc_final: 0.8907 (t70) REVERT: Y 131 LYS cc_start: 0.9160 (ttmt) cc_final: 0.8933 (ptpt) REVERT: d 15 ILE cc_start: 0.8021 (pt) cc_final: 0.7546 (mp) REVERT: d 25 LYS cc_start: 0.9273 (tttt) cc_final: 0.9032 (tptp) REVERT: d 39 MET cc_start: 0.8931 (mtm) cc_final: 0.7986 (mtt) REVERT: d 67 GLN cc_start: 0.9241 (tp-100) cc_final: 0.8775 (mt0) REVERT: d 68 MET cc_start: 0.8986 (mmm) cc_final: 0.8739 (mmp) REVERT: d 76 GLU cc_start: 0.9538 (mm-30) cc_final: 0.9200 (mt-10) REVERT: d 143 ARG cc_start: 0.8828 (tpt170) cc_final: 0.8601 (tpt170) REVERT: d 168 PHE cc_start: 0.9350 (t80) cc_final: 0.9088 (t80) REVERT: d 203 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8557 (mtmt) REVERT: e 10 MET cc_start: 0.9042 (mmm) cc_final: 0.8526 (tpp) REVERT: e 23 TRP cc_start: 0.9387 (t-100) cc_final: 0.8838 (t-100) REVERT: e 39 MET cc_start: 0.9694 (mtm) cc_final: 0.9263 (mtm) REVERT: e 55 MET cc_start: 0.9571 (mtp) cc_final: 0.9273 (tpp) REVERT: e 57 ASN cc_start: 0.9604 (m110) cc_final: 0.9336 (p0) REVERT: e 104 ILE cc_start: 0.8370 (mt) cc_final: 0.7800 (mt) REVERT: e 140 LYS cc_start: 0.9709 (mttt) cc_final: 0.9002 (mttp) REVERT: e 166 ASP cc_start: 0.8927 (t0) cc_final: 0.8695 (t0) REVERT: e 167 ARG cc_start: 0.8477 (ptp-110) cc_final: 0.8184 (mtm110) REVERT: e 169 TYR cc_start: 0.9673 (m-10) cc_final: 0.8944 (m-10) REVERT: e 170 LYS cc_start: 0.9751 (tttt) cc_final: 0.9501 (pptt) REVERT: e 182 LYS cc_start: 0.9589 (mttt) cc_final: 0.9158 (mmmm) REVERT: e 205 LEU cc_start: 0.7685 (mp) cc_final: 0.5589 (tp) REVERT: j 153 ILE cc_start: 0.8733 (tp) cc_final: 0.8392 (tp) REVERT: j 172 LEU cc_start: 0.9738 (tp) cc_final: 0.9523 (mm) REVERT: j 182 LYS cc_start: 0.9395 (mttt) cc_final: 0.9084 (mmtp) REVERT: k 52 LEU cc_start: 0.9618 (mt) cc_final: 0.9308 (mt) REVERT: k 56 LEU cc_start: 0.9584 (mt) cc_final: 0.9317 (mt) REVERT: k 66 MET cc_start: 0.9627 (tpt) cc_final: 0.9217 (tpt) REVERT: k 68 MET cc_start: 0.9378 (mtp) cc_final: 0.9163 (mtp) REVERT: k 81 ASP cc_start: 0.9614 (t70) cc_final: 0.9408 (m-30) REVERT: k 104 ILE cc_start: 0.8619 (mm) cc_final: 0.8241 (mm) REVERT: k 111 LEU cc_start: 0.9222 (tp) cc_final: 0.8661 (tp) REVERT: k 115 ILE cc_start: 0.9583 (mm) cc_final: 0.9178 (mm) REVERT: k 130 TYR cc_start: 0.9440 (t80) cc_final: 0.9180 (t80) REVERT: k 140 LYS cc_start: 0.9597 (mttt) cc_final: 0.8884 (tptp) REVERT: k 159 GLU cc_start: 0.8579 (mp0) cc_final: 0.7923 (pt0) REVERT: k 168 PHE cc_start: 0.9582 (t80) cc_final: 0.9142 (t80) REVERT: k 179 GLN cc_start: 0.9483 (tp-100) cc_final: 0.9161 (tp-100) REVERT: k 180 GLU cc_start: 0.9508 (mp0) cc_final: 0.9234 (mp0) REVERT: k 185 MET cc_start: 0.9323 (mtm) cc_final: 0.9079 (mtm) REVERT: k 187 GLU cc_start: 0.9647 (mt-10) cc_final: 0.9281 (pt0) REVERT: k 193 ASN cc_start: 0.9081 (m110) cc_final: 0.7821 (t0) REVERT: k 203 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8685 (mmtt) REVERT: k 214 MET cc_start: 0.9196 (mmp) cc_final: 0.8860 (mmp) outliers start: 7 outliers final: 2 residues processed: 934 average time/residue: 0.1664 time to fit residues: 220.7313 Evaluate side-chains 725 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 722 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 9.9990 chunk 31 optimal weight: 40.0000 chunk 78 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 70 optimal weight: 30.0000 chunk 48 optimal weight: 7.9990 chunk 116 optimal weight: 30.0000 chunk 148 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS B 87 HIS B 95 GLN G 53 ASN ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 7 GLN ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 ASN j 155 GLN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.084541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.059626 restraints weight = 73227.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061775 restraints weight = 49754.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.063397 restraints weight = 37455.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.064585 restraints weight = 30193.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.065533 restraints weight = 25570.789| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18834 Z= 0.160 Angle : 0.676 9.097 25587 Z= 0.349 Chirality : 0.046 0.304 2848 Planarity : 0.005 0.083 3345 Dihedral : 4.261 20.596 2500 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.15 % Allowed : 4.30 % Favored : 95.55 % 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: -0.08 (0.17), residues: 2338 helix: 0.23 (0.13), residues: 1450 sheet: -1.52 (0.61), residues: 73 loop : -0.16 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG e 100 TYR 0.015 0.002 TYR C 130 PHE 0.029 0.002 PHE H 168 TRP 0.030 0.002 TRP e 117 HIS 0.003 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00351 (18824) covalent geometry : angle 0.67616 (25567) SS BOND : bond 0.00297 ( 10) SS BOND : angle 0.98005 ( 20) hydrogen bonds : bond 0.04434 ( 1037) hydrogen bonds : angle 4.64596 ( 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 872 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 869 time to evaluate : 0.656 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: A 9 GLN cc_start: 0.9462 (mp10) cc_final: 0.9058 (pp30) REVERT: A 23 TRP cc_start: 0.9208 (t-100) cc_final: 0.8897 (t-100) REVERT: A 27 VAL cc_start: 0.9747 (t) cc_final: 0.9273 (t) REVERT: A 28 GLU cc_start: 0.9614 (mm-30) cc_final: 0.9314 (mm-30) REVERT: A 67 GLN cc_start: 0.9617 (tp40) cc_final: 0.9315 (tm-30) REVERT: A 72 THR cc_start: 0.9837 (m) cc_final: 0.9093 (m) REVERT: A 100 ARG cc_start: 0.9618 (ttm-80) cc_final: 0.9359 (tpp80) REVERT: A 103 ASP cc_start: 0.9586 (m-30) cc_final: 0.9128 (m-30) REVERT: A 114 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8649 (pt0) REVERT: A 141 ILE cc_start: 0.9355 (mm) cc_final: 0.8923 (mm) REVERT: B 5 ASN cc_start: 0.9137 (t0) cc_final: 0.8822 (m110) REVERT: B 20 LEU cc_start: 0.9622 (mt) cc_final: 0.9410 (mt) REVERT: B 23 TRP cc_start: 0.9097 (t-100) cc_final: 0.8628 (t-100) REVERT: B 30 LYS cc_start: 0.8885 (mmtp) cc_final: 0.8333 (mppt) REVERT: B 39 MET cc_start: 0.9643 (tpp) cc_final: 0.9168 (tpt) REVERT: B 100 ARG cc_start: 0.8981 (ttp-110) cc_final: 0.8708 (ttp80) REVERT: B 118 MET cc_start: 0.9587 (mtm) cc_final: 0.9249 (mmm) REVERT: B 128 GLU cc_start: 0.9420 (mp0) cc_final: 0.9131 (mp0) REVERT: B 132 ARG cc_start: 0.9601 (ptp90) cc_final: 0.9305 (ptp-170) REVERT: B 133 TRP cc_start: 0.8812 (m-10) cc_final: 0.8262 (m-10) REVERT: B 169 TYR cc_start: 0.9348 (m-10) cc_final: 0.8882 (m-10) REVERT: B 181 VAL cc_start: 0.9642 (t) cc_final: 0.9110 (p) REVERT: B 185 MET cc_start: 0.9664 (ptp) cc_final: 0.9436 (ptt) REVERT: B 213 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9030 (pt0) REVERT: C 52 LEU cc_start: 0.9749 (mt) cc_final: 0.9506 (mt) REVERT: C 75 GLU cc_start: 0.9535 (mt-10) cc_final: 0.8991 (pt0) REVERT: C 76 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9047 (mm-30) REVERT: C 96 MET cc_start: -0.5245 (mmt) cc_final: -0.5620 (mtm) REVERT: C 140 LYS cc_start: 0.9389 (mttt) cc_final: 0.8924 (tptp) REVERT: C 166 ASP cc_start: 0.8574 (t0) cc_final: 0.7956 (t0) REVERT: C 175 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7979 (tm-30) REVERT: D 10 MET cc_start: 0.7304 (mpp) cc_final: 0.6382 (mmt) REVERT: D 21 ASN cc_start: 0.9574 (t0) cc_final: 0.9330 (t0) REVERT: D 23 TRP cc_start: 0.9512 (t-100) cc_final: 0.8976 (t60) REVERT: D 25 LYS cc_start: 0.9791 (ttpt) cc_final: 0.9550 (ptmt) REVERT: D 52 LEU cc_start: 0.9678 (mt) cc_final: 0.9303 (mt) REVERT: D 53 ASN cc_start: 0.9221 (m-40) cc_final: 0.8899 (m110) REVERT: D 55 MET cc_start: 0.9533 (mtp) cc_final: 0.9199 (ttp) REVERT: D 66 MET cc_start: 0.9699 (mmp) cc_final: 0.9480 (mmm) REVERT: D 129 ILE cc_start: 0.9555 (mt) cc_final: 0.9284 (tp) REVERT: D 130 TYR cc_start: 0.8746 (t80) cc_final: 0.8401 (t80) REVERT: D 131 LYS cc_start: 0.9481 (ttmt) cc_final: 0.8931 (mttt) REVERT: D 140 LYS cc_start: 0.9622 (mttt) cc_final: 0.9335 (tptp) REVERT: D 144 MET cc_start: 0.4961 (ttt) cc_final: 0.4666 (ttt) REVERT: D 205 LEU cc_start: 0.8773 (tt) cc_final: 0.8469 (tt) REVERT: D 215 MET cc_start: 0.8407 (mtm) cc_final: 0.7575 (mtm) REVERT: G 11 VAL cc_start: 0.8535 (t) cc_final: 0.8148 (t) REVERT: G 18 ARG cc_start: 0.9470 (mmm-85) cc_final: 0.9263 (mmp80) REVERT: G 25 LYS cc_start: 0.9387 (ptpp) cc_final: 0.9156 (ptpp) REVERT: G 140 LYS cc_start: 0.9684 (mtpp) cc_final: 0.9431 (mtpp) REVERT: G 168 PHE cc_start: 0.9336 (t80) cc_final: 0.8987 (t80) REVERT: G 215 MET cc_start: 0.8644 (ppp) cc_final: 0.8440 (ppp) REVERT: H 25 LYS cc_start: 0.9732 (tttt) cc_final: 0.9267 (tppt) REVERT: H 39 MET cc_start: 0.9096 (mtt) cc_final: 0.8861 (mtt) REVERT: H 52 LEU cc_start: 0.9769 (mt) cc_final: 0.9548 (mt) REVERT: H 66 MET cc_start: 0.9467 (mmm) cc_final: 0.9098 (mmm) REVERT: H 67 GLN cc_start: 0.9350 (tp40) cc_final: 0.8920 (mt0) REVERT: H 100 ARG cc_start: 0.9129 (ttt-90) cc_final: 0.8558 (mmp-170) REVERT: H 111 LEU cc_start: 0.9451 (pt) cc_final: 0.9087 (pt) REVERT: H 114 GLN cc_start: 0.9577 (mm-40) cc_final: 0.9126 (pt0) REVERT: H 118 MET cc_start: 0.8432 (mmm) cc_final: 0.8000 (mmm) REVERT: H 128 GLU cc_start: 0.9610 (mm-30) cc_final: 0.9277 (mp0) REVERT: H 143 ARG cc_start: 0.9470 (mtt180) cc_final: 0.9241 (mtm180) REVERT: H 145 TYR cc_start: 0.9123 (m-80) cc_final: 0.8676 (m-10) REVERT: H 152 ASP cc_start: 0.9459 (m-30) cc_final: 0.8905 (p0) REVERT: H 182 LYS cc_start: 0.9788 (pttp) cc_final: 0.9586 (pttm) REVERT: H 184 TRP cc_start: 0.9591 (t60) cc_final: 0.9384 (t60) REVERT: J 22 PHE cc_start: 0.9473 (m-80) cc_final: 0.8624 (m-80) REVERT: J 29 VAL cc_start: 0.9121 (t) cc_final: 0.8742 (p) REVERT: J 36 PHE cc_start: 0.9668 (t80) cc_final: 0.9289 (t80) REVERT: J 40 SER cc_start: 0.8698 (m) cc_final: 0.7709 (p) REVERT: J 60 PHE cc_start: 0.7775 (t80) cc_final: 0.7259 (t80) REVERT: J 61 MET cc_start: 0.7150 (ppp) cc_final: 0.6569 (ppp) REVERT: J 98 LEU cc_start: 0.9207 (mt) cc_final: 0.8517 (mt) REVERT: J 100 MET cc_start: 0.9321 (mtm) cc_final: 0.9095 (mtm) REVERT: J 119 THR cc_start: 0.7659 (p) cc_final: 0.6922 (m) REVERT: J 138 ILE cc_start: 0.5274 (mm) cc_final: 0.4403 (mm) REVERT: J 142 MET cc_start: 0.9130 (mtt) cc_final: 0.8548 (mmm) REVERT: J 158 ILE cc_start: 0.9241 (mt) cc_final: 0.8920 (mt) REVERT: N 166 ASP cc_start: 0.8792 (t70) cc_final: 0.8503 (t70) REVERT: N 170 LYS cc_start: 0.8906 (tptt) cc_final: 0.8684 (tppt) REVERT: N 178 SER cc_start: 0.8672 (p) cc_final: 0.8219 (t) REVERT: Y 10 MET cc_start: 0.9055 (pmm) cc_final: 0.8724 (mmp) REVERT: Y 63 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8773 (mp10) REVERT: Y 67 GLN cc_start: 0.9744 (mm-40) cc_final: 0.9515 (mm-40) REVERT: Y 68 MET cc_start: 0.9286 (mtm) cc_final: 0.9031 (mtp) REVERT: Y 71 GLU cc_start: 0.9567 (mt-10) cc_final: 0.9227 (mt-10) REVERT: Y 100 ARG cc_start: 0.9235 (ttm-80) cc_final: 0.8926 (tpp80) REVERT: Y 103 ASP cc_start: 0.9252 (t0) cc_final: 0.9010 (t0) REVERT: Y 129 ILE cc_start: 0.9427 (mt) cc_final: 0.9076 (mt) REVERT: Y 131 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8857 (ptpt) REVERT: Y 136 LEU cc_start: 0.9757 (mt) cc_final: 0.9503 (mt) REVERT: d 15 ILE cc_start: 0.8008 (pt) cc_final: 0.7605 (mp) REVERT: d 21 ASN cc_start: 0.9503 (m-40) cc_final: 0.9271 (m-40) REVERT: d 25 LYS cc_start: 0.9247 (tttt) cc_final: 0.9001 (tptp) REVERT: d 30 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7523 (ttpp) REVERT: d 39 MET cc_start: 0.8830 (mtm) cc_final: 0.7948 (mtt) REVERT: d 57 ASN cc_start: 0.9428 (m-40) cc_final: 0.9028 (t0) REVERT: d 66 MET cc_start: 0.9579 (mpp) cc_final: 0.9345 (mpp) REVERT: d 67 GLN cc_start: 0.9187 (tp-100) cc_final: 0.8743 (mt0) REVERT: d 76 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9174 (mt-10) REVERT: d 132 ARG cc_start: 0.9354 (ttm110) cc_final: 0.9090 (ttp-110) REVERT: d 143 ARG cc_start: 0.8727 (tpt170) cc_final: 0.8491 (tpt170) REVERT: d 215 MET cc_start: 0.3570 (mmt) cc_final: 0.3096 (mtp) REVERT: e 4 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8579 (tp40) REVERT: e 10 MET cc_start: 0.8966 (mmm) cc_final: 0.8640 (tpp) REVERT: e 23 TRP cc_start: 0.9498 (t-100) cc_final: 0.9296 (t-100) REVERT: e 39 MET cc_start: 0.9750 (mtm) cc_final: 0.9246 (mtm) REVERT: e 50 GLN cc_start: 0.9312 (mt0) cc_final: 0.8960 (mt0) REVERT: e 57 ASN cc_start: 0.9607 (m110) cc_final: 0.9312 (p0) REVERT: e 104 ILE cc_start: 0.8415 (mt) cc_final: 0.8011 (mt) REVERT: e 111 LEU cc_start: 0.9407 (tp) cc_final: 0.9092 (tp) REVERT: e 131 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8746 (ttmt) REVERT: e 140 LYS cc_start: 0.9512 (mttt) cc_final: 0.9049 (mttp) REVERT: e 141 ILE cc_start: 0.9600 (tp) cc_final: 0.9355 (tp) REVERT: e 170 LYS cc_start: 0.9735 (tttt) cc_final: 0.9458 (tppt) REVERT: e 182 LYS cc_start: 0.9721 (mttt) cc_final: 0.9190 (mmmm) REVERT: e 185 MET cc_start: 0.9836 (ptp) cc_final: 0.9508 (ptt) REVERT: e 203 LYS cc_start: 0.8044 (ptpt) cc_final: 0.7407 (tttt) REVERT: j 188 THR cc_start: 0.7919 (m) cc_final: 0.7550 (m) REVERT: j 215 MET cc_start: 0.8583 (ppp) cc_final: 0.8316 (ppp) REVERT: k 21 ASN cc_start: 0.9387 (t0) cc_final: 0.9102 (t0) REVERT: k 52 LEU cc_start: 0.9547 (mt) cc_final: 0.9258 (mt) REVERT: k 56 LEU cc_start: 0.9626 (mt) cc_final: 0.9403 (mt) REVERT: k 66 MET cc_start: 0.9600 (tpt) cc_final: 0.9252 (tpt) REVERT: k 76 GLU cc_start: 0.9436 (mm-30) cc_final: 0.9158 (mm-30) REVERT: k 81 ASP cc_start: 0.9708 (t70) cc_final: 0.9346 (m-30) REVERT: k 100 ARG cc_start: 0.8997 (ptp-110) cc_final: 0.8658 (ptp-110) REVERT: k 104 ILE cc_start: 0.8700 (mm) cc_final: 0.8331 (mm) REVERT: k 131 LYS cc_start: 0.9395 (tttt) cc_final: 0.9040 (tttt) REVERT: k 140 LYS cc_start: 0.9601 (mttt) cc_final: 0.8814 (tptp) REVERT: k 168 PHE cc_start: 0.9556 (t80) cc_final: 0.9207 (t80) REVERT: k 179 GLN cc_start: 0.9514 (tp-100) cc_final: 0.8893 (tp-100) REVERT: k 180 GLU cc_start: 0.9490 (mp0) cc_final: 0.9200 (mp0) REVERT: k 182 LYS cc_start: 0.9482 (ttmm) cc_final: 0.8869 (ttpp) REVERT: k 185 MET cc_start: 0.9322 (mtm) cc_final: 0.8939 (mtt) REVERT: k 193 ASN cc_start: 0.9127 (m110) cc_final: 0.7981 (t0) REVERT: k 203 LYS cc_start: 0.8994 (mmtm) cc_final: 0.8689 (mmtt) REVERT: k 214 MET cc_start: 0.9253 (mmp) cc_final: 0.9050 (mmp) outliers start: 3 outliers final: 1 residues processed: 871 average time/residue: 0.1639 time to fit residues: 203.0775 Evaluate side-chains 679 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 678 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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: 30.0000 chunk 14 optimal weight: 40.0000 chunk 85 optimal weight: 20.0000 chunk 147 optimal weight: 50.0000 chunk 206 optimal weight: 20.0000 chunk 182 optimal weight: 40.0000 chunk 195 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 228 optimal weight: 5.9990 chunk 198 optimal weight: 30.0000 chunk 215 optimal weight: 0.8980 overall best weight: 10.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 87 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN C 183 ASN G 13 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS Y 13 GLN ** Y 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 155 GLN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.078471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.055130 restraints weight = 79023.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.057081 restraints weight = 53256.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058532 restraints weight = 39993.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.059623 restraints weight = 32260.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.060428 restraints weight = 27387.008| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18834 Z= 0.257 Angle : 0.756 8.261 25587 Z= 0.404 Chirality : 0.047 0.212 2848 Planarity : 0.006 0.063 3345 Dihedral : 4.630 24.193 2500 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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: -0.54 (0.16), residues: 2338 helix: -0.15 (0.13), residues: 1465 sheet: -1.68 (0.54), residues: 73 loop : -0.30 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG k 82 TYR 0.027 0.003 TYR J 48 PHE 0.031 0.003 PHE H 168 TRP 0.028 0.003 TRP B 184 HIS 0.009 0.002 HIS k 12 Details of bonding type rmsd covalent geometry : bond 0.00518 (18824) covalent geometry : angle 0.75500 (25567) SS BOND : bond 0.00623 ( 10) SS BOND : angle 1.42186 ( 20) hydrogen bonds : bond 0.04695 ( 1037) hydrogen bonds : angle 5.11056 ( 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 831 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 831 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 9 GLN cc_start: 0.9435 (mp10) cc_final: 0.9228 (pm20) REVERT: A 15 ILE cc_start: 0.8924 (mm) cc_final: 0.8673 (mm) REVERT: A 23 TRP cc_start: 0.9360 (t-100) cc_final: 0.8954 (t-100) REVERT: A 67 GLN cc_start: 0.9594 (tp40) cc_final: 0.9353 (tm-30) REVERT: A 68 MET cc_start: 0.9193 (ptp) cc_final: 0.8892 (ptp) REVERT: A 96 MET cc_start: 0.6648 (mtp) cc_final: 0.6135 (mtp) REVERT: A 100 ARG cc_start: 0.9696 (ttm-80) cc_final: 0.9479 (tpp80) REVERT: A 103 ASP cc_start: 0.9659 (m-30) cc_final: 0.9123 (m-30) REVERT: A 114 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8847 (pt0) REVERT: B 5 ASN cc_start: 0.9429 (t0) cc_final: 0.9001 (m110) REVERT: B 30 LYS cc_start: 0.8991 (mmtp) cc_final: 0.8573 (mmmt) REVERT: B 39 MET cc_start: 0.9645 (tpp) cc_final: 0.9266 (tpt) REVERT: B 100 ARG cc_start: 0.9007 (ttp-110) cc_final: 0.8547 (ttp80) REVERT: B 108 THR cc_start: 0.9221 (p) cc_final: 0.8919 (p) REVERT: B 118 MET cc_start: 0.9612 (mtm) cc_final: 0.9341 (mmm) REVERT: B 158 LYS cc_start: 0.8544 (tptt) cc_final: 0.8022 (mmtt) REVERT: B 169 TYR cc_start: 0.9414 (m-10) cc_final: 0.8802 (m-10) REVERT: B 181 VAL cc_start: 0.9691 (t) cc_final: 0.9137 (t) REVERT: B 185 MET cc_start: 0.9777 (ptp) cc_final: 0.9285 (ptp) REVERT: B 213 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9120 (pt0) REVERT: C 10 MET cc_start: 0.8504 (tpp) cc_final: 0.7912 (tpp) REVERT: C 52 LEU cc_start: 0.9770 (mt) cc_final: 0.9568 (mt) REVERT: C 55 MET cc_start: 0.9508 (ttt) cc_final: 0.9307 (ttm) REVERT: C 59 VAL cc_start: 0.8652 (t) cc_final: 0.8297 (p) REVERT: C 76 GLU cc_start: 0.9505 (mm-30) cc_final: 0.9056 (mm-30) REVERT: C 79 GLU cc_start: 0.8992 (pt0) cc_final: 0.8773 (pt0) REVERT: C 96 MET cc_start: -0.4874 (mmt) cc_final: -0.5363 (mtm) REVERT: C 133 TRP cc_start: 0.9019 (m-10) cc_final: 0.8484 (m-10) REVERT: C 140 LYS cc_start: 0.9396 (mttt) cc_final: 0.8930 (tptp) REVERT: C 166 ASP cc_start: 0.8760 (t0) cc_final: 0.7791 (t0) REVERT: C 175 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8328 (tm-30) REVERT: C 185 MET cc_start: 0.9342 (mtt) cc_final: 0.9048 (mtt) REVERT: C 215 MET cc_start: 0.9494 (tmm) cc_final: 0.9007 (tmm) REVERT: D 21 ASN cc_start: 0.9610 (t0) cc_final: 0.9212 (t0) REVERT: D 25 LYS cc_start: 0.9782 (ttpt) cc_final: 0.9526 (ptmt) REVERT: D 52 LEU cc_start: 0.9688 (mt) cc_final: 0.9393 (mt) REVERT: D 53 ASN cc_start: 0.9298 (m-40) cc_final: 0.8959 (m110) REVERT: D 128 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8878 (mp0) REVERT: D 129 ILE cc_start: 0.9617 (mt) cc_final: 0.9352 (tp) REVERT: D 130 TYR cc_start: 0.8877 (t80) cc_final: 0.8581 (t80) REVERT: D 131 LYS cc_start: 0.9525 (ttmt) cc_final: 0.9105 (ptpt) REVERT: D 140 LYS cc_start: 0.9646 (mttt) cc_final: 0.9349 (tptp) REVERT: D 144 MET cc_start: 0.4549 (ttt) cc_final: 0.4228 (ttt) REVERT: D 215 MET cc_start: 0.8543 (mtm) cc_final: 0.7916 (mtp) REVERT: G 15 ILE cc_start: 0.9168 (pt) cc_final: 0.8962 (mm) REVERT: G 18 ARG cc_start: 0.9562 (mmm-85) cc_final: 0.9295 (mmp80) REVERT: G 23 TRP cc_start: 0.9522 (t-100) cc_final: 0.8677 (t60) REVERT: G 55 MET cc_start: 0.9550 (ttp) cc_final: 0.9127 (tmm) REVERT: G 58 THR cc_start: 0.9309 (p) cc_final: 0.8604 (p) REVERT: G 68 MET cc_start: 0.8693 (mtt) cc_final: 0.8170 (ptp) REVERT: G 128 GLU cc_start: 0.9644 (pm20) cc_final: 0.9398 (pm20) REVERT: G 140 LYS cc_start: 0.9701 (mtpp) cc_final: 0.9470 (mtpp) REVERT: G 141 ILE cc_start: 0.9055 (mt) cc_final: 0.8836 (mt) REVERT: G 168 PHE cc_start: 0.9398 (t80) cc_final: 0.9092 (t80) REVERT: G 188 THR cc_start: 0.9411 (p) cc_final: 0.9187 (p) REVERT: H 13 GLN cc_start: 0.9385 (pp30) cc_final: 0.9162 (pm20) REVERT: H 25 LYS cc_start: 0.9611 (tttt) cc_final: 0.9157 (tppt) REVERT: H 29 GLU cc_start: 0.7978 (pm20) cc_final: 0.7776 (pm20) REVERT: H 52 LEU cc_start: 0.9805 (mt) cc_final: 0.9588 (mt) REVERT: H 55 MET cc_start: 0.9203 (mmp) cc_final: 0.8807 (mmm) REVERT: H 67 GLN cc_start: 0.9380 (tp40) cc_final: 0.9110 (mt0) REVERT: H 87 HIS cc_start: 0.7957 (m-70) cc_final: 0.7022 (t-90) REVERT: H 118 MET cc_start: 0.8463 (mmm) cc_final: 0.8005 (mmm) REVERT: H 128 GLU cc_start: 0.9612 (mm-30) cc_final: 0.9283 (mp0) REVERT: H 143 ARG cc_start: 0.9558 (mtt180) cc_final: 0.9348 (mtm180) REVERT: H 145 TYR cc_start: 0.9239 (m-80) cc_final: 0.8701 (m-10) REVERT: H 184 TRP cc_start: 0.9658 (t60) cc_final: 0.9373 (t60) REVERT: H 185 MET cc_start: 0.9475 (mtm) cc_final: 0.9152 (mtm) REVERT: J 29 VAL cc_start: 0.9250 (t) cc_final: 0.8972 (p) REVERT: J 37 ARG cc_start: 0.9447 (ptm-80) cc_final: 0.9223 (ptm-80) REVERT: J 40 SER cc_start: 0.8970 (m) cc_final: 0.7777 (p) REVERT: J 48 TYR cc_start: 0.8852 (m-80) cc_final: 0.8282 (m-80) REVERT: J 57 ILE cc_start: 0.7783 (tt) cc_final: 0.6588 (tt) REVERT: J 60 PHE cc_start: 0.8000 (t80) cc_final: 0.7372 (t80) REVERT: J 61 MET cc_start: 0.6935 (ppp) cc_final: 0.5944 (ppp) REVERT: J 119 THR cc_start: 0.7617 (p) cc_final: 0.6772 (m) REVERT: J 122 LEU cc_start: 0.8751 (mt) cc_final: 0.8433 (mt) REVERT: J 142 MET cc_start: 0.9181 (mtt) cc_final: 0.8809 (mtp) REVERT: N 178 SER cc_start: 0.8824 (p) cc_final: 0.8467 (t) REVERT: N 180 GLU cc_start: 0.9170 (pm20) cc_final: 0.8950 (pm20) REVERT: N 215 MET cc_start: 0.8827 (tmm) cc_final: 0.8469 (tmm) REVERT: Y 10 MET cc_start: 0.9102 (pmm) cc_final: 0.8743 (mmp) REVERT: Y 63 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8665 (mp10) REVERT: Y 66 MET cc_start: 0.8861 (ptp) cc_final: 0.8537 (ptp) REVERT: Y 67 GLN cc_start: 0.9766 (mm-40) cc_final: 0.9484 (mm-40) REVERT: Y 68 MET cc_start: 0.9355 (mtm) cc_final: 0.9057 (mtp) REVERT: Y 71 GLU cc_start: 0.9529 (mt-10) cc_final: 0.9144 (mt-10) REVERT: Y 79 GLU cc_start: 0.9509 (tp30) cc_final: 0.9140 (tp30) REVERT: Y 100 ARG cc_start: 0.9327 (ttm-80) cc_final: 0.9058 (tpp80) REVERT: Y 115 ILE cc_start: 0.9377 (mm) cc_final: 0.8745 (mm) REVERT: Y 124 ILE cc_start: 0.8927 (tp) cc_final: 0.8682 (tp) REVERT: Y 128 GLU cc_start: 0.9211 (pp20) cc_final: 0.8498 (pm20) REVERT: Y 129 ILE cc_start: 0.9487 (mt) cc_final: 0.8892 (mm) REVERT: Y 136 LEU cc_start: 0.9749 (mt) cc_final: 0.9507 (mt) REVERT: d 21 ASN cc_start: 0.9476 (m-40) cc_final: 0.9221 (m-40) REVERT: d 23 TRP cc_start: 0.9531 (t-100) cc_final: 0.8890 (t-100) REVERT: d 25 LYS cc_start: 0.9295 (tttt) cc_final: 0.9072 (tptp) REVERT: d 30 LYS cc_start: 0.8347 (mtpt) cc_final: 0.8125 (mtpt) REVERT: d 39 MET cc_start: 0.9004 (mtm) cc_final: 0.8164 (mtt) REVERT: d 55 MET cc_start: 0.9642 (ptm) cc_final: 0.9204 (ppp) REVERT: d 67 GLN cc_start: 0.9164 (tp-100) cc_final: 0.8670 (tp40) REVERT: d 76 GLU cc_start: 0.9615 (mm-30) cc_final: 0.9396 (mt-10) REVERT: d 111 LEU cc_start: 0.9602 (pp) cc_final: 0.9251 (pp) REVERT: d 130 TYR cc_start: 0.9047 (t80) cc_final: 0.8748 (t80) REVERT: d 132 ARG cc_start: 0.9401 (ttm110) cc_final: 0.9095 (ttp-110) REVERT: d 168 PHE cc_start: 0.9349 (t80) cc_final: 0.9022 (t80) REVERT: d 215 MET cc_start: 0.4031 (mmt) cc_final: 0.3569 (mtm) REVERT: e 23 TRP cc_start: 0.9474 (t-100) cc_final: 0.9083 (t-100) REVERT: e 30 LYS cc_start: 0.9397 (mmtp) cc_final: 0.9126 (mmmm) REVERT: e 32 PHE cc_start: 0.8930 (m-80) cc_final: 0.8718 (m-80) REVERT: e 35 GLU cc_start: 0.9296 (pm20) cc_final: 0.8982 (pm20) REVERT: e 39 MET cc_start: 0.9726 (mtm) cc_final: 0.9174 (mtm) REVERT: e 50 GLN cc_start: 0.9327 (mt0) cc_final: 0.8832 (mt0) REVERT: e 55 MET cc_start: 0.9543 (mtp) cc_final: 0.9213 (tpp) REVERT: e 57 ASN cc_start: 0.9646 (m110) cc_final: 0.9272 (p0) REVERT: e 76 GLU cc_start: 0.9625 (mm-30) cc_final: 0.9286 (mm-30) REVERT: e 79 GLU cc_start: 0.9595 (mt-10) cc_final: 0.9366 (mm-30) REVERT: e 104 ILE cc_start: 0.8435 (mt) cc_final: 0.7983 (mt) REVERT: e 111 LEU cc_start: 0.9401 (tp) cc_final: 0.8985 (tp) REVERT: e 118 MET cc_start: 0.9336 (mmt) cc_final: 0.9002 (ptp) REVERT: e 128 GLU cc_start: 0.9456 (pm20) cc_final: 0.8731 (pm20) REVERT: e 129 ILE cc_start: 0.9814 (mt) cc_final: 0.9390 (mm) REVERT: e 130 TYR cc_start: 0.9668 (t80) cc_final: 0.9444 (t80) REVERT: e 132 ARG cc_start: 0.9395 (ptp-110) cc_final: 0.8715 (ptp-170) REVERT: e 141 ILE cc_start: 0.9569 (tp) cc_final: 0.9328 (tp) REVERT: e 170 LYS cc_start: 0.9730 (tttt) cc_final: 0.9486 (tppt) REVERT: e 185 MET cc_start: 0.9828 (ptp) cc_final: 0.9477 (ptt) REVERT: e 205 LEU cc_start: 0.8023 (mt) cc_final: 0.7432 (mt) REVERT: e 211 LEU cc_start: 0.9413 (tp) cc_final: 0.9054 (tp) REVERT: e 214 MET cc_start: 0.8988 (tpp) cc_final: 0.8779 (tpp) REVERT: j 150 ILE cc_start: 0.9538 (tp) cc_final: 0.9319 (tp) REVERT: j 172 LEU cc_start: 0.9768 (tp) cc_final: 0.9511 (mm) REVERT: j 182 LYS cc_start: 0.9361 (mmtt) cc_final: 0.8902 (mmtt) REVERT: j 188 THR cc_start: 0.8036 (m) cc_final: 0.7701 (m) REVERT: k 43 LEU cc_start: 0.9710 (mp) cc_final: 0.8724 (mp) REVERT: k 52 LEU cc_start: 0.9645 (mt) cc_final: 0.9363 (mt) REVERT: k 76 GLU cc_start: 0.9586 (mm-30) cc_final: 0.9271 (mm-30) REVERT: k 81 ASP cc_start: 0.9750 (t70) cc_final: 0.9414 (m-30) REVERT: k 100 ARG cc_start: 0.9095 (ptp-110) cc_final: 0.8884 (ptp-110) REVERT: k 104 ILE cc_start: 0.8564 (mm) cc_final: 0.8317 (mm) REVERT: k 131 LYS cc_start: 0.9421 (tttt) cc_final: 0.9062 (tptt) REVERT: k 167 ARG cc_start: 0.8905 (mtm110) cc_final: 0.8633 (ptp-170) REVERT: k 168 PHE cc_start: 0.9590 (t80) cc_final: 0.9345 (t80) REVERT: k 185 MET cc_start: 0.9289 (mtm) cc_final: 0.8976 (mtt) REVERT: k 193 ASN cc_start: 0.9349 (m110) cc_final: 0.8290 (t0) REVERT: k 199 LYS cc_start: 0.9596 (tttt) cc_final: 0.9362 (tttm) REVERT: k 203 LYS cc_start: 0.9199 (mmtm) cc_final: 0.8883 (mmtt) REVERT: k 214 MET cc_start: 0.9381 (mmp) cc_final: 0.9122 (mmt) outliers start: 0 outliers final: 0 residues processed: 831 average time/residue: 0.1628 time to fit residues: 192.9091 Evaluate side-chains 672 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 672 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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: 7.9990 chunk 115 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 136 optimal weight: 30.0000 chunk 203 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS B 95 GLN G 193 ASN ** N 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 GLN ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 155 GLN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.081377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057130 restraints weight = 75610.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.059188 restraints weight = 51611.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.060726 restraints weight = 38989.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.061877 restraints weight = 31499.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.062730 restraints weight = 26774.594| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18834 Z= 0.145 Angle : 0.669 8.359 25587 Z= 0.349 Chirality : 0.046 0.254 2848 Planarity : 0.005 0.053 3345 Dihedral : 4.484 21.628 2500 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.45 % 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: -0.23 (0.17), residues: 2338 helix: 0.13 (0.13), residues: 1467 sheet: -1.60 (0.51), residues: 79 loop : -0.24 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 167 TYR 0.016 0.002 TYR J 48 PHE 0.032 0.002 PHE H 168 TRP 0.026 0.002 TRP H 23 HIS 0.005 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00319 (18824) covalent geometry : angle 0.66795 (25567) SS BOND : bond 0.00564 ( 10) SS BOND : angle 1.38175 ( 20) hydrogen bonds : bond 0.04276 ( 1037) hydrogen bonds : angle 4.72816 ( 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 847 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 845 time to evaluate : 0.744 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 9 GLN cc_start: 0.9435 (mp10) cc_final: 0.9205 (pm20) REVERT: A 23 TRP cc_start: 0.9363 (t-100) cc_final: 0.8954 (t-100) REVERT: A 39 MET cc_start: 0.9056 (mtt) cc_final: 0.8787 (mtt) REVERT: A 63 GLN cc_start: 0.9387 (tp-100) cc_final: 0.9135 (tp-100) REVERT: A 67 GLN cc_start: 0.9616 (tp40) cc_final: 0.9163 (tm-30) REVERT: A 68 MET cc_start: 0.9163 (ptp) cc_final: 0.8749 (ptm) REVERT: A 96 MET cc_start: 0.6716 (mtp) cc_final: 0.6333 (mtp) REVERT: A 103 ASP cc_start: 0.9563 (m-30) cc_final: 0.9071 (m-30) REVERT: A 114 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8833 (pt0) REVERT: A 132 ARG cc_start: 0.9454 (mtm110) cc_final: 0.9215 (mtm180) REVERT: A 135 ILE cc_start: 0.9476 (mt) cc_final: 0.9276 (mt) REVERT: B 5 ASN cc_start: 0.9372 (t0) cc_final: 0.8938 (m110) REVERT: B 30 LYS cc_start: 0.8782 (mmtp) cc_final: 0.8370 (mmmt) REVERT: B 39 MET cc_start: 0.9606 (tpp) cc_final: 0.9209 (tpt) REVERT: B 100 ARG cc_start: 0.8940 (ttp-110) cc_final: 0.8451 (ttp80) REVERT: B 108 THR cc_start: 0.9135 (p) cc_final: 0.8862 (p) REVERT: B 118 MET cc_start: 0.9665 (mtm) cc_final: 0.9333 (mmm) REVERT: B 158 LYS cc_start: 0.8534 (tptt) cc_final: 0.8033 (mmtt) REVERT: B 159 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8684 (tm-30) REVERT: B 169 TYR cc_start: 0.9421 (m-10) cc_final: 0.8748 (m-10) REVERT: B 170 LYS cc_start: 0.9466 (tppt) cc_final: 0.9228 (tppt) REVERT: B 181 VAL cc_start: 0.9684 (t) cc_final: 0.9152 (p) REVERT: B 185 MET cc_start: 0.9716 (ptp) cc_final: 0.9366 (ptt) REVERT: B 187 GLU cc_start: 0.9473 (mt-10) cc_final: 0.9184 (pp20) REVERT: B 213 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9156 (pt0) REVERT: C 10 MET cc_start: 0.8460 (tpp) cc_final: 0.7888 (tpp) REVERT: C 40 PHE cc_start: 0.9747 (t80) cc_final: 0.9434 (t80) REVERT: C 52 LEU cc_start: 0.9708 (mt) cc_final: 0.9461 (mt) REVERT: C 55 MET cc_start: 0.9561 (ttt) cc_final: 0.9323 (ttt) REVERT: C 59 VAL cc_start: 0.8397 (t) cc_final: 0.8052 (p) REVERT: C 71 GLU cc_start: 0.9472 (mp0) cc_final: 0.9108 (mp0) REVERT: C 75 GLU cc_start: 0.9441 (mt-10) cc_final: 0.9224 (mt-10) REVERT: C 76 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9044 (mt-10) REVERT: C 96 MET cc_start: -0.5093 (mmt) cc_final: -0.5524 (mtm) REVERT: C 129 ILE cc_start: 0.9727 (mt) cc_final: 0.9311 (mt) REVERT: C 133 TRP cc_start: 0.8935 (m-10) cc_final: 0.8483 (m-10) REVERT: C 144 MET cc_start: 0.8386 (tmm) cc_final: 0.7978 (tmm) REVERT: C 166 ASP cc_start: 0.8804 (t0) cc_final: 0.7862 (t0) REVERT: C 175 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8348 (tm-30) REVERT: C 185 MET cc_start: 0.9349 (mtt) cc_final: 0.8997 (mtt) REVERT: C 203 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8784 (mmmm) REVERT: C 215 MET cc_start: 0.9252 (tmm) cc_final: 0.8967 (tmm) REVERT: D 10 MET cc_start: 0.7673 (mpp) cc_final: 0.6697 (mmt) REVERT: D 21 ASN cc_start: 0.9581 (t0) cc_final: 0.9251 (t0) REVERT: D 25 LYS cc_start: 0.9764 (ttpt) cc_final: 0.9464 (ptmt) REVERT: D 52 LEU cc_start: 0.9653 (mt) cc_final: 0.9423 (mt) REVERT: D 53 ASN cc_start: 0.9293 (m-40) cc_final: 0.8991 (m110) REVERT: D 68 MET cc_start: 0.8555 (mtt) cc_final: 0.8350 (mtp) REVERT: D 128 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8833 (mm-30) REVERT: D 129 ILE cc_start: 0.9574 (mt) cc_final: 0.9302 (tp) REVERT: D 130 TYR cc_start: 0.8841 (t80) cc_final: 0.8493 (t80) REVERT: D 131 LYS cc_start: 0.9487 (ttmt) cc_final: 0.9013 (ptpt) REVERT: D 140 LYS cc_start: 0.9624 (mttt) cc_final: 0.9321 (tptp) REVERT: D 144 MET cc_start: 0.4165 (ttt) cc_final: 0.3813 (ttt) REVERT: G 68 MET cc_start: 0.8652 (mtt) cc_final: 0.8123 (ptp) REVERT: G 128 GLU cc_start: 0.9610 (pm20) cc_final: 0.9312 (pm20) REVERT: G 140 LYS cc_start: 0.9690 (mtpp) cc_final: 0.9470 (mtpp) REVERT: G 141 ILE cc_start: 0.8783 (mt) cc_final: 0.8537 (mt) REVERT: G 168 PHE cc_start: 0.9384 (t80) cc_final: 0.9068 (t80) REVERT: G 188 THR cc_start: 0.9440 (p) cc_final: 0.9222 (p) REVERT: H 13 GLN cc_start: 0.9430 (pp30) cc_final: 0.9199 (pm20) REVERT: H 25 LYS cc_start: 0.9602 (tttt) cc_final: 0.9233 (tppt) REVERT: H 55 MET cc_start: 0.9331 (mmp) cc_final: 0.8379 (mmm) REVERT: H 66 MET cc_start: 0.9530 (mmp) cc_final: 0.9161 (mmm) REVERT: H 67 GLN cc_start: 0.9425 (tp40) cc_final: 0.8900 (mt0) REVERT: H 68 MET cc_start: 0.9376 (mmt) cc_final: 0.9084 (mmt) REVERT: H 87 HIS cc_start: 0.7983 (m-70) cc_final: 0.7046 (t-90) REVERT: H 100 ARG cc_start: 0.9064 (ttt-90) cc_final: 0.8462 (mmp-170) REVERT: H 118 MET cc_start: 0.8525 (mmm) cc_final: 0.8074 (mmm) REVERT: H 124 ILE cc_start: 0.6559 (mm) cc_final: 0.6238 (mp) REVERT: H 128 GLU cc_start: 0.9637 (mm-30) cc_final: 0.9299 (mp0) REVERT: H 145 TYR cc_start: 0.9136 (m-80) cc_final: 0.8713 (m-10) REVERT: H 152 ASP cc_start: 0.9602 (m-30) cc_final: 0.9327 (m-30) REVERT: H 182 LYS cc_start: 0.9786 (pttp) cc_final: 0.9469 (pmtt) REVERT: J 36 PHE cc_start: 0.9727 (t80) cc_final: 0.9516 (t80) REVERT: J 40 SER cc_start: 0.8848 (m) cc_final: 0.8126 (p) REVERT: J 41 THR cc_start: 0.6768 (t) cc_final: 0.6533 (t) REVERT: J 48 TYR cc_start: 0.8772 (m-80) cc_final: 0.8258 (m-80) REVERT: J 49 LYS cc_start: 0.9290 (ttmm) cc_final: 0.9031 (tppp) REVERT: J 57 ILE cc_start: 0.7578 (tt) cc_final: 0.6054 (tt) REVERT: J 60 PHE cc_start: 0.8068 (t80) cc_final: 0.7458 (t80) REVERT: J 61 MET cc_start: 0.5841 (ppp) cc_final: 0.5604 (ppp) REVERT: J 142 MET cc_start: 0.9264 (mtt) cc_final: 0.8845 (mtp) REVERT: N 162 ARG cc_start: 0.9423 (mmm-85) cc_final: 0.9112 (mmm-85) REVERT: N 166 ASP cc_start: 0.8862 (t70) cc_final: 0.8599 (t70) REVERT: N 178 SER cc_start: 0.8847 (p) cc_final: 0.8379 (t) REVERT: N 180 GLU cc_start: 0.9114 (pm20) cc_final: 0.8840 (pm20) REVERT: Y 10 MET cc_start: 0.9122 (pmm) cc_final: 0.8775 (mmp) REVERT: Y 63 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8667 (mp10) REVERT: Y 67 GLN cc_start: 0.9779 (mm-40) cc_final: 0.9331 (mm-40) REVERT: Y 68 MET cc_start: 0.9252 (mtm) cc_final: 0.8950 (mtp) REVERT: Y 71 GLU cc_start: 0.9502 (mt-10) cc_final: 0.9136 (mt-10) REVERT: Y 136 LEU cc_start: 0.9709 (mt) cc_final: 0.9471 (mt) REVERT: d 15 ILE cc_start: 0.7365 (pt) cc_final: 0.6774 (mp) REVERT: d 23 TRP cc_start: 0.9463 (t-100) cc_final: 0.8783 (t-100) REVERT: d 25 LYS cc_start: 0.9213 (tttt) cc_final: 0.8976 (tptp) REVERT: d 30 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7921 (ttpt) REVERT: d 39 MET cc_start: 0.8970 (mtm) cc_final: 0.8072 (mtt) REVERT: d 51 ASP cc_start: 0.8205 (m-30) cc_final: 0.7873 (m-30) REVERT: d 55 MET cc_start: 0.9662 (ptm) cc_final: 0.9156 (ppp) REVERT: d 57 ASN cc_start: 0.9463 (m-40) cc_final: 0.9102 (t0) REVERT: d 58 THR cc_start: 0.9314 (p) cc_final: 0.9099 (p) REVERT: d 67 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8647 (tp40) REVERT: d 76 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9171 (mt-10) REVERT: d 111 LEU cc_start: 0.9470 (pp) cc_final: 0.9197 (pp) REVERT: d 132 ARG cc_start: 0.9385 (ttm110) cc_final: 0.9101 (ttp-110) REVERT: d 215 MET cc_start: 0.4363 (mmt) cc_final: 0.3766 (mtp) REVERT: e 10 MET cc_start: 0.9170 (mmm) cc_final: 0.8802 (tpp) REVERT: e 23 TRP cc_start: 0.9507 (t-100) cc_final: 0.9062 (t-100) REVERT: e 30 LYS cc_start: 0.9414 (mmtp) cc_final: 0.9031 (mmmm) REVERT: e 32 PHE cc_start: 0.8859 (m-80) cc_final: 0.8584 (m-80) REVERT: e 35 GLU cc_start: 0.9288 (pm20) cc_final: 0.8940 (pm20) REVERT: e 39 MET cc_start: 0.9639 (mtm) cc_final: 0.9160 (mtm) REVERT: e 50 GLN cc_start: 0.9262 (mt0) cc_final: 0.8859 (mt0) REVERT: e 55 MET cc_start: 0.9637 (mtp) cc_final: 0.9075 (tpp) REVERT: e 104 ILE cc_start: 0.8440 (mt) cc_final: 0.8085 (mt) REVERT: e 111 LEU cc_start: 0.9427 (tp) cc_final: 0.9065 (tp) REVERT: e 118 MET cc_start: 0.9367 (mmt) cc_final: 0.9000 (ptp) REVERT: e 128 GLU cc_start: 0.9467 (pm20) cc_final: 0.8767 (pm20) REVERT: e 129 ILE cc_start: 0.9806 (mt) cc_final: 0.9275 (mm) REVERT: e 132 ARG cc_start: 0.9385 (ptp-110) cc_final: 0.8750 (ptp-170) REVERT: e 141 ILE cc_start: 0.9583 (tp) cc_final: 0.9338 (tp) REVERT: e 169 TYR cc_start: 0.9639 (m-10) cc_final: 0.9310 (m-10) REVERT: e 170 LYS cc_start: 0.9738 (tttt) cc_final: 0.9462 (tppt) REVERT: e 185 MET cc_start: 0.9789 (ptp) cc_final: 0.9497 (ptt) REVERT: e 203 LYS cc_start: 0.7996 (ptpt) cc_final: 0.7318 (tttt) REVERT: e 211 LEU cc_start: 0.9359 (tp) cc_final: 0.9121 (tp) REVERT: e 214 MET cc_start: 0.8893 (tpp) cc_final: 0.8628 (tpp) REVERT: j 188 THR cc_start: 0.8228 (m) cc_final: 0.7800 (m) REVERT: j 215 MET cc_start: 0.8479 (ppp) cc_final: 0.8228 (ppp) REVERT: k 21 ASN cc_start: 0.9514 (t0) cc_final: 0.9185 (t0) REVERT: k 25 LYS cc_start: 0.9775 (ptmm) cc_final: 0.9453 (ptmt) REVERT: k 39 MET cc_start: 0.9336 (tpt) cc_final: 0.8926 (tpt) REVERT: k 43 LEU cc_start: 0.9542 (mp) cc_final: 0.8953 (mp) REVERT: k 52 LEU cc_start: 0.9622 (mt) cc_final: 0.9336 (mt) REVERT: k 66 MET cc_start: 0.9615 (tpp) cc_final: 0.9410 (tpp) REVERT: k 76 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9071 (mm-30) REVERT: k 81 ASP cc_start: 0.9761 (t70) cc_final: 0.9363 (m-30) REVERT: k 131 LYS cc_start: 0.9400 (tttt) cc_final: 0.8954 (tptt) REVERT: k 143 ARG cc_start: 0.9399 (mtt180) cc_final: 0.9165 (ttm110) REVERT: k 159 GLU cc_start: 0.8806 (mp0) cc_final: 0.8120 (mp0) REVERT: k 167 ARG cc_start: 0.8880 (mtm110) cc_final: 0.8463 (ptt180) REVERT: k 173 ARG cc_start: 0.8882 (ttt180) cc_final: 0.8636 (ttp-170) REVERT: k 179 GLN cc_start: 0.9551 (tp-100) cc_final: 0.9232 (tp-100) REVERT: k 185 MET cc_start: 0.9256 (mtm) cc_final: 0.8901 (mtt) REVERT: k 193 ASN cc_start: 0.9306 (m110) cc_final: 0.8288 (t0) REVERT: k 199 LYS cc_start: 0.9579 (tttt) cc_final: 0.9379 (tttm) REVERT: k 203 LYS cc_start: 0.9152 (mmtm) cc_final: 0.8679 (mptt) outliers start: 2 outliers final: 1 residues processed: 847 average time/residue: 0.1665 time to fit residues: 200.2776 Evaluate side-chains 682 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 681 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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: 8.9990 chunk 233 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 131 optimal weight: 50.0000 chunk 84 optimal weight: 30.0000 chunk 210 optimal weight: 20.0000 chunk 228 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 219 GLN Y 13 GLN d 21 ASN d 62 HIS e 95 GLN ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 155 GLN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.079283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.056038 restraints weight = 78182.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.058010 restraints weight = 52775.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.059467 restraints weight = 39538.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.060552 restraints weight = 31806.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.061356 restraints weight = 26977.200| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.7348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18834 Z= 0.192 Angle : 0.711 9.604 25587 Z= 0.379 Chirality : 0.046 0.213 2848 Planarity : 0.005 0.049 3345 Dihedral : 4.617 23.200 2500 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.10 % Allowed : 1.85 % Favored : 98.05 % 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: -0.44 (0.17), residues: 2338 helix: -0.01 (0.13), residues: 1474 sheet: -1.93 (0.46), residues: 91 loop : -0.32 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG d 173 TYR 0.019 0.002 TYR H 130 PHE 0.033 0.003 PHE H 168 TRP 0.029 0.002 TRP Y 23 HIS 0.007 0.002 HIS d 62 Details of bonding type rmsd covalent geometry : bond 0.00407 (18824) covalent geometry : angle 0.71068 (25567) SS BOND : bond 0.00632 ( 10) SS BOND : angle 1.13635 ( 20) hydrogen bonds : bond 0.04446 ( 1037) hydrogen bonds : angle 4.93011 ( 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 841 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 839 time to evaluate : 0.665 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: A 9 GLN cc_start: 0.9452 (mp10) cc_final: 0.9220 (pm20) REVERT: A 25 LYS cc_start: 0.9627 (tptp) cc_final: 0.9414 (tppt) REVERT: A 39 MET cc_start: 0.9131 (mtt) cc_final: 0.8841 (mtt) REVERT: A 63 GLN cc_start: 0.9374 (tp-100) cc_final: 0.9130 (tp-100) REVERT: A 67 GLN cc_start: 0.9550 (tp40) cc_final: 0.9246 (tm-30) REVERT: A 68 MET cc_start: 0.9394 (ptp) cc_final: 0.9087 (ptp) REVERT: A 96 MET cc_start: 0.6810 (mtp) cc_final: 0.6448 (mtp) REVERT: A 100 ARG cc_start: 0.9683 (ttm-80) cc_final: 0.9382 (tpp80) REVERT: A 103 ASP cc_start: 0.9606 (m-30) cc_final: 0.9260 (m-30) REVERT: A 135 ILE cc_start: 0.9451 (mt) cc_final: 0.9190 (mt) REVERT: B 5 ASN cc_start: 0.9401 (t0) cc_final: 0.9166 (m110) REVERT: B 16 SER cc_start: 0.9074 (m) cc_final: 0.8832 (m) REVERT: B 20 LEU cc_start: 0.9499 (mt) cc_final: 0.9281 (mt) REVERT: B 23 TRP cc_start: 0.9186 (t-100) cc_final: 0.8649 (t-100) REVERT: B 30 LYS cc_start: 0.8975 (mmtp) cc_final: 0.8488 (mppt) REVERT: B 39 MET cc_start: 0.9581 (tpp) cc_final: 0.9204 (tpt) REVERT: B 40 PHE cc_start: 0.9433 (t80) cc_final: 0.8993 (t80) REVERT: B 96 MET cc_start: 0.8828 (tpt) cc_final: 0.8245 (ptp) REVERT: B 113 GLU cc_start: 0.9689 (mp0) cc_final: 0.9485 (mp0) REVERT: B 117 TRP cc_start: 0.8413 (m-10) cc_final: 0.7691 (m-90) REVERT: B 118 MET cc_start: 0.9656 (mtm) cc_final: 0.9192 (ptp) REVERT: B 128 GLU cc_start: 0.9325 (pm20) cc_final: 0.9116 (pm20) REVERT: B 132 ARG cc_start: 0.9583 (ptp90) cc_final: 0.9347 (ptp-170) REVERT: B 158 LYS cc_start: 0.8554 (tptt) cc_final: 0.8014 (mmtt) REVERT: B 169 TYR cc_start: 0.9404 (m-10) cc_final: 0.8917 (m-10) REVERT: B 170 LYS cc_start: 0.9503 (tppt) cc_final: 0.9253 (tppt) REVERT: C 10 MET cc_start: 0.8460 (tpp) cc_final: 0.8005 (tpp) REVERT: C 52 LEU cc_start: 0.9726 (mt) cc_final: 0.9476 (mt) REVERT: C 59 VAL cc_start: 0.8653 (t) cc_final: 0.8346 (p) REVERT: C 71 GLU cc_start: 0.9454 (mp0) cc_final: 0.9008 (mp0) REVERT: C 76 GLU cc_start: 0.9568 (mm-30) cc_final: 0.9007 (mm-30) REVERT: C 79 GLU cc_start: 0.9539 (mt-10) cc_final: 0.9315 (pt0) REVERT: C 96 MET cc_start: -0.5001 (mmt) cc_final: -0.5446 (mtm) REVERT: C 133 TRP cc_start: 0.9006 (m-10) cc_final: 0.8457 (m-10) REVERT: C 144 MET cc_start: 0.8148 (tmm) cc_final: 0.7691 (tmm) REVERT: C 163 ASP cc_start: 0.9067 (m-30) cc_final: 0.8698 (t0) REVERT: C 166 ASP cc_start: 0.8885 (t0) cc_final: 0.7893 (t0) REVERT: C 167 ARG cc_start: 0.8821 (mmp80) cc_final: 0.8388 (mmp80) REVERT: C 175 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8408 (tm-30) REVERT: C 185 MET cc_start: 0.9337 (mtt) cc_final: 0.9094 (mtt) REVERT: C 203 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8853 (mmmm) REVERT: D 21 ASN cc_start: 0.9616 (t0) cc_final: 0.9234 (t0) REVERT: D 25 LYS cc_start: 0.9781 (ttpt) cc_final: 0.9510 (ptmt) REVERT: D 52 LEU cc_start: 0.9604 (mt) cc_final: 0.9384 (mt) REVERT: D 53 ASN cc_start: 0.9300 (m-40) cc_final: 0.8985 (m-40) REVERT: D 96 MET cc_start: 0.6937 (ttt) cc_final: 0.6171 (ttt) REVERT: D 103 ASP cc_start: 0.9640 (t0) cc_final: 0.9433 (t0) REVERT: D 129 ILE cc_start: 0.9592 (mt) cc_final: 0.9152 (tp) REVERT: D 130 TYR cc_start: 0.8976 (t80) cc_final: 0.8676 (t80) REVERT: D 131 LYS cc_start: 0.9477 (ttmt) cc_final: 0.8900 (mttt) REVERT: D 132 ARG cc_start: 0.9707 (ttt180) cc_final: 0.9439 (tpp80) REVERT: D 140 LYS cc_start: 0.9643 (mttt) cc_final: 0.9339 (tptp) REVERT: D 144 MET cc_start: 0.4019 (ttt) cc_final: 0.3647 (ttt) REVERT: D 161 PHE cc_start: 0.8338 (t80) cc_final: 0.8096 (t80) REVERT: D 215 MET cc_start: 0.8200 (mtm) cc_final: 0.7300 (mtm) REVERT: G 23 TRP cc_start: 0.9483 (t-100) cc_final: 0.9273 (t60) REVERT: G 25 LYS cc_start: 0.9381 (ptpp) cc_final: 0.9116 (ptpp) REVERT: G 68 MET cc_start: 0.8844 (mtt) cc_final: 0.8373 (ptp) REVERT: G 168 PHE cc_start: 0.9412 (t80) cc_final: 0.9109 (t80) REVERT: G 188 THR cc_start: 0.9447 (p) cc_final: 0.9232 (p) REVERT: H 13 GLN cc_start: 0.9484 (pp30) cc_final: 0.9232 (pm20) REVERT: H 23 TRP cc_start: 0.9396 (t60) cc_final: 0.8914 (t60) REVERT: H 25 LYS cc_start: 0.9587 (tttt) cc_final: 0.9252 (tppt) REVERT: H 30 LYS cc_start: 0.8725 (ptmt) cc_final: 0.8496 (ptmt) REVERT: H 32 PHE cc_start: 0.7108 (m-10) cc_final: 0.6733 (m-10) REVERT: H 39 MET cc_start: 0.9146 (mpp) cc_final: 0.8933 (mpp) REVERT: H 55 MET cc_start: 0.9223 (mmp) cc_final: 0.8939 (mmp) REVERT: H 66 MET cc_start: 0.9554 (mmp) cc_final: 0.9204 (mmm) REVERT: H 67 GLN cc_start: 0.9404 (tp40) cc_final: 0.8768 (mt0) REVERT: H 68 MET cc_start: 0.9360 (mmt) cc_final: 0.8885 (mmm) REVERT: H 87 HIS cc_start: 0.8069 (m-70) cc_final: 0.6945 (t-170) REVERT: H 100 ARG cc_start: 0.9128 (ttt-90) cc_final: 0.8466 (mmp-170) REVERT: H 118 MET cc_start: 0.8560 (mmm) cc_final: 0.8064 (mmt) REVERT: H 124 ILE cc_start: 0.6734 (mm) cc_final: 0.6349 (mp) REVERT: H 128 GLU cc_start: 0.9591 (mm-30) cc_final: 0.9248 (mp0) REVERT: H 145 TYR cc_start: 0.9159 (m-80) cc_final: 0.8739 (m-10) REVERT: H 152 ASP cc_start: 0.9638 (m-30) cc_final: 0.9365 (m-30) REVERT: H 182 LYS cc_start: 0.9786 (pttp) cc_final: 0.9469 (pttt) REVERT: H 185 MET cc_start: 0.9554 (mtm) cc_final: 0.9315 (mtm) REVERT: J 29 VAL cc_start: 0.9362 (t) cc_final: 0.9123 (p) REVERT: J 36 PHE cc_start: 0.9709 (t80) cc_final: 0.9502 (t80) REVERT: J 40 SER cc_start: 0.9103 (m) cc_final: 0.8161 (p) REVERT: J 48 TYR cc_start: 0.8917 (m-80) cc_final: 0.8369 (m-80) REVERT: J 49 LYS cc_start: 0.9323 (ttmm) cc_final: 0.9077 (tppp) REVERT: J 60 PHE cc_start: 0.8280 (t80) cc_final: 0.7801 (t80) REVERT: J 61 MET cc_start: 0.5859 (ppp) cc_final: 0.5391 (ppp) REVERT: J 142 MET cc_start: 0.9262 (mtt) cc_final: 0.8766 (mtp) REVERT: J 158 ILE cc_start: 0.9283 (mm) cc_final: 0.8948 (mt) REVERT: N 162 ARG cc_start: 0.9371 (mmm-85) cc_final: 0.9121 (mmm-85) REVERT: N 178 SER cc_start: 0.8924 (p) cc_final: 0.8509 (t) REVERT: N 180 GLU cc_start: 0.9112 (pm20) cc_final: 0.8832 (pm20) REVERT: Y 10 MET cc_start: 0.9127 (pmm) cc_final: 0.8813 (mmp) REVERT: Y 43 LEU cc_start: 0.9483 (mm) cc_final: 0.9276 (mm) REVERT: Y 53 ASN cc_start: 0.9448 (m110) cc_final: 0.9157 (m-40) REVERT: Y 63 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8526 (mp10) REVERT: Y 67 GLN cc_start: 0.9760 (mm-40) cc_final: 0.9314 (mm-40) REVERT: Y 68 MET cc_start: 0.9287 (mtm) cc_final: 0.8854 (mtp) REVERT: Y 71 GLU cc_start: 0.9511 (mt-10) cc_final: 0.9081 (mt-10) REVERT: Y 115 ILE cc_start: 0.9498 (mm) cc_final: 0.9079 (mm) REVERT: Y 118 MET cc_start: 0.9197 (mmp) cc_final: 0.8970 (ptm) REVERT: Y 124 ILE cc_start: 0.8939 (tp) cc_final: 0.8654 (tp) REVERT: Y 136 LEU cc_start: 0.9701 (mt) cc_final: 0.9453 (mt) REVERT: d 10 MET cc_start: 0.2752 (ptt) cc_final: 0.2173 (ttp) REVERT: d 15 ILE cc_start: 0.7367 (pt) cc_final: 0.6727 (pt) REVERT: d 23 TRP cc_start: 0.9489 (t-100) cc_final: 0.8798 (t-100) REVERT: d 25 LYS cc_start: 0.9235 (tttt) cc_final: 0.9002 (tptp) REVERT: d 30 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8017 (tttt) REVERT: d 39 MET cc_start: 0.9081 (mtm) cc_final: 0.8211 (mtt) REVERT: d 55 MET cc_start: 0.9669 (ptm) cc_final: 0.9218 (ppp) REVERT: d 57 ASN cc_start: 0.9458 (m-40) cc_final: 0.9065 (t0) REVERT: d 58 THR cc_start: 0.9307 (p) cc_final: 0.9097 (p) REVERT: d 67 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8587 (tp40) REVERT: d 111 LEU cc_start: 0.9485 (pp) cc_final: 0.9273 (pp) REVERT: d 130 TYR cc_start: 0.8943 (t80) cc_final: 0.8694 (t80) REVERT: d 132 ARG cc_start: 0.9402 (ttm110) cc_final: 0.8955 (ttp-110) REVERT: d 168 PHE cc_start: 0.9272 (t80) cc_final: 0.8994 (t80) REVERT: d 215 MET cc_start: 0.4332 (mmt) cc_final: 0.4005 (mtm) REVERT: e 30 LYS cc_start: 0.9416 (mmtp) cc_final: 0.9162 (mmmm) REVERT: e 32 PHE cc_start: 0.9019 (m-80) cc_final: 0.8745 (m-80) REVERT: e 39 MET cc_start: 0.9616 (mtm) cc_final: 0.9228 (mtm) REVERT: e 50 GLN cc_start: 0.9314 (mt0) cc_final: 0.8864 (mt0) REVERT: e 55 MET cc_start: 0.9697 (mtp) cc_final: 0.9063 (tpp) REVERT: e 63 GLN cc_start: 0.9627 (mp10) cc_final: 0.9363 (mp10) REVERT: e 76 GLU cc_start: 0.9621 (mm-30) cc_final: 0.9315 (mm-30) REVERT: e 100 ARG cc_start: 0.7963 (mmp80) cc_final: 0.7660 (mmp-170) REVERT: e 104 ILE cc_start: 0.8498 (mt) cc_final: 0.8053 (mt) REVERT: e 111 LEU cc_start: 0.9399 (tp) cc_final: 0.8733 (tp) REVERT: e 141 ILE cc_start: 0.9612 (tp) cc_final: 0.9390 (tp) REVERT: e 169 TYR cc_start: 0.9664 (m-10) cc_final: 0.9291 (m-10) REVERT: e 170 LYS cc_start: 0.9750 (tttt) cc_final: 0.9471 (tppt) REVERT: e 185 MET cc_start: 0.9786 (ptp) cc_final: 0.9496 (ptt) REVERT: e 203 LYS cc_start: 0.7960 (ptpt) cc_final: 0.7222 (tttt) REVERT: e 214 MET cc_start: 0.9016 (tpp) cc_final: 0.8767 (tpp) REVERT: j 188 THR cc_start: 0.8156 (m) cc_final: 0.7737 (m) REVERT: j 215 MET cc_start: 0.8586 (ppp) cc_final: 0.8379 (ppp) REVERT: k 25 LYS cc_start: 0.9770 (ptmm) cc_final: 0.9453 (ptmt) REVERT: k 39 MET cc_start: 0.9433 (tpt) cc_final: 0.9078 (tpt) REVERT: k 43 LEU cc_start: 0.9615 (mp) cc_final: 0.9013 (mp) REVERT: k 52 LEU cc_start: 0.9636 (mt) cc_final: 0.9386 (mt) REVERT: k 66 MET cc_start: 0.9655 (tpp) cc_final: 0.9413 (tpp) REVERT: k 76 GLU cc_start: 0.9524 (mm-30) cc_final: 0.9168 (mm-30) REVERT: k 81 ASP cc_start: 0.9748 (t70) cc_final: 0.9382 (m-30) REVERT: k 131 LYS cc_start: 0.9360 (tttt) cc_final: 0.8934 (tptt) REVERT: k 139 ASN cc_start: 0.9683 (m110) cc_final: 0.9459 (m110) REVERT: k 140 LYS cc_start: 0.9696 (mttt) cc_final: 0.9437 (mttm) REVERT: k 173 ARG cc_start: 0.8936 (ttt180) cc_final: 0.8623 (ttp-170) REVERT: k 185 MET cc_start: 0.9226 (mtm) cc_final: 0.8914 (mtt) REVERT: k 193 ASN cc_start: 0.9300 (m110) cc_final: 0.8273 (t0) outliers start: 2 outliers final: 0 residues processed: 840 average time/residue: 0.1618 time to fit residues: 193.7607 Evaluate side-chains 673 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 673 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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: 6.9990 chunk 135 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 218 optimal weight: 7.9990 chunk 165 optimal weight: 40.0000 chunk 208 optimal weight: 10.0000 chunk 150 optimal weight: 0.0050 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS B 95 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS e 95 GLN ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 ASN j 155 GLN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 74 ASN ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.080782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.056449 restraints weight = 76462.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058498 restraints weight = 51483.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.060017 restraints weight = 38674.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061138 restraints weight = 31142.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.061939 restraints weight = 26420.569| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.7598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18834 Z= 0.149 Angle : 0.701 8.654 25587 Z= 0.368 Chirality : 0.047 0.270 2848 Planarity : 0.005 0.052 3345 Dihedral : 4.553 21.633 2500 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.05 % Allowed : 1.05 % Favored : 98.90 % 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: -0.30 (0.17), residues: 2338 helix: 0.11 (0.13), residues: 1466 sheet: -1.88 (0.46), residues: 91 loop : -0.29 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 132 TYR 0.023 0.002 TYR H 169 PHE 0.035 0.002 PHE H 168 TRP 0.028 0.002 TRP A 23 HIS 0.004 0.001 HIS J 92 Details of bonding type rmsd covalent geometry : bond 0.00328 (18824) covalent geometry : angle 0.70046 (25567) SS BOND : bond 0.00407 ( 10) SS BOND : angle 1.33630 ( 20) hydrogen bonds : bond 0.04319 ( 1037) hydrogen bonds : angle 4.84231 ( 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 840 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 839 time to evaluate : 0.711 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: A 9 GLN cc_start: 0.9453 (mp10) cc_final: 0.9228 (pm20) REVERT: A 30 LYS cc_start: 0.9555 (mmtm) cc_final: 0.9222 (mmmt) REVERT: A 39 MET cc_start: 0.9147 (mtt) cc_final: 0.8777 (mtt) REVERT: A 40 PHE cc_start: 0.9628 (t80) cc_final: 0.9354 (t80) REVERT: A 63 GLN cc_start: 0.9368 (tp-100) cc_final: 0.9149 (tp-100) REVERT: A 67 GLN cc_start: 0.9592 (tp40) cc_final: 0.9288 (tm-30) REVERT: A 96 MET cc_start: 0.6653 (mtp) cc_final: 0.6286 (mtp) REVERT: A 100 ARG cc_start: 0.9684 (ttm-80) cc_final: 0.9378 (tpp80) REVERT: A 114 GLN cc_start: 0.9245 (mt0) cc_final: 0.9013 (mt0) REVERT: A 135 ILE cc_start: 0.9439 (mt) cc_final: 0.9224 (mt) REVERT: A 141 ILE cc_start: 0.9681 (mm) cc_final: 0.9209 (mm) REVERT: B 2 ILE cc_start: 0.9396 (tt) cc_final: 0.9059 (tt) REVERT: B 20 LEU cc_start: 0.9527 (mt) cc_final: 0.9303 (mt) REVERT: B 23 TRP cc_start: 0.9186 (t-100) cc_final: 0.8621 (t-100) REVERT: B 30 LYS cc_start: 0.8955 (mmtp) cc_final: 0.8449 (mppt) REVERT: B 39 MET cc_start: 0.9592 (tpp) cc_final: 0.9194 (tpt) REVERT: B 118 MET cc_start: 0.9642 (mtm) cc_final: 0.9238 (ptp) REVERT: B 132 ARG cc_start: 0.9558 (ptp90) cc_final: 0.9313 (ptp-170) REVERT: B 144 MET cc_start: 0.9128 (tpp) cc_final: 0.8611 (tpp) REVERT: B 158 LYS cc_start: 0.8590 (tptt) cc_final: 0.8030 (mmtt) REVERT: B 169 TYR cc_start: 0.9523 (m-10) cc_final: 0.9005 (m-10) REVERT: B 170 LYS cc_start: 0.9471 (tppt) cc_final: 0.9190 (tppt) REVERT: C 10 MET cc_start: 0.8432 (tpp) cc_final: 0.8035 (tpp) REVERT: C 39 MET cc_start: 0.9731 (mmm) cc_final: 0.9195 (mtt) REVERT: C 40 PHE cc_start: 0.9776 (t80) cc_final: 0.9575 (t80) REVERT: C 52 LEU cc_start: 0.9694 (mt) cc_final: 0.9443 (mt) REVERT: C 59 VAL cc_start: 0.8556 (t) cc_final: 0.8271 (p) REVERT: C 71 GLU cc_start: 0.9549 (mp0) cc_final: 0.9192 (mp0) REVERT: C 76 GLU cc_start: 0.9557 (mm-30) cc_final: 0.9029 (mm-30) REVERT: C 79 GLU cc_start: 0.9540 (mt-10) cc_final: 0.9317 (tp30) REVERT: C 96 MET cc_start: -0.5039 (mmt) cc_final: -0.5557 (mtm) REVERT: C 144 MET cc_start: 0.8127 (tmm) cc_final: 0.7630 (tmm) REVERT: C 150 ILE cc_start: 0.8861 (tp) cc_final: 0.8630 (tp) REVERT: C 153 ILE cc_start: 0.9231 (mt) cc_final: 0.8969 (mt) REVERT: C 163 ASP cc_start: 0.9037 (m-30) cc_final: 0.8638 (t0) REVERT: C 166 ASP cc_start: 0.8938 (t0) cc_final: 0.7993 (t0) REVERT: C 167 ARG cc_start: 0.8922 (mmp80) cc_final: 0.8501 (mmp80) REVERT: C 185 MET cc_start: 0.9328 (mtt) cc_final: 0.9029 (mtt) REVERT: C 203 LYS cc_start: 0.9155 (mmtt) cc_final: 0.8863 (mmmm) REVERT: D 10 MET cc_start: 0.6721 (mmp) cc_final: 0.6429 (mmm) REVERT: D 21 ASN cc_start: 0.9594 (t0) cc_final: 0.9241 (t0) REVERT: D 25 LYS cc_start: 0.9761 (ttpt) cc_final: 0.9476 (ptmt) REVERT: D 52 LEU cc_start: 0.9601 (mt) cc_final: 0.9330 (mt) REVERT: D 53 ASN cc_start: 0.9288 (m-40) cc_final: 0.8955 (m110) REVERT: D 68 MET cc_start: 0.8666 (mtt) cc_final: 0.8173 (mtp) REVERT: D 96 MET cc_start: 0.7597 (ttt) cc_final: 0.6982 (ttt) REVERT: D 112 GLN cc_start: 0.9666 (mp-120) cc_final: 0.9268 (pp30) REVERT: D 129 ILE cc_start: 0.9521 (mt) cc_final: 0.9258 (tp) REVERT: D 130 TYR cc_start: 0.8962 (t80) cc_final: 0.8718 (t80) REVERT: D 131 LYS cc_start: 0.9351 (ttmt) cc_final: 0.8779 (mttt) REVERT: D 140 LYS cc_start: 0.9612 (mttt) cc_final: 0.9264 (tptp) REVERT: D 161 PHE cc_start: 0.8282 (t80) cc_final: 0.8080 (t80) REVERT: D 215 MET cc_start: 0.8287 (mtm) cc_final: 0.7306 (mtm) REVERT: G 68 MET cc_start: 0.8821 (mtt) cc_final: 0.8598 (mtp) REVERT: G 128 GLU cc_start: 0.9507 (pm20) cc_final: 0.9237 (pm20) REVERT: G 132 ARG cc_start: 0.9651 (ptp90) cc_final: 0.9193 (ptt-90) REVERT: G 168 PHE cc_start: 0.9368 (t80) cc_final: 0.9062 (t80) REVERT: G 188 THR cc_start: 0.9446 (p) cc_final: 0.9217 (p) REVERT: H 13 GLN cc_start: 0.9477 (pp30) cc_final: 0.9231 (pm20) REVERT: H 23 TRP cc_start: 0.9437 (t60) cc_final: 0.8718 (t60) REVERT: H 25 LYS cc_start: 0.9653 (tttt) cc_final: 0.9280 (tppt) REVERT: H 32 PHE cc_start: 0.7008 (m-10) cc_final: 0.6668 (m-10) REVERT: H 39 MET cc_start: 0.9157 (mpp) cc_final: 0.8829 (mpp) REVERT: H 55 MET cc_start: 0.9272 (mmp) cc_final: 0.8713 (mmp) REVERT: H 66 MET cc_start: 0.9547 (mmp) cc_final: 0.9196 (mmm) REVERT: H 67 GLN cc_start: 0.9361 (tp40) cc_final: 0.8961 (mt0) REVERT: H 68 MET cc_start: 0.9360 (mmt) cc_final: 0.8813 (mmm) REVERT: H 87 HIS cc_start: 0.8036 (m-70) cc_final: 0.7092 (t-170) REVERT: H 100 ARG cc_start: 0.9060 (ttt-90) cc_final: 0.8435 (mmp-170) REVERT: H 118 MET cc_start: 0.8611 (mmm) cc_final: 0.8267 (mmt) REVERT: H 128 GLU cc_start: 0.9633 (mm-30) cc_final: 0.9308 (mp0) REVERT: H 145 TYR cc_start: 0.8927 (m-80) cc_final: 0.8617 (m-10) REVERT: H 152 ASP cc_start: 0.9633 (m-30) cc_final: 0.9367 (m-30) REVERT: H 182 LYS cc_start: 0.9801 (pttp) cc_final: 0.9469 (pttt) REVERT: J 24 LEU cc_start: 0.9694 (mt) cc_final: 0.9451 (mt) REVERT: J 36 PHE cc_start: 0.9700 (t80) cc_final: 0.9452 (t80) REVERT: J 37 ARG cc_start: 0.9249 (ptm160) cc_final: 0.9040 (ptm-80) REVERT: J 40 SER cc_start: 0.8944 (m) cc_final: 0.7966 (p) REVERT: J 48 TYR cc_start: 0.8793 (m-80) cc_final: 0.8167 (m-80) REVERT: J 57 ILE cc_start: 0.7818 (tt) cc_final: 0.6355 (tt) REVERT: J 60 PHE cc_start: 0.8210 (t80) cc_final: 0.7773 (t80) REVERT: J 61 MET cc_start: 0.6052 (ppp) cc_final: 0.5723 (ppp) REVERT: J 78 ILE cc_start: 0.9292 (pt) cc_final: 0.9010 (pt) REVERT: J 133 LYS cc_start: 0.9381 (tppt) cc_final: 0.9085 (mttt) REVERT: J 136 MET cc_start: 0.8406 (tpp) cc_final: 0.8204 (tpp) REVERT: J 142 MET cc_start: 0.9241 (mtt) cc_final: 0.8991 (mtp) REVERT: N 162 ARG cc_start: 0.9340 (mmm-85) cc_final: 0.9135 (mmp80) REVERT: N 178 SER cc_start: 0.8928 (p) cc_final: 0.8381 (t) REVERT: N 180 GLU cc_start: 0.9184 (pm20) cc_final: 0.8894 (pm20) REVERT: Y 10 MET cc_start: 0.9133 (pmm) cc_final: 0.8865 (mmp) REVERT: Y 23 TRP cc_start: 0.9499 (t60) cc_final: 0.9179 (t60) REVERT: Y 25 LYS cc_start: 0.9693 (tppt) cc_final: 0.9293 (tptm) REVERT: Y 32 PHE cc_start: 0.7822 (m-80) cc_final: 0.7540 (m-80) REVERT: Y 43 LEU cc_start: 0.9431 (mm) cc_final: 0.9172 (mm) REVERT: Y 58 THR cc_start: 0.9564 (p) cc_final: 0.8974 (p) REVERT: Y 67 GLN cc_start: 0.9779 (mm-40) cc_final: 0.9457 (mm-40) REVERT: Y 68 MET cc_start: 0.9115 (mtm) cc_final: 0.8794 (mtp) REVERT: Y 71 GLU cc_start: 0.9446 (mt-10) cc_final: 0.9072 (mt-10) REVERT: Y 115 ILE cc_start: 0.9509 (mm) cc_final: 0.8999 (mm) REVERT: Y 118 MET cc_start: 0.9243 (mmp) cc_final: 0.9024 (ptm) REVERT: Y 124 ILE cc_start: 0.8969 (tp) cc_final: 0.8661 (tp) REVERT: Y 131 LYS cc_start: 0.9048 (mttm) cc_final: 0.8819 (mttt) REVERT: Y 132 ARG cc_start: 0.9674 (ptp-170) cc_final: 0.9414 (ptp-170) REVERT: Y 136 LEU cc_start: 0.9712 (mt) cc_final: 0.9492 (mt) REVERT: d 10 MET cc_start: 0.2941 (ptt) cc_final: 0.2335 (ttp) REVERT: d 15 ILE cc_start: 0.7330 (pt) cc_final: 0.6923 (pt) REVERT: d 23 TRP cc_start: 0.9499 (t-100) cc_final: 0.8839 (t-100) REVERT: d 25 LYS cc_start: 0.9243 (tttt) cc_final: 0.9012 (tptp) REVERT: d 30 LYS cc_start: 0.8325 (mtpt) cc_final: 0.8018 (tttt) REVERT: d 39 MET cc_start: 0.9013 (mtm) cc_final: 0.8155 (mtt) REVERT: d 55 MET cc_start: 0.9679 (ptm) cc_final: 0.9216 (ppp) REVERT: d 57 ASN cc_start: 0.9473 (m-40) cc_final: 0.9127 (t0) REVERT: d 67 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8576 (tp40) REVERT: d 111 LEU cc_start: 0.9479 (pp) cc_final: 0.9265 (pp) REVERT: d 132 ARG cc_start: 0.9402 (ttm110) cc_final: 0.8944 (ttp-110) REVERT: d 144 MET cc_start: 0.9047 (tmm) cc_final: 0.8839 (tmm) REVERT: d 168 PHE cc_start: 0.9329 (t80) cc_final: 0.9069 (t80) REVERT: d 215 MET cc_start: 0.4822 (mmt) cc_final: 0.4437 (mtm) REVERT: e 10 MET cc_start: 0.9102 (mmm) cc_final: 0.8741 (tpp) REVERT: e 23 TRP cc_start: 0.9538 (t-100) cc_final: 0.9010 (t-100) REVERT: e 30 LYS cc_start: 0.9355 (mmtp) cc_final: 0.9042 (mmmm) REVERT: e 32 PHE cc_start: 0.8909 (m-80) cc_final: 0.8613 (m-80) REVERT: e 39 MET cc_start: 0.9643 (mtm) cc_final: 0.9238 (mtm) REVERT: e 50 GLN cc_start: 0.9332 (mt0) cc_final: 0.8915 (mt0) REVERT: e 55 MET cc_start: 0.9700 (mtp) cc_final: 0.9080 (tpp) REVERT: e 63 GLN cc_start: 0.9611 (mp10) cc_final: 0.9395 (mp10) REVERT: e 76 GLU cc_start: 0.9651 (mm-30) cc_final: 0.9365 (mm-30) REVERT: e 104 ILE cc_start: 0.8539 (mt) cc_final: 0.8090 (mt) REVERT: e 111 LEU cc_start: 0.9434 (tp) cc_final: 0.9064 (tp) REVERT: e 129 ILE cc_start: 0.9786 (mt) cc_final: 0.9585 (mm) REVERT: e 170 LYS cc_start: 0.9735 (tttt) cc_final: 0.9485 (tppt) REVERT: e 185 MET cc_start: 0.9790 (ptp) cc_final: 0.9512 (ptt) REVERT: e 203 LYS cc_start: 0.7924 (ptpt) cc_final: 0.7176 (tttt) REVERT: e 211 LEU cc_start: 0.9452 (tp) cc_final: 0.9136 (tp) REVERT: j 150 ILE cc_start: 0.9382 (tp) cc_final: 0.9178 (tp) REVERT: j 172 LEU cc_start: 0.9665 (tp) cc_final: 0.9430 (mm) REVERT: j 182 LYS cc_start: 0.9353 (mmtt) cc_final: 0.9016 (mmtt) REVERT: j 188 THR cc_start: 0.8246 (m) cc_final: 0.7803 (m) REVERT: k 21 ASN cc_start: 0.9480 (t0) cc_final: 0.9183 (t0) REVERT: k 25 LYS cc_start: 0.9735 (ptmm) cc_final: 0.9448 (ptmt) REVERT: k 39 MET cc_start: 0.9505 (tpt) cc_final: 0.9018 (tpt) REVERT: k 43 LEU cc_start: 0.9569 (mp) cc_final: 0.8815 (mp) REVERT: k 52 LEU cc_start: 0.9656 (mt) cc_final: 0.9416 (mt) REVERT: k 66 MET cc_start: 0.9699 (tpp) cc_final: 0.9447 (tpp) REVERT: k 76 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9168 (mm-30) REVERT: k 81 ASP cc_start: 0.9764 (t70) cc_final: 0.9373 (m-30) REVERT: k 104 ILE cc_start: 0.8187 (mm) cc_final: 0.7944 (mm) REVERT: k 159 GLU cc_start: 0.8842 (mp0) cc_final: 0.8401 (mp0) REVERT: k 163 ASP cc_start: 0.9407 (m-30) cc_final: 0.9010 (m-30) REVERT: k 168 PHE cc_start: 0.9514 (t80) cc_final: 0.9314 (t80) REVERT: k 185 MET cc_start: 0.9251 (mtm) cc_final: 0.8909 (mtm) REVERT: k 193 ASN cc_start: 0.9299 (m110) cc_final: 0.7916 (t0) REVERT: k 203 LYS cc_start: 0.9209 (mmtm) cc_final: 0.8763 (mmtt) outliers start: 1 outliers final: 0 residues processed: 840 average time/residue: 0.1684 time to fit residues: 201.6677 Evaluate side-chains 674 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 674 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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: 20.0000 chunk 28 optimal weight: 20.0000 chunk 125 optimal weight: 50.0000 chunk 226 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 77 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: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS B 95 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 155 GLN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.079262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.055206 restraints weight = 77771.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.057176 restraints weight = 53366.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.058619 restraints weight = 40418.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.059696 restraints weight = 32823.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.060488 restraints weight = 28004.257| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.7951 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= 0.182 Angle : 0.733 9.913 25587 Z= 0.389 Chirality : 0.047 0.250 2848 Planarity : 0.006 0.128 3345 Dihedral : 4.641 22.823 2500 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.05 % Allowed : 1.25 % Favored : 98.70 % 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: -0.39 (0.17), residues: 2338 helix: 0.01 (0.13), residues: 1461 sheet: -1.79 (0.46), residues: 91 loop : -0.29 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 143 TYR 0.043 0.002 TYR C 169 PHE 0.035 0.002 PHE H 168 TRP 0.032 0.002 TRP N 184 HIS 0.005 0.001 HIS k 12 Details of bonding type rmsd covalent geometry : bond 0.00394 (18824) covalent geometry : angle 0.73260 (25567) SS BOND : bond 0.00215 ( 10) SS BOND : angle 1.18830 ( 20) hydrogen bonds : bond 0.04421 ( 1037) hydrogen bonds : angle 5.00767 ( 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 819 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 818 time to evaluate : 0.723 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: A 9 GLN cc_start: 0.9465 (mp10) cc_final: 0.9222 (pm20) REVERT: A 25 LYS cc_start: 0.9686 (tptt) cc_final: 0.9419 (tppt) REVERT: A 30 LYS cc_start: 0.9454 (mmtm) cc_final: 0.9221 (mmmt) REVERT: A 39 MET cc_start: 0.9184 (mtt) cc_final: 0.8860 (mtt) REVERT: A 40 PHE cc_start: 0.9640 (t80) cc_final: 0.9181 (t80) REVERT: A 63 GLN cc_start: 0.9358 (tp-100) cc_final: 0.8621 (tp-100) REVERT: A 67 GLN cc_start: 0.9595 (tp40) cc_final: 0.9315 (tm-30) REVERT: A 68 MET cc_start: 0.9253 (ptp) cc_final: 0.9009 (ptp) REVERT: A 70 LYS cc_start: 0.9528 (pttm) cc_final: 0.8893 (pttm) REVERT: A 96 MET cc_start: 0.6669 (mtp) cc_final: 0.6281 (mtp) REVERT: A 100 ARG cc_start: 0.9674 (ttm-80) cc_final: 0.9360 (tpp80) REVERT: A 114 GLN cc_start: 0.9260 (mt0) cc_final: 0.9033 (mt0) REVERT: A 135 ILE cc_start: 0.9444 (mt) cc_final: 0.9188 (mt) REVERT: A 141 ILE cc_start: 0.9680 (mm) cc_final: 0.9405 (mm) REVERT: B 23 TRP cc_start: 0.9104 (t-100) cc_final: 0.8532 (t-100) REVERT: B 30 LYS cc_start: 0.9092 (mmtp) cc_final: 0.8600 (mmmt) REVERT: B 39 MET cc_start: 0.9576 (tpp) cc_final: 0.9215 (tpt) REVERT: B 114 GLN cc_start: 0.9386 (pt0) cc_final: 0.9107 (pt0) REVERT: B 117 TRP cc_start: 0.8909 (m-10) cc_final: 0.7785 (m-90) REVERT: B 118 MET cc_start: 0.9647 (mtm) cc_final: 0.9225 (ptp) REVERT: B 128 GLU cc_start: 0.9477 (mp0) cc_final: 0.9213 (pm20) REVERT: B 132 ARG cc_start: 0.9556 (ptp90) cc_final: 0.9318 (ptp-170) REVERT: B 158 LYS cc_start: 0.8632 (tptt) cc_final: 0.8092 (mmtt) REVERT: B 169 TYR cc_start: 0.9532 (m-10) cc_final: 0.9039 (m-10) REVERT: B 170 LYS cc_start: 0.9486 (tppt) cc_final: 0.9216 (tppt) REVERT: B 181 VAL cc_start: 0.9700 (t) cc_final: 0.9394 (t) REVERT: B 185 MET cc_start: 0.9375 (ptt) cc_final: 0.8993 (ptt) REVERT: C 10 MET cc_start: 0.8445 (tpp) cc_final: 0.8005 (tpp) REVERT: C 39 MET cc_start: 0.9699 (mmm) cc_final: 0.9196 (mtm) REVERT: C 52 LEU cc_start: 0.9710 (mt) cc_final: 0.9482 (mt) REVERT: C 59 VAL cc_start: 0.8727 (t) cc_final: 0.8487 (p) REVERT: C 71 GLU cc_start: 0.9550 (mp0) cc_final: 0.9050 (mp0) REVERT: C 76 GLU cc_start: 0.9596 (mm-30) cc_final: 0.9166 (mm-30) REVERT: C 96 MET cc_start: -0.4988 (mmt) cc_final: -0.5527 (mtm) REVERT: C 144 MET cc_start: 0.8098 (tmm) cc_final: 0.7593 (tmm) REVERT: C 150 ILE cc_start: 0.8915 (tp) cc_final: 0.8707 (tp) REVERT: C 153 ILE cc_start: 0.9230 (mt) cc_final: 0.8981 (mt) REVERT: C 167 ARG cc_start: 0.8894 (mmp80) cc_final: 0.8441 (mmp80) REVERT: C 185 MET cc_start: 0.9349 (mtt) cc_final: 0.9119 (mtt) REVERT: D 10 MET cc_start: 0.6886 (mmp) cc_final: 0.6536 (mmm) REVERT: D 21 ASN cc_start: 0.9604 (t0) cc_final: 0.9216 (t0) REVERT: D 25 LYS cc_start: 0.9765 (ttpt) cc_final: 0.9471 (ptmt) REVERT: D 40 PHE cc_start: 0.9597 (t80) cc_final: 0.9170 (t80) REVERT: D 53 ASN cc_start: 0.9344 (m-40) cc_final: 0.9024 (m-40) REVERT: D 68 MET cc_start: 0.8687 (mtt) cc_final: 0.8201 (mtp) REVERT: D 96 MET cc_start: 0.7562 (ttt) cc_final: 0.6609 (ttt) REVERT: D 129 ILE cc_start: 0.9515 (mt) cc_final: 0.9195 (tp) REVERT: D 130 TYR cc_start: 0.9047 (t80) cc_final: 0.8831 (t80) REVERT: D 131 LYS cc_start: 0.9396 (ttmt) cc_final: 0.8631 (tttt) REVERT: D 140 LYS cc_start: 0.9630 (mttt) cc_final: 0.9281 (tptp) REVERT: D 161 PHE cc_start: 0.8317 (t80) cc_final: 0.8015 (t80) REVERT: D 215 MET cc_start: 0.8259 (mtm) cc_final: 0.7192 (mtm) REVERT: G 23 TRP cc_start: 0.9463 (t60) cc_final: 0.8966 (t60) REVERT: G 25 LYS cc_start: 0.9360 (ptpp) cc_final: 0.9034 (ptpp) REVERT: G 58 THR cc_start: 0.9284 (p) cc_final: 0.8582 (p) REVERT: G 68 MET cc_start: 0.8792 (mtt) cc_final: 0.8529 (mtp) REVERT: G 168 PHE cc_start: 0.9383 (t80) cc_final: 0.9060 (t80) REVERT: G 188 THR cc_start: 0.9430 (p) cc_final: 0.9206 (p) REVERT: H 13 GLN cc_start: 0.9451 (pp30) cc_final: 0.9220 (pm20) REVERT: H 25 LYS cc_start: 0.9656 (tttt) cc_final: 0.9284 (tppt) REVERT: H 32 PHE cc_start: 0.7314 (m-10) cc_final: 0.7100 (m-10) REVERT: H 39 MET cc_start: 0.9210 (mpp) cc_final: 0.8964 (mpp) REVERT: H 66 MET cc_start: 0.9536 (mmp) cc_final: 0.9179 (mmm) REVERT: H 67 GLN cc_start: 0.9350 (tp40) cc_final: 0.8918 (mt0) REVERT: H 68 MET cc_start: 0.9353 (mmt) cc_final: 0.8876 (mmm) REVERT: H 87 HIS cc_start: 0.8155 (m-70) cc_final: 0.7198 (t-170) REVERT: H 118 MET cc_start: 0.8654 (mmm) cc_final: 0.8324 (mmt) REVERT: H 128 GLU cc_start: 0.9615 (mm-30) cc_final: 0.9282 (mp0) REVERT: H 145 TYR cc_start: 0.9051 (m-80) cc_final: 0.8741 (m-10) REVERT: H 152 ASP cc_start: 0.9637 (m-30) cc_final: 0.9376 (m-30) REVERT: H 182 LYS cc_start: 0.9793 (pttp) cc_final: 0.9587 (pttm) REVERT: J 40 SER cc_start: 0.9114 (m) cc_final: 0.8349 (p) REVERT: J 48 TYR cc_start: 0.8900 (m-80) cc_final: 0.8323 (m-80) REVERT: J 57 ILE cc_start: 0.7928 (tt) cc_final: 0.6438 (tt) REVERT: J 60 PHE cc_start: 0.8111 (t80) cc_final: 0.7721 (t80) REVERT: J 61 MET cc_start: 0.6057 (ppp) cc_final: 0.5751 (ppp) REVERT: J 78 ILE cc_start: 0.9266 (pt) cc_final: 0.8857 (pt) REVERT: J 136 MET cc_start: 0.8379 (tpp) cc_final: 0.8071 (tpp) REVERT: J 140 GLU cc_start: 0.9325 (mt-10) cc_final: 0.9013 (mt-10) REVERT: J 142 MET cc_start: 0.9295 (mtt) cc_final: 0.8983 (mtp) REVERT: N 162 ARG cc_start: 0.9326 (mmm-85) cc_final: 0.9006 (tpp80) REVERT: N 166 ASP cc_start: 0.8813 (t70) cc_final: 0.8586 (t70) REVERT: N 180 GLU cc_start: 0.9253 (pm20) cc_final: 0.8954 (pm20) REVERT: Y 10 MET cc_start: 0.9115 (pmm) cc_final: 0.8857 (mmp) REVERT: Y 39 MET cc_start: 0.9404 (tmm) cc_final: 0.9163 (tmm) REVERT: Y 53 ASN cc_start: 0.9397 (m110) cc_final: 0.9139 (m110) REVERT: Y 67 GLN cc_start: 0.9764 (mm-40) cc_final: 0.9399 (mm-40) REVERT: Y 103 ASP cc_start: 0.9367 (t70) cc_final: 0.9070 (t70) REVERT: Y 124 ILE cc_start: 0.9007 (tp) cc_final: 0.8669 (tp) REVERT: Y 132 ARG cc_start: 0.9681 (ptp-170) cc_final: 0.9394 (ptp-170) REVERT: Y 136 LEU cc_start: 0.9683 (mt) cc_final: 0.9448 (mt) REVERT: d 15 ILE cc_start: 0.7377 (pt) cc_final: 0.6499 (pt) REVERT: d 23 TRP cc_start: 0.9519 (t-100) cc_final: 0.8840 (t-100) REVERT: d 25 LYS cc_start: 0.9228 (tttt) cc_final: 0.8993 (tptp) REVERT: d 30 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8108 (tttt) REVERT: d 39 MET cc_start: 0.9091 (mtm) cc_final: 0.8279 (mtt) REVERT: d 55 MET cc_start: 0.9681 (ptm) cc_final: 0.9133 (ppp) REVERT: d 57 ASN cc_start: 0.9468 (m-40) cc_final: 0.9074 (t0) REVERT: d 58 THR cc_start: 0.9342 (p) cc_final: 0.9140 (p) REVERT: d 67 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8474 (tp40) REVERT: d 68 MET cc_start: 0.8991 (mmm) cc_final: 0.8419 (mmm) REVERT: d 76 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9116 (mt-10) REVERT: d 130 TYR cc_start: 0.8930 (t80) cc_final: 0.8681 (t80) REVERT: d 215 MET cc_start: 0.4616 (mmt) cc_final: 0.4315 (mtm) REVERT: e 23 TRP cc_start: 0.9564 (t-100) cc_final: 0.8987 (t-100) REVERT: e 30 LYS cc_start: 0.9380 (mmtp) cc_final: 0.9147 (mmmm) REVERT: e 39 MET cc_start: 0.9614 (mtm) cc_final: 0.9236 (mtm) REVERT: e 50 GLN cc_start: 0.9319 (mt0) cc_final: 0.8837 (mt0) REVERT: e 55 MET cc_start: 0.9727 (mtp) cc_final: 0.9100 (tpp) REVERT: e 63 GLN cc_start: 0.9628 (mp10) cc_final: 0.9310 (mp10) REVERT: e 76 GLU cc_start: 0.9685 (mm-30) cc_final: 0.9373 (mm-30) REVERT: e 104 ILE cc_start: 0.8553 (mt) cc_final: 0.8343 (mt) REVERT: e 111 LEU cc_start: 0.9450 (tp) cc_final: 0.9068 (tp) REVERT: e 114 GLN cc_start: 0.9483 (pt0) cc_final: 0.8717 (pt0) REVERT: e 128 GLU cc_start: 0.9388 (pm20) cc_final: 0.8842 (pm20) REVERT: e 129 ILE cc_start: 0.9755 (mt) cc_final: 0.9332 (mt) REVERT: e 132 ARG cc_start: 0.9354 (ptp-110) cc_final: 0.8790 (ptp-170) REVERT: e 185 MET cc_start: 0.9787 (ptp) cc_final: 0.9473 (ptt) REVERT: e 203 LYS cc_start: 0.8048 (ptpt) cc_final: 0.7277 (tttt) REVERT: j 150 ILE cc_start: 0.9393 (tp) cc_final: 0.9180 (tp) REVERT: j 172 LEU cc_start: 0.9686 (tp) cc_final: 0.9443 (mm) REVERT: j 182 LYS cc_start: 0.9358 (mmtt) cc_final: 0.8988 (mmtt) REVERT: j 188 THR cc_start: 0.8228 (m) cc_final: 0.7785 (m) REVERT: j 215 MET cc_start: 0.8724 (ppp) cc_final: 0.8509 (ppp) REVERT: k 25 LYS cc_start: 0.9743 (ptmm) cc_final: 0.9462 (ptmt) REVERT: k 39 MET cc_start: 0.9567 (tpt) cc_final: 0.9028 (tpt) REVERT: k 43 LEU cc_start: 0.9604 (mp) cc_final: 0.8893 (mp) REVERT: k 52 LEU cc_start: 0.9691 (mt) cc_final: 0.9446 (mt) REVERT: k 66 MET cc_start: 0.9648 (tpp) cc_final: 0.9382 (tpp) REVERT: k 76 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9161 (mm-30) REVERT: k 131 LYS cc_start: 0.9511 (tttp) cc_final: 0.9115 (tptt) REVERT: k 159 GLU cc_start: 0.8855 (mp0) cc_final: 0.8497 (mp0) REVERT: k 173 ARG cc_start: 0.8927 (ttt180) cc_final: 0.8605 (ttt180) REVERT: k 185 MET cc_start: 0.9220 (mtm) cc_final: 0.8898 (mtt) REVERT: k 193 ASN cc_start: 0.9323 (m110) cc_final: 0.7971 (t0) REVERT: k 203 LYS cc_start: 0.9207 (mmtm) cc_final: 0.8683 (mmtt) outliers start: 1 outliers final: 0 residues processed: 819 average time/residue: 0.1591 time to fit residues: 187.1436 Evaluate side-chains 667 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 667 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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: 20.0000 chunk 187 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 174 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 133 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS B 95 GLN B 139 ASN B 183 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 21 ASN d 12 HIS ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 155 GLN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.078170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.054945 restraints weight = 78326.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.056889 restraints weight = 53201.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.058304 restraints weight = 40155.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.059419 restraints weight = 32458.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060118 restraints weight = 27577.737| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.8228 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 : 0.758 16.504 25587 Z= 0.400 Chirality : 0.048 0.224 2848 Planarity : 0.005 0.058 3345 Dihedral : 4.746 26.724 2500 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.05 % Allowed : 0.75 % Favored : 99.20 % 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: -0.53 (0.17), residues: 2338 helix: -0.08 (0.13), residues: 1443 sheet: -1.67 (0.47), residues: 91 loop : -0.39 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 167 TYR 0.019 0.002 TYR d 130 PHE 0.034 0.002 PHE H 168 TRP 0.046 0.002 TRP D 23 HIS 0.007 0.001 HIS J 92 Details of bonding type rmsd covalent geometry : bond 0.00390 (18824) covalent geometry : angle 0.75780 (25567) SS BOND : bond 0.00178 ( 10) SS BOND : angle 1.18033 ( 20) hydrogen bonds : bond 0.04447 ( 1037) hydrogen bonds : angle 5.08638 ( 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 818 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 817 time to evaluate : 0.776 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 9 GLN cc_start: 0.9453 (mp10) cc_final: 0.9216 (pm20) REVERT: A 25 LYS cc_start: 0.9683 (tptt) cc_final: 0.9445 (tppt) REVERT: A 29 GLU cc_start: 0.9166 (pm20) cc_final: 0.8677 (pm20) REVERT: A 30 LYS cc_start: 0.9462 (mmtm) cc_final: 0.9223 (mmmt) REVERT: A 39 MET cc_start: 0.9218 (mtt) cc_final: 0.8874 (mtt) REVERT: A 40 PHE cc_start: 0.9666 (t80) cc_final: 0.9199 (t80) REVERT: A 67 GLN cc_start: 0.9606 (tp40) cc_final: 0.9375 (tm-30) REVERT: A 68 MET cc_start: 0.9318 (ptp) cc_final: 0.8950 (ptp) REVERT: A 96 MET cc_start: 0.6586 (mtp) cc_final: 0.4673 (mtp) REVERT: A 100 ARG cc_start: 0.9670 (ttm-80) cc_final: 0.9354 (tpp80) REVERT: A 114 GLN cc_start: 0.9179 (mt0) cc_final: 0.8944 (mt0) REVERT: A 135 ILE cc_start: 0.9462 (mt) cc_final: 0.9184 (mt) REVERT: B 20 LEU cc_start: 0.9538 (mt) cc_final: 0.9316 (mt) REVERT: B 23 TRP cc_start: 0.9154 (t-100) cc_final: 0.8937 (t-100) REVERT: B 30 LYS cc_start: 0.9056 (mmtp) cc_final: 0.8538 (mmmt) REVERT: B 39 MET cc_start: 0.9578 (tpp) cc_final: 0.9217 (tpt) REVERT: B 114 GLN cc_start: 0.9415 (pt0) cc_final: 0.9150 (pt0) REVERT: B 117 TRP cc_start: 0.8930 (m-10) cc_final: 0.7699 (m-90) REVERT: B 118 MET cc_start: 0.9649 (mtm) cc_final: 0.9243 (ptp) REVERT: B 132 ARG cc_start: 0.9563 (ptp90) cc_final: 0.9330 (ptp-170) REVERT: B 144 MET cc_start: 0.9077 (tpp) cc_final: 0.8447 (tpp) REVERT: B 158 LYS cc_start: 0.8677 (tptt) cc_final: 0.8121 (mmtt) REVERT: B 169 TYR cc_start: 0.9550 (m-10) cc_final: 0.9012 (m-10) REVERT: B 170 LYS cc_start: 0.9484 (tppt) cc_final: 0.9201 (tppt) REVERT: B 181 VAL cc_start: 0.9656 (t) cc_final: 0.9370 (t) REVERT: B 185 MET cc_start: 0.9343 (ptt) cc_final: 0.9050 (ptt) REVERT: B 211 LEU cc_start: 0.7260 (tt) cc_final: 0.6498 (tt) REVERT: C 10 MET cc_start: 0.8471 (tpp) cc_final: 0.7952 (tpp) REVERT: C 52 LEU cc_start: 0.9683 (mt) cc_final: 0.9463 (mt) REVERT: C 71 GLU cc_start: 0.9628 (mp0) cc_final: 0.9328 (mp0) REVERT: C 75 GLU cc_start: 0.9339 (pm20) cc_final: 0.9070 (pm20) REVERT: C 76 GLU cc_start: 0.9479 (mm-30) cc_final: 0.8887 (mm-30) REVERT: C 79 GLU cc_start: 0.9399 (tp30) cc_final: 0.9168 (tp30) REVERT: C 96 MET cc_start: -0.4661 (mmt) cc_final: -0.5403 (mtm) REVERT: C 103 ASP cc_start: 0.9328 (m-30) cc_final: 0.8455 (t70) REVERT: C 104 ILE cc_start: 0.9017 (tt) cc_final: 0.8720 (tt) REVERT: C 129 ILE cc_start: 0.9709 (mt) cc_final: 0.9212 (mt) REVERT: C 133 TRP cc_start: 0.8982 (m-10) cc_final: 0.8631 (m-10) REVERT: C 144 MET cc_start: 0.8071 (tmm) cc_final: 0.7675 (tmm) REVERT: C 167 ARG cc_start: 0.8828 (mmp80) cc_final: 0.8398 (mmp80) REVERT: C 185 MET cc_start: 0.9403 (mtt) cc_final: 0.9160 (mtt) REVERT: D 10 MET cc_start: 0.6926 (mmp) cc_final: 0.6544 (mmm) REVERT: D 21 ASN cc_start: 0.9581 (t0) cc_final: 0.9168 (t0) REVERT: D 25 LYS cc_start: 0.9748 (ttpt) cc_final: 0.9440 (ptmt) REVERT: D 39 MET cc_start: 0.9708 (tpt) cc_final: 0.9502 (tpt) REVERT: D 53 ASN cc_start: 0.9306 (m-40) cc_final: 0.9046 (m-40) REVERT: D 68 MET cc_start: 0.8731 (mtt) cc_final: 0.8255 (mtp) REVERT: D 96 MET cc_start: 0.7640 (ttt) cc_final: 0.6678 (ttt) REVERT: D 129 ILE cc_start: 0.9437 (mt) cc_final: 0.9133 (tp) REVERT: D 131 LYS cc_start: 0.9430 (ttmt) cc_final: 0.9074 (mttt) REVERT: G 23 TRP cc_start: 0.9528 (t60) cc_final: 0.9189 (t60) REVERT: G 68 MET cc_start: 0.8865 (mtt) cc_final: 0.8598 (mtp) REVERT: G 128 GLU cc_start: 0.9530 (pm20) cc_final: 0.9154 (pm20) REVERT: G 132 ARG cc_start: 0.9644 (ptp90) cc_final: 0.9205 (ptt-90) REVERT: G 168 PHE cc_start: 0.9383 (t80) cc_final: 0.9027 (t80) REVERT: G 188 THR cc_start: 0.9429 (p) cc_final: 0.9205 (p) REVERT: G 215 MET cc_start: 0.9148 (ptt) cc_final: 0.8724 (ptt) REVERT: H 13 GLN cc_start: 0.9441 (pp30) cc_final: 0.9152 (pm20) REVERT: H 23 TRP cc_start: 0.9483 (t60) cc_final: 0.8841 (t60) REVERT: H 25 LYS cc_start: 0.9519 (tttt) cc_final: 0.9095 (tppt) REVERT: H 29 GLU cc_start: 0.8433 (pm20) cc_final: 0.8102 (pm20) REVERT: H 32 PHE cc_start: 0.7280 (m-10) cc_final: 0.7051 (m-10) REVERT: H 39 MET cc_start: 0.9210 (mpp) cc_final: 0.8967 (mpp) REVERT: H 55 MET cc_start: 0.9191 (mmp) cc_final: 0.8912 (mmm) REVERT: H 66 MET cc_start: 0.9537 (mmp) cc_final: 0.9187 (mmm) REVERT: H 67 GLN cc_start: 0.9339 (tp40) cc_final: 0.8896 (mt0) REVERT: H 68 MET cc_start: 0.9333 (mmt) cc_final: 0.8798 (mmm) REVERT: H 87 HIS cc_start: 0.8228 (m-70) cc_final: 0.7205 (t-170) REVERT: H 118 MET cc_start: 0.8693 (mmm) cc_final: 0.8380 (mmt) REVERT: H 128 GLU cc_start: 0.9648 (mm-30) cc_final: 0.9274 (mp0) REVERT: H 130 TYR cc_start: 0.9221 (t80) cc_final: 0.9020 (t80) REVERT: H 145 TYR cc_start: 0.9037 (m-80) cc_final: 0.8753 (m-10) REVERT: H 152 ASP cc_start: 0.9657 (m-30) cc_final: 0.9401 (m-30) REVERT: H 182 LYS cc_start: 0.9803 (pttp) cc_final: 0.9497 (pttt) REVERT: J 40 SER cc_start: 0.8970 (m) cc_final: 0.8574 (p) REVERT: J 41 THR cc_start: 0.7563 (t) cc_final: 0.7225 (t) REVERT: J 48 TYR cc_start: 0.8597 (m-80) cc_final: 0.8238 (m-80) REVERT: J 57 ILE cc_start: 0.7819 (tt) cc_final: 0.6348 (tt) REVERT: J 60 PHE cc_start: 0.8160 (t80) cc_final: 0.7810 (t80) REVERT: J 61 MET cc_start: 0.5928 (ppp) cc_final: 0.5545 (ppp) REVERT: J 136 MET cc_start: 0.8379 (tpp) cc_final: 0.8135 (tpp) REVERT: J 142 MET cc_start: 0.9143 (mtt) cc_final: 0.8812 (mtp) REVERT: N 162 ARG cc_start: 0.9339 (mmm-85) cc_final: 0.9016 (tpp80) REVERT: N 166 ASP cc_start: 0.8851 (t70) cc_final: 0.8633 (t70) REVERT: N 180 GLU cc_start: 0.9283 (pm20) cc_final: 0.8982 (pm20) REVERT: N 186 THR cc_start: 0.9547 (t) cc_final: 0.9318 (t) REVERT: Y 39 MET cc_start: 0.9367 (tmm) cc_final: 0.9153 (tmm) REVERT: Y 53 ASN cc_start: 0.9394 (m110) cc_final: 0.9142 (m110) REVERT: Y 67 GLN cc_start: 0.9773 (mm-40) cc_final: 0.9453 (mm-40) REVERT: Y 68 MET cc_start: 0.9333 (mtt) cc_final: 0.9058 (mtt) REVERT: Y 71 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9072 (mt-10) REVERT: Y 132 ARG cc_start: 0.9700 (ptp-170) cc_final: 0.9411 (ptp-170) REVERT: Y 136 LEU cc_start: 0.9689 (mt) cc_final: 0.9483 (mt) REVERT: d 25 LYS cc_start: 0.9235 (tttt) cc_final: 0.8994 (tptp) REVERT: d 30 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8103 (tttt) REVERT: d 39 MET cc_start: 0.9019 (mtm) cc_final: 0.8267 (mtt) REVERT: d 51 ASP cc_start: 0.9124 (t0) cc_final: 0.8539 (m-30) REVERT: d 55 MET cc_start: 0.9663 (ptm) cc_final: 0.9392 (ppp) REVERT: d 57 ASN cc_start: 0.9467 (m-40) cc_final: 0.9154 (t0) REVERT: d 67 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8540 (tp40) REVERT: d 75 GLU cc_start: 0.9128 (pp20) cc_final: 0.8771 (pp20) REVERT: d 76 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9065 (mt-10) REVERT: d 80 TRP cc_start: 0.9631 (t60) cc_final: 0.9374 (t60) REVERT: d 128 GLU cc_start: 0.9376 (mm-30) cc_final: 0.8976 (pp20) REVERT: d 132 ARG cc_start: 0.9437 (ttm110) cc_final: 0.8879 (mtp85) REVERT: d 144 MET cc_start: 0.9078 (tmm) cc_final: 0.8878 (tmm) REVERT: d 215 MET cc_start: 0.4889 (mmt) cc_final: 0.4437 (mtm) REVERT: e 23 TRP cc_start: 0.9532 (t-100) cc_final: 0.8906 (t-100) REVERT: e 30 LYS cc_start: 0.9385 (mmtp) cc_final: 0.9064 (mmmm) REVERT: e 35 GLU cc_start: 0.9418 (pm20) cc_final: 0.9151 (pm20) REVERT: e 39 MET cc_start: 0.9617 (mtm) cc_final: 0.9253 (mtm) REVERT: e 50 GLN cc_start: 0.9340 (mt0) cc_final: 0.8848 (mt0) REVERT: e 55 MET cc_start: 0.9734 (mtp) cc_final: 0.9084 (tpp) REVERT: e 63 GLN cc_start: 0.9622 (mp10) cc_final: 0.9287 (mp10) REVERT: e 76 GLU cc_start: 0.9654 (mm-30) cc_final: 0.9228 (mm-30) REVERT: e 111 LEU cc_start: 0.9474 (tp) cc_final: 0.9089 (tp) REVERT: e 114 GLN cc_start: 0.9490 (pt0) cc_final: 0.8739 (pt0) REVERT: e 128 GLU cc_start: 0.9441 (pm20) cc_final: 0.8708 (pm20) REVERT: e 132 ARG cc_start: 0.9337 (ptp-110) cc_final: 0.8778 (ptp-170) REVERT: e 185 MET cc_start: 0.9798 (ptp) cc_final: 0.9402 (ptp) REVERT: e 203 LYS cc_start: 0.8003 (ptpt) cc_final: 0.7159 (tttt) REVERT: e 211 LEU cc_start: 0.9458 (tp) cc_final: 0.9212 (tp) REVERT: j 150 ILE cc_start: 0.9374 (tp) cc_final: 0.9172 (tp) REVERT: j 172 LEU cc_start: 0.9685 (tp) cc_final: 0.9426 (mm) REVERT: j 182 LYS cc_start: 0.9377 (mmtt) cc_final: 0.8991 (mmtt) REVERT: j 188 THR cc_start: 0.8243 (m) cc_final: 0.7798 (m) REVERT: j 215 MET cc_start: 0.8788 (ppp) cc_final: 0.8557 (ppp) REVERT: k 25 LYS cc_start: 0.9743 (ptmm) cc_final: 0.9522 (ptmm) REVERT: k 39 MET cc_start: 0.9636 (tpt) cc_final: 0.9062 (tpt) REVERT: k 43 LEU cc_start: 0.9579 (mp) cc_final: 0.8866 (mp) REVERT: k 52 LEU cc_start: 0.9680 (mt) cc_final: 0.9430 (mt) REVERT: k 66 MET cc_start: 0.9632 (tpp) cc_final: 0.9351 (tpp) REVERT: k 76 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9190 (mm-30) REVERT: k 131 LYS cc_start: 0.9490 (tttp) cc_final: 0.9072 (tptt) REVERT: k 139 ASN cc_start: 0.9670 (m110) cc_final: 0.9343 (m110) REVERT: k 163 ASP cc_start: 0.9357 (m-30) cc_final: 0.8771 (m-30) REVERT: k 167 ARG cc_start: 0.8730 (mtm-85) cc_final: 0.8299 (ptt-90) REVERT: k 185 MET cc_start: 0.9295 (mtm) cc_final: 0.8957 (mtt) REVERT: k 193 ASN cc_start: 0.9339 (m110) cc_final: 0.7966 (t0) REVERT: k 203 LYS cc_start: 0.9196 (mmtm) cc_final: 0.8726 (mmtt) outliers start: 1 outliers final: 0 residues processed: 818 average time/residue: 0.1588 time to fit residues: 186.3763 Evaluate side-chains 660 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 6.9990 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 193 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 114 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS B 95 GLN C 139 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS Y 21 ASN e 57 ASN j 155 GLN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 74 ASN ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 179 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.079521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.056120 restraints weight = 77696.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.058120 restraints weight = 52738.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.059557 restraints weight = 39652.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060709 restraints weight = 31993.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.061518 restraints weight = 27152.365| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.8372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18834 Z= 0.157 Angle : 0.763 11.499 25587 Z= 0.401 Chirality : 0.048 0.214 2848 Planarity : 0.005 0.059 3345 Dihedral : 4.755 22.758 2500 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.05 % Allowed : 0.15 % Favored : 99.80 % 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: -0.46 (0.17), residues: 2338 helix: -0.07 (0.13), residues: 1436 sheet: -1.29 (0.59), residues: 64 loop : -0.38 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG k 143 TYR 0.018 0.002 TYR d 130 PHE 0.033 0.002 PHE H 168 TRP 0.056 0.002 TRP G 117 HIS 0.006 0.001 HIS J 92 Details of bonding type rmsd covalent geometry : bond 0.00346 (18824) covalent geometry : angle 0.76238 (25567) SS BOND : bond 0.00155 ( 10) SS BOND : angle 1.15034 ( 20) hydrogen bonds : bond 0.04388 ( 1037) hydrogen bonds : angle 5.05561 ( 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 814 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 813 time to evaluate : 0.693 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: A 9 GLN cc_start: 0.9454 (mp10) cc_final: 0.9206 (pm20) REVERT: A 39 MET cc_start: 0.9223 (mtt) cc_final: 0.8914 (mtt) REVERT: A 40 PHE cc_start: 0.9641 (t80) cc_final: 0.9101 (t80) REVERT: A 67 GLN cc_start: 0.9589 (tp40) cc_final: 0.9362 (tm-30) REVERT: A 68 MET cc_start: 0.9306 (ptp) cc_final: 0.8920 (ptp) REVERT: A 114 GLN cc_start: 0.9135 (mt0) cc_final: 0.8861 (mt0) REVERT: A 119 THR cc_start: 0.8771 (t) cc_final: 0.8565 (t) REVERT: A 135 ILE cc_start: 0.9448 (mt) cc_final: 0.9151 (mt) REVERT: B 20 LEU cc_start: 0.9486 (mt) cc_final: 0.9265 (mt) REVERT: B 23 TRP cc_start: 0.9160 (t-100) cc_final: 0.8944 (t-100) REVERT: B 30 LYS cc_start: 0.8995 (mmtp) cc_final: 0.8459 (mmmt) REVERT: B 39 MET cc_start: 0.9567 (tpp) cc_final: 0.9211 (tpt) REVERT: B 114 GLN cc_start: 0.9424 (pt0) cc_final: 0.8977 (pt0) REVERT: B 118 MET cc_start: 0.9644 (mtm) cc_final: 0.9228 (ptp) REVERT: B 132 ARG cc_start: 0.9576 (ptp90) cc_final: 0.9346 (ptp-170) REVERT: B 144 MET cc_start: 0.9054 (tpp) cc_final: 0.8265 (tpp) REVERT: B 158 LYS cc_start: 0.8631 (tptt) cc_final: 0.8107 (mmtt) REVERT: B 169 TYR cc_start: 0.9532 (m-10) cc_final: 0.8983 (m-10) REVERT: B 170 LYS cc_start: 0.9471 (tppt) cc_final: 0.9182 (tppt) REVERT: B 211 LEU cc_start: 0.7443 (tt) cc_final: 0.6695 (tt) REVERT: C 10 MET cc_start: 0.8476 (tpp) cc_final: 0.8096 (tpp) REVERT: C 76 GLU cc_start: 0.9464 (mm-30) cc_final: 0.8823 (mm-30) REVERT: C 79 GLU cc_start: 0.9394 (tp30) cc_final: 0.9189 (tp30) REVERT: C 96 MET cc_start: -0.5041 (mmt) cc_final: -0.5651 (mtm) REVERT: C 104 ILE cc_start: 0.9033 (tt) cc_final: 0.8797 (tt) REVERT: C 129 ILE cc_start: 0.9693 (mt) cc_final: 0.9398 (pt) REVERT: C 133 TRP cc_start: 0.9017 (m-10) cc_final: 0.8729 (m-10) REVERT: C 144 MET cc_start: 0.8126 (tmm) cc_final: 0.7876 (tmm) REVERT: C 150 ILE cc_start: 0.8871 (tp) cc_final: 0.8594 (tp) REVERT: C 153 ILE cc_start: 0.8861 (mm) cc_final: 0.8577 (mt) REVERT: C 167 ARG cc_start: 0.8823 (mmp80) cc_final: 0.8346 (mmp80) REVERT: C 185 MET cc_start: 0.9327 (mtt) cc_final: 0.9092 (mtt) REVERT: C 199 LYS cc_start: 0.9011 (tppp) cc_final: 0.8720 (tptp) REVERT: D 10 MET cc_start: 0.7071 (mmp) cc_final: 0.6688 (mmm) REVERT: D 21 ASN cc_start: 0.9567 (t0) cc_final: 0.9171 (t0) REVERT: D 25 LYS cc_start: 0.9719 (ttpt) cc_final: 0.9439 (ptmt) REVERT: D 39 MET cc_start: 0.9709 (tpt) cc_final: 0.9505 (tpt) REVERT: D 68 MET cc_start: 0.8780 (mtt) cc_final: 0.8318 (mtp) REVERT: D 96 MET cc_start: 0.7621 (ttt) cc_final: 0.6804 (ttt) REVERT: D 129 ILE cc_start: 0.9538 (mt) cc_final: 0.9309 (tp) REVERT: G 23 TRP cc_start: 0.9484 (t60) cc_final: 0.8985 (t60) REVERT: G 58 THR cc_start: 0.9269 (p) cc_final: 0.8608 (p) REVERT: G 68 MET cc_start: 0.8798 (mtt) cc_final: 0.8522 (mtp) REVERT: G 140 LYS cc_start: 0.9634 (mtpp) cc_final: 0.9402 (mtpp) REVERT: G 168 PHE cc_start: 0.9370 (t80) cc_final: 0.9013 (t80) REVERT: G 188 THR cc_start: 0.9444 (p) cc_final: 0.9228 (p) REVERT: H 13 GLN cc_start: 0.9450 (pp30) cc_final: 0.9190 (pm20) REVERT: H 25 LYS cc_start: 0.9495 (tttt) cc_final: 0.9163 (tppt) REVERT: H 53 ASN cc_start: 0.9621 (m-40) cc_final: 0.9401 (m-40) REVERT: H 66 MET cc_start: 0.9524 (mmp) cc_final: 0.9186 (mmm) REVERT: H 67 GLN cc_start: 0.9336 (tp40) cc_final: 0.8916 (mt0) REVERT: H 68 MET cc_start: 0.9322 (mmt) cc_final: 0.9092 (mmt) REVERT: H 79 GLU cc_start: 0.9771 (mm-30) cc_final: 0.9538 (mm-30) REVERT: H 80 TRP cc_start: 0.9597 (t-100) cc_final: 0.9111 (t60) REVERT: H 87 HIS cc_start: 0.8271 (m-70) cc_final: 0.7214 (t-170) REVERT: H 118 MET cc_start: 0.8619 (mmm) cc_final: 0.8277 (mmt) REVERT: H 128 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9276 (mp0) REVERT: H 130 TYR cc_start: 0.9239 (t80) cc_final: 0.8981 (t80) REVERT: H 145 TYR cc_start: 0.9067 (m-80) cc_final: 0.8729 (m-10) REVERT: H 152 ASP cc_start: 0.9637 (m-30) cc_final: 0.9390 (m-30) REVERT: H 167 ARG cc_start: 0.9178 (ptt180) cc_final: 0.8883 (ptt90) REVERT: H 182 LYS cc_start: 0.9813 (pttp) cc_final: 0.9512 (pttt) REVERT: J 40 SER cc_start: 0.9121 (m) cc_final: 0.8280 (p) REVERT: J 48 TYR cc_start: 0.8794 (m-80) cc_final: 0.8232 (m-80) REVERT: J 57 ILE cc_start: 0.7786 (tt) cc_final: 0.6295 (tt) REVERT: J 60 PHE cc_start: 0.8141 (t80) cc_final: 0.7797 (t80) REVERT: J 61 MET cc_start: 0.6092 (ppp) cc_final: 0.5743 (ppp) REVERT: J 136 MET cc_start: 0.8369 (tpp) cc_final: 0.8113 (tpp) REVERT: J 142 MET cc_start: 0.9182 (mtt) cc_final: 0.8832 (mtp) REVERT: N 180 GLU cc_start: 0.9298 (pm20) cc_final: 0.8991 (pm20) REVERT: N 203 LYS cc_start: 0.7809 (pttt) cc_final: 0.7342 (pttt) REVERT: Y 25 LYS cc_start: 0.9559 (tptm) cc_final: 0.9272 (tptm) REVERT: Y 39 MET cc_start: 0.9361 (tmm) cc_final: 0.9142 (tmm) REVERT: Y 53 ASN cc_start: 0.9406 (m110) cc_final: 0.9111 (m110) REVERT: Y 67 GLN cc_start: 0.9744 (mm-40) cc_final: 0.9495 (mm-40) REVERT: Y 68 MET cc_start: 0.9290 (mtt) cc_final: 0.8939 (mtt) REVERT: Y 71 GLU cc_start: 0.9439 (mt-10) cc_final: 0.9045 (mt-10) REVERT: Y 124 ILE cc_start: 0.9066 (tp) cc_final: 0.8537 (pt) REVERT: Y 132 ARG cc_start: 0.9686 (ptp-170) cc_final: 0.9387 (ptp-170) REVERT: Y 144 MET cc_start: 0.8509 (ttp) cc_final: 0.7884 (ptm) REVERT: d 23 TRP cc_start: 0.9494 (t-100) cc_final: 0.8856 (t-100) REVERT: d 25 LYS cc_start: 0.9222 (tttt) cc_final: 0.8977 (tptp) REVERT: d 30 LYS cc_start: 0.8390 (mtpt) cc_final: 0.8093 (tttt) REVERT: d 39 MET cc_start: 0.8983 (mtm) cc_final: 0.8228 (mtt) REVERT: d 51 ASP cc_start: 0.9052 (t0) cc_final: 0.8592 (m-30) REVERT: d 55 MET cc_start: 0.9659 (ptm) cc_final: 0.9187 (ppp) REVERT: d 66 MET cc_start: 0.9620 (mpp) cc_final: 0.9306 (mpp) REVERT: d 67 GLN cc_start: 0.9069 (tp-100) cc_final: 0.8492 (tm-30) REVERT: d 68 MET cc_start: 0.9025 (mmt) cc_final: 0.8117 (mmm) REVERT: d 75 GLU cc_start: 0.9136 (pp20) cc_final: 0.8841 (pp20) REVERT: d 80 TRP cc_start: 0.9624 (t60) cc_final: 0.9372 (t60) REVERT: d 128 GLU cc_start: 0.9400 (mm-30) cc_final: 0.8975 (pp20) REVERT: d 132 ARG cc_start: 0.9440 (ttm110) cc_final: 0.8810 (mtp85) REVERT: d 144 MET cc_start: 0.9076 (tmm) cc_final: 0.8760 (tmm) REVERT: d 215 MET cc_start: 0.4726 (mmt) cc_final: 0.4160 (mtm) REVERT: e 23 TRP cc_start: 0.9530 (t-100) cc_final: 0.8889 (t-100) REVERT: e 30 LYS cc_start: 0.9366 (mmtp) cc_final: 0.8971 (mmmm) REVERT: e 35 GLU cc_start: 0.9398 (pm20) cc_final: 0.9140 (pm20) REVERT: e 39 MET cc_start: 0.9604 (mtm) cc_final: 0.9237 (mtm) REVERT: e 50 GLN cc_start: 0.9340 (mt0) cc_final: 0.8873 (mt0) REVERT: e 55 MET cc_start: 0.9747 (mtp) cc_final: 0.9086 (tpp) REVERT: e 63 GLN cc_start: 0.9598 (mp10) cc_final: 0.9278 (mp10) REVERT: e 76 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9355 (mm-30) REVERT: e 111 LEU cc_start: 0.9472 (tp) cc_final: 0.9093 (tp) REVERT: e 114 GLN cc_start: 0.9501 (pt0) cc_final: 0.8766 (pt0) REVERT: e 128 GLU cc_start: 0.9506 (pm20) cc_final: 0.9205 (pm20) REVERT: e 129 ILE cc_start: 0.9837 (mt) cc_final: 0.9611 (mm) REVERT: e 185 MET cc_start: 0.9767 (ptp) cc_final: 0.9459 (ptt) REVERT: e 203 LYS cc_start: 0.7758 (ptpt) cc_final: 0.6869 (tttt) REVERT: e 211 LEU cc_start: 0.9387 (tp) cc_final: 0.9145 (tp) REVERT: e 215 MET cc_start: 0.8949 (ppp) cc_final: 0.8254 (ppp) REVERT: j 172 LEU cc_start: 0.9663 (tp) cc_final: 0.9400 (mm) REVERT: j 182 LYS cc_start: 0.9354 (mmtt) cc_final: 0.8975 (mmtt) REVERT: j 188 THR cc_start: 0.8257 (m) cc_final: 0.7825 (m) REVERT: j 215 MET cc_start: 0.8830 (ppp) cc_final: 0.8514 (ppp) REVERT: k 25 LYS cc_start: 0.9747 (ptmm) cc_final: 0.9530 (ptmm) REVERT: k 39 MET cc_start: 0.9685 (tpt) cc_final: 0.9085 (tpt) REVERT: k 43 LEU cc_start: 0.9557 (mp) cc_final: 0.8798 (mp) REVERT: k 52 LEU cc_start: 0.9656 (mt) cc_final: 0.9397 (mt) REVERT: k 76 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9190 (mm-30) REVERT: k 81 ASP cc_start: 0.9766 (t70) cc_final: 0.9419 (m-30) REVERT: k 131 LYS cc_start: 0.9436 (tttp) cc_final: 0.8993 (tptt) REVERT: k 173 ARG cc_start: 0.8918 (ttt180) cc_final: 0.8578 (ttt-90) REVERT: k 179 GLN cc_start: 0.9546 (tp40) cc_final: 0.9094 (tp-100) REVERT: k 182 LYS cc_start: 0.9549 (ttmm) cc_final: 0.9183 (mtmt) REVERT: k 185 MET cc_start: 0.9304 (mtm) cc_final: 0.8901 (mtm) REVERT: k 193 ASN cc_start: 0.9277 (m110) cc_final: 0.7834 (t0) outliers start: 1 outliers final: 0 residues processed: 814 average time/residue: 0.1605 time to fit residues: 187.9387 Evaluate side-chains 657 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 657 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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: 8.9990 chunk 18 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 44 optimal weight: 0.0970 chunk 152 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 95 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 219 GLN e 4 GLN j 155 GLN j 193 ASN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 74 ASN ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.078786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.055507 restraints weight = 78539.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.057475 restraints weight = 53557.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.058955 restraints weight = 40373.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.060028 restraints weight = 32594.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.060882 restraints weight = 27692.080| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.8579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18834 Z= 0.166 Angle : 0.760 12.174 25587 Z= 0.402 Chirality : 0.047 0.239 2848 Planarity : 0.006 0.102 3345 Dihedral : 4.799 23.737 2500 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.15 % Allowed : 0.35 % Favored : 99.50 % 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: -0.49 (0.17), residues: 2338 helix: -0.13 (0.13), residues: 1450 sheet: -1.31 (0.59), residues: 64 loop : -0.30 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG G 143 TYR 0.026 0.002 TYR C 169 PHE 0.031 0.002 PHE H 168 TRP 0.044 0.002 TRP N 184 HIS 0.006 0.001 HIS J 92 Details of bonding type rmsd covalent geometry : bond 0.00365 (18824) covalent geometry : angle 0.75954 (25567) SS BOND : bond 0.00159 ( 10) SS BOND : angle 1.01309 ( 20) hydrogen bonds : bond 0.04404 ( 1037) hydrogen bonds : angle 5.09952 ( 3081) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3966.30 seconds wall clock time: 69 minutes 1.57 seconds (4141.57 seconds total)