Starting phenix.real_space_refine on Thu Mar 5 01:09:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y9w_10739/03_2026/6y9w_10739.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y9w_10739/03_2026/6y9w_10739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y9w_10739/03_2026/6y9w_10739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y9w_10739/03_2026/6y9w_10739.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y9w_10739/03_2026/6y9w_10739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y9w_10739/03_2026/6y9w_10739.map" } resolution = 4.1 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 69 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.31, per 1000 atoms: 0.23 Number of scatterers: 18418 At special positions: 0 Unit cell: (136.74, 184.44, 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: 1.52 Conformation dependent library (CDL) restraints added in 666.7 milliseconds 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB ARG C 18 " Number of C-beta restraints generated: 4400 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 8 sheets defined 64.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.526A 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: 3.791A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.595A 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: 3.537A 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: 3.960A 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: 3.701A pdb=" N GLN D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 146 removed outlier: 3.602A pdb=" N ARG D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.765A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 145 Processing helix chain 'G' and resid 160 through 175 Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.895A pdb=" N TRP G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'G' and resid 210 through 218 Processing helix chain 'H' and resid 16 through 31 Processing helix chain 'H' and resid 35 through 44 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 62 through 84 Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'H' and resid 160 through 175 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.894A 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: 3.525A 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: 3.790A pdb=" N TRP N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N 187 " --> pdb=" O ASN N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 206 removed outlier: 3.593A pdb=" N LEU N 205 " --> pdb=" O ILE N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 removed outlier: 3.801A 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: 3.601A pdb=" N ARG Y 132 " --> pdb=" O GLU Y 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 30 removed outlier: 3.673A pdb=" N LEU d 20 " --> pdb=" O SER d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 44 Processing helix chain 'd' and resid 48 through 58 Processing helix chain 'd' and resid 62 through 83 Processing helix chain 'd' and resid 100 through 105 Processing helix chain 'd' and resid 110 through 118 removed outlier: 3.700A pdb=" N GLN d 114 " --> pdb=" O THR d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 146 removed outlier: 3.602A pdb=" N ARG d 132 " --> pdb=" O GLU d 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 174 Processing helix chain 'd' and resid 178 through 193 removed outlier: 4.765A pdb=" N LEU d 190 " --> pdb=" O THR d 186 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 206 Processing helix chain 'd' and resid 210 through 218 Processing helix chain '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: 3.904A pdb=" N ILE j 201 " --> pdb=" O ASP j 197 " (cutoff:3.500A) Processing helix chain 'j' and resid 210 through 218 removed outlier: 3.511A pdb=" N MET j 214 " --> pdb=" O THR j 210 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 31 removed outlier: 3.524A pdb=" N LEU k 20 " --> pdb=" O SER k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 36 through 44 Processing helix chain 'k' and resid 48 through 58 Processing helix chain 'k' and resid 62 through 84 Processing helix chain 'k' and resid 100 through 105 Processing helix chain 'k' and resid 110 through 119 Processing helix chain 'k' and resid 125 through 145 Processing helix chain 'k' and resid 160 through 176 Processing helix chain 'k' and resid 179 through 193 removed outlier: 4.360A pdb=" N LEU k 190 " --> pdb=" O THR k 186 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL k 191 " --> pdb=" O GLU k 187 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN k 193 " --> pdb=" O LEU k 189 " (cutoff:3.500A) Processing helix chain 'k' and resid 195 through 204 Processing helix chain 'k' and resid 210 through 219 removed outlier: 3.921A 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: 3.669A 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: 3.765A pdb=" N VAL e 11 " --> pdb=" O VAL e 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'k' and resid 3 through 4 removed outlier: 3.540A pdb=" N VAL k 3 " --> pdb=" O VAL k 11 " (cutoff:3.500A) removed outlier: 3.531A 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: 2.69 Time building geometry restraints manager: 2.05 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: 7782 1.44 - 1.67: 10787 1.67 - 1.90: 252 1.90 - 2.13: 0 2.13 - 2.37: 3 Bond restraints: 18824 Sorted by residual: bond pdb=" C PRO C 147 " pdb=" N THR C 148 " ideal model delta sigma weight residual 1.331 2.238 -0.907 1.23e-02 6.61e+03 5.44e+03 bond pdb=" CA ARG C 18 " pdb=" C ARG C 18 " ideal model delta sigma weight residual 1.522 2.365 -0.844 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 -0.817 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 2.24e+02 bond pdb=" CD2 HIS J 54 " pdb=" NE2 HIS J 54 " ideal model delta sigma weight residual 1.374 1.293 0.081 1.10e-02 8.26e+03 5.41e+01 ... (remaining 18819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.82: 25548 9.82 - 19.64: 15 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 91.99 27.28 1.17e+00 7.31e-01 5.44e+02 angle pdb=" CA ARG C 18 " pdb=" C ARG C 18 " pdb=" N THR C 19 " ideal model delta sigma weight residual 118.21 145.55 -27.34 1.36e+00 5.41e-01 4.04e+02 angle pdb=" O PRO C 147 " pdb=" C PRO C 147 " pdb=" N THR C 148 " ideal model delta sigma weight residual 122.30 108.79 13.51 1.36e+00 5.41e-01 9.87e+01 angle pdb=" C HIS e 84 " pdb=" N PRO e 85 " pdb=" CA PRO e 85 " ideal model delta sigma weight residual 120.03 129.85 -9.82 9.90e-01 1.02e+00 9.84e+01 ... (remaining 25562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10637 17.99 - 35.99: 709 35.99 - 53.98: 179 53.98 - 71.97: 19 71.97 - 89.97: 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 -163.12 40.52 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 122.80 158.65 -35.85 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 -134.79 48.79 1 1.00e+01 1.00e-02 3.28e+01 ... (remaining 11554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.946: 2846 0.946 - 1.891: 1 1.891 - 2.837: 0 2.837 - 3.782: 0 3.782 - 4.728: 1 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA ARG C 18 " pdb=" N ARG C 18 " pdb=" C ARG C 18 " pdb=" CB ARG C 18 " both_signs ideal model delta sigma weight residual False 2.51 7.24 -4.73 2.00e-01 2.50e+01 5.59e+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 6.56e+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 4.57e+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 7.92e-02 1.10e+02 pdb=" CG PHE J 60 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE J 60 " -0.094 2.00e-02 2.50e+03 pdb=" CD2 PHE J 60 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE J 60 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE J 60 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE J 60 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 147 " -0.064 2.00e-02 2.50e+03 9.96e-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 7.86e-02 6.18e+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: 1.91 - 2.51: 80 2.51 - 3.11: 13700 3.11 - 3.70: 28195 3.70 - 4.30: 37715 4.30 - 4.90: 61472 Nonbonded interactions: 141162 Sorted by model distance: nonbonded pdb=" OE1 GLN G 7 " pdb=" NE2 GLN k 9 " model vdw 1.911 3.120 nonbonded pdb=" OE1 GLU D 180 " pdb=" CG2 VAL H 181 " model vdw 2.020 3.460 nonbonded pdb=" CD1 LEU G 151 " pdb=" OE1 GLN d 192 " model vdw 2.028 3.460 nonbonded pdb=" CD1 LEU D 151 " pdb=" OE1 GLN H 192 " model vdw 2.094 3.460 nonbonded pdb=" NH2 ARG C 143 " pdb=" O GLN C 176 " model vdw 2.125 3.120 ... (remaining 141157 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.190 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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= 0.921 Angle : 1.068 49.088 25587 Z= 0.726 Chirality : 0.108 4.728 2848 Planarity : 0.007 0.100 3345 Dihedral : 13.054 89.965 7127 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.99 % Rotamer: Outliers : 0.45 % Allowed : 3.05 % Favored : 96.50 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.16), residues: 2336 helix: -0.33 (0.13), residues: 1402 sheet: -1.56 (0.60), residues: 65 loop : -0.85 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 37 TYR 0.100 0.003 TYR J 48 PHE 0.124 0.009 PHE J 60 TRP 0.019 0.001 TRP J 121 HIS 0.009 0.001 HIS J 70 Details of bonding type rmsd covalent geometry : bond 0.01239 (18824) covalent geometry : angle 1.06779 (25567) SS BOND : bond 0.00290 ( 10) SS BOND : angle 0.97259 ( 20) hydrogen bonds : bond 0.13585 ( 1037) hydrogen bonds : angle 5.13693 ( 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 1243 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1234 time to evaluate : 0.609 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 43 LEU cc_start: 0.8944 (mt) cc_final: 0.8665 (mp) REVERT: A 51 ASP cc_start: 0.9119 (m-30) cc_final: 0.8898 (m-30) REVERT: A 67 GLN cc_start: 0.9135 (tp40) cc_final: 0.8882 (tt0) REVERT: A 76 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9220 (mm-30) REVERT: A 86 VAL cc_start: 0.6828 (t) cc_final: 0.6094 (m) REVERT: A 145 TYR cc_start: 0.8844 (m-80) cc_final: 0.8527 (m-80) REVERT: B 21 ASN cc_start: 0.9511 (m-40) cc_final: 0.9238 (m110) REVERT: B 35 GLU cc_start: 0.9263 (pm20) cc_final: 0.8975 (mp0) REVERT: B 43 LEU cc_start: 0.8827 (mt) cc_final: 0.8558 (mt) REVERT: B 51 ASP cc_start: 0.9034 (m-30) cc_final: 0.8683 (m-30) REVERT: B 71 GLU cc_start: 0.9175 (tt0) cc_final: 0.8270 (tt0) REVERT: B 74 ASN cc_start: 0.9412 (m-40) cc_final: 0.9153 (m110) REVERT: B 75 GLU cc_start: 0.9243 (tt0) cc_final: 0.8975 (mt-10) REVERT: B 131 LYS cc_start: 0.9634 (ttmt) cc_final: 0.9366 (mttt) REVERT: B 144 MET cc_start: 0.9488 (ttt) cc_final: 0.9204 (ttt) REVERT: B 153 ILE cc_start: 0.9140 (mm) cc_final: 0.8535 (mt) REVERT: B 163 ASP cc_start: 0.9225 (m-30) cc_final: 0.8348 (t70) REVERT: B 173 ARG cc_start: 0.9095 (ttt180) cc_final: 0.8696 (ptm160) REVERT: B 180 GLU cc_start: 0.9453 (mp0) cc_final: 0.9250 (pm20) REVERT: B 181 VAL cc_start: 0.9815 (t) cc_final: 0.9345 (p) REVERT: B 182 LYS cc_start: 0.9638 (mttt) cc_final: 0.9207 (mtpt) REVERT: B 205 LEU cc_start: 0.7703 (mp) cc_final: 0.4867 (mp) REVERT: B 214 MET cc_start: 0.9407 (mtt) cc_final: 0.9169 (mmp) REVERT: C 25 LYS cc_start: 0.9498 (mttt) cc_final: 0.9204 (ptmm) REVERT: C 35 GLU cc_start: 0.9231 (pm20) cc_final: 0.8127 (pp20) REVERT: C 56 LEU cc_start: 0.9613 (mt) cc_final: 0.9341 (mt) REVERT: C 59 VAL cc_start: 0.9050 (t) cc_final: 0.8150 (p) REVERT: C 72 THR cc_start: 0.9308 (m) cc_final: 0.8968 (m) REVERT: C 75 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8598 (pp20) REVERT: C 103 ASP cc_start: 0.8892 (m-30) cc_final: 0.8343 (m-30) REVERT: C 140 LYS cc_start: 0.9762 (mttt) cc_final: 0.9459 (tptp) REVERT: C 153 ILE cc_start: 0.8213 (mt) cc_final: 0.7918 (mm) REVERT: C 178 SER cc_start: 0.7627 (m) cc_final: 0.7042 (t) REVERT: C 182 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8816 (mttm) REVERT: C 192 GLN cc_start: 0.9056 (mt0) cc_final: 0.8753 (mm-40) REVERT: C 215 MET cc_start: 0.9063 (mtm) cc_final: 0.8301 (mtm) REVERT: D 28 GLU cc_start: 0.9240 (tt0) cc_final: 0.9032 (pt0) REVERT: D 41 SER cc_start: 0.9571 (t) cc_final: 0.9071 (p) REVERT: D 53 ASN cc_start: 0.9427 (m-40) cc_final: 0.9079 (m110) REVERT: D 57 ASN cc_start: 0.9432 (m-40) cc_final: 0.9173 (m-40) REVERT: D 62 HIS cc_start: 0.8439 (m-70) cc_final: 0.8186 (m90) REVERT: D 66 MET cc_start: 0.9035 (mmm) cc_final: 0.8780 (ptp) REVERT: D 103 ASP cc_start: 0.8455 (t0) cc_final: 0.8049 (m-30) REVERT: D 128 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8530 (tm-30) REVERT: D 129 ILE cc_start: 0.9557 (mt) cc_final: 0.8479 (tt) REVERT: D 164 TYR cc_start: 0.7810 (t80) cc_final: 0.7308 (t80) REVERT: D 168 PHE cc_start: 0.8613 (t80) cc_final: 0.8377 (t80) REVERT: D 172 LEU cc_start: 0.9186 (tp) cc_final: 0.8718 (tp) REVERT: D 182 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8115 (mttm) REVERT: D 190 LEU cc_start: 0.9523 (tp) cc_final: 0.9174 (tp) REVERT: D 215 MET cc_start: 0.8777 (mtm) cc_final: 0.8255 (mmm) REVERT: G 16 SER cc_start: 0.8882 (m) cc_final: 0.8341 (p) REVERT: G 55 MET cc_start: 0.9395 (mtp) cc_final: 0.9158 (mtm) REVERT: G 57 ASN cc_start: 0.9284 (m-40) cc_final: 0.9000 (m110) REVERT: G 59 VAL cc_start: 0.7983 (t) cc_final: 0.7766 (p) REVERT: G 62 HIS cc_start: 0.7960 (m-70) cc_final: 0.7395 (m90) REVERT: G 79 GLU cc_start: 0.9318 (tm-30) cc_final: 0.8962 (tm-30) REVERT: G 96 MET cc_start: 0.4939 (mpp) cc_final: 0.4174 (mpp) REVERT: G 166 ASP cc_start: 0.8751 (m-30) cc_final: 0.8316 (m-30) REVERT: G 170 LYS cc_start: 0.8995 (tttt) cc_final: 0.8794 (mptt) REVERT: G 171 THR cc_start: 0.8807 (m) cc_final: 0.8006 (p) REVERT: G 187 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9098 (mp0) REVERT: G 197 ASP cc_start: 0.9376 (m-30) cc_final: 0.9164 (p0) REVERT: G 214 MET cc_start: 0.9382 (mtm) cc_final: 0.9011 (mtt) REVERT: G 215 MET cc_start: 0.8112 (mtm) cc_final: 0.7672 (mtm) REVERT: H 23 TRP cc_start: 0.9057 (t-100) cc_final: 0.8585 (t-100) REVERT: H 68 MET cc_start: 0.9358 (mtp) cc_final: 0.8985 (ttm) REVERT: H 80 TRP cc_start: 0.9125 (t-100) cc_final: 0.8305 (t60) REVERT: H 102 SER cc_start: 0.8754 (m) cc_final: 0.8466 (t) REVERT: J 5 THR cc_start: 0.7170 (m) cc_final: 0.6472 (p) REVERT: J 22 PHE cc_start: 0.8817 (m-80) cc_final: 0.8135 (m-10) REVERT: J 29 VAL cc_start: 0.6639 (OUTLIER) cc_final: 0.5557 (p) REVERT: J 31 LYS cc_start: 0.9002 (tttm) cc_final: 0.8559 (mmmt) REVERT: J 53 PHE cc_start: 0.9016 (m-80) cc_final: 0.8560 (m-10) REVERT: J 61 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6779 (pp-130) REVERT: J 84 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6263 (pm20) REVERT: J 100 MET cc_start: 0.8964 (mmt) cc_final: 0.8739 (tpt) REVERT: J 108 ASN cc_start: 0.8442 (m-40) cc_final: 0.8034 (m110) REVERT: J 119 THR cc_start: 0.8478 (p) cc_final: 0.8259 (m) REVERT: J 122 LEU cc_start: 0.8582 (mt) cc_final: 0.8247 (mt) REVERT: J 138 ILE cc_start: 0.7739 (mm) cc_final: 0.7360 (mt) REVERT: J 160 ASP cc_start: 0.8409 (t0) cc_final: 0.8108 (t0) REVERT: J 164 LEU cc_start: 0.7098 (mt) cc_final: 0.6711 (mp) REVERT: J 165 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: N 153 ILE cc_start: 0.9210 (mm) cc_final: 0.8656 (mm) REVERT: N 163 ASP cc_start: 0.8834 (m-30) cc_final: 0.7690 (t0) REVERT: N 182 LYS cc_start: 0.9557 (mttt) cc_final: 0.8938 (mmmt) REVERT: N 212 GLU cc_start: 0.9304 (pt0) cc_final: 0.9074 (pm20) REVERT: Y 13 GLN cc_start: 0.9033 (tt0) cc_final: 0.8604 (tm-30) REVERT: Y 33 SER cc_start: 0.8036 (m) cc_final: 0.7718 (p) REVERT: Y 41 SER cc_start: 0.9617 (t) cc_final: 0.9347 (p) REVERT: Y 43 LEU cc_start: 0.9364 (mt) cc_final: 0.8973 (mt) REVERT: Y 49 PRO cc_start: 0.9428 (Cg_exo) cc_final: 0.9222 (Cg_endo) REVERT: Y 51 ASP cc_start: 0.9328 (m-30) cc_final: 0.8577 (m-30) REVERT: Y 52 LEU cc_start: 0.9537 (mt) cc_final: 0.9155 (mp) REVERT: Y 53 ASN cc_start: 0.9527 (m-40) cc_final: 0.9271 (m-40) REVERT: Y 67 GLN cc_start: 0.9041 (tp-100) cc_final: 0.8353 (mt0) REVERT: Y 68 MET cc_start: 0.9189 (mtp) cc_final: 0.8615 (mmt) REVERT: Y 69 LEU cc_start: 0.9588 (tp) cc_final: 0.9319 (tp) REVERT: Y 71 GLU cc_start: 0.9393 (tm-30) cc_final: 0.9103 (mt-10) REVERT: Y 72 THR cc_start: 0.9599 (m) cc_final: 0.9053 (p) REVERT: Y 75 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8830 (pt0) REVERT: Y 96 MET cc_start: 0.3438 (mpp) cc_final: 0.2625 (mtp) REVERT: Y 104 ILE cc_start: 0.8590 (tt) cc_final: 0.8294 (pt) REVERT: Y 113 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8289 (mp0) REVERT: Y 117 TRP cc_start: 0.8273 (m-10) cc_final: 0.7768 (m-10) REVERT: Y 129 ILE cc_start: 0.9487 (mt) cc_final: 0.9264 (pt) REVERT: d 2 ILE cc_start: 0.6151 (mt) cc_final: 0.5910 (mm) REVERT: d 23 TRP cc_start: 0.9256 (t-100) cc_final: 0.9012 (t-100) REVERT: d 67 GLN cc_start: 0.9521 (tp-100) cc_final: 0.9087 (tt0) REVERT: d 74 ASN cc_start: 0.9373 (m-40) cc_final: 0.9148 (m110) REVERT: d 91 ILE cc_start: 0.3991 (mm) cc_final: 0.3741 (tt) REVERT: d 103 ASP cc_start: 0.8717 (t0) cc_final: 0.8150 (t0) REVERT: d 128 GLU cc_start: 0.9607 (mm-30) cc_final: 0.9266 (mp0) REVERT: d 129 ILE cc_start: 0.9416 (mt) cc_final: 0.9107 (tp) REVERT: d 130 TYR cc_start: 0.8506 (t80) cc_final: 0.8199 (t80) REVERT: d 139 ASN cc_start: 0.9663 (m-40) cc_final: 0.9446 (m-40) REVERT: d 143 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8841 (ttm-80) REVERT: d 183 ASN cc_start: 0.9572 (m-40) cc_final: 0.9323 (m110) REVERT: d 193 ASN cc_start: 0.8314 (m-40) cc_final: 0.7859 (t0) REVERT: e 6 ILE cc_start: 0.9062 (mt) cc_final: 0.8799 (tp) REVERT: e 41 SER cc_start: 0.9237 (m) cc_final: 0.8835 (p) REVERT: e 58 THR cc_start: 0.9169 (p) cc_final: 0.8937 (p) REVERT: e 59 VAL cc_start: 0.9281 (p) cc_final: 0.9038 (m) REVERT: e 74 ASN cc_start: 0.9693 (m-40) cc_final: 0.9359 (m110) REVERT: e 76 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8663 (mm-30) REVERT: e 79 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8177 (pp20) REVERT: e 96 MET cc_start: 0.5059 (mpp) cc_final: 0.4718 (mpp) REVERT: e 104 ILE cc_start: 0.8661 (mt) cc_final: 0.8243 (mt) REVERT: e 124 ILE cc_start: 0.8634 (mm) cc_final: 0.8127 (mm) REVERT: e 128 GLU cc_start: 0.9288 (mp0) cc_final: 0.8827 (mp0) REVERT: e 129 ILE cc_start: 0.9564 (mt) cc_final: 0.9303 (mm) REVERT: e 153 ILE cc_start: 0.8813 (mm) cc_final: 0.8602 (mm) REVERT: e 158 LYS cc_start: 0.8367 (tptt) cc_final: 0.8126 (tppt) REVERT: e 181 VAL cc_start: 0.9677 (t) cc_final: 0.9465 (t) REVERT: e 183 ASN cc_start: 0.9595 (m-40) cc_final: 0.9163 (m-40) REVERT: e 186 THR cc_start: 0.9548 (t) cc_final: 0.9171 (p) REVERT: j 153 ILE cc_start: 0.8793 (mm) cc_final: 0.8414 (mm) REVERT: j 189 LEU cc_start: 0.8917 (tp) cc_final: 0.8648 (tp) REVERT: j 199 LYS cc_start: 0.9212 (tttt) cc_final: 0.8892 (ttmm) REVERT: k 25 LYS cc_start: 0.9489 (mttt) cc_final: 0.9176 (ptmm) REVERT: k 32 PHE cc_start: 0.8459 (m-80) cc_final: 0.8191 (m-80) REVERT: k 40 PHE cc_start: 0.9421 (t80) cc_final: 0.9164 (t80) REVERT: k 43 LEU cc_start: 0.9337 (mt) cc_final: 0.9091 (mp) REVERT: k 55 MET cc_start: 0.9576 (mtp) cc_final: 0.9012 (ttm) REVERT: k 72 THR cc_start: 0.9014 (m) cc_final: 0.8530 (m) REVERT: k 76 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8912 (mm-30) REVERT: k 79 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8832 (tp30) REVERT: k 82 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8265 (ttp80) REVERT: k 103 ASP cc_start: 0.8836 (m-30) cc_final: 0.8599 (m-30) REVERT: k 111 LEU cc_start: 0.8269 (tp) cc_final: 0.7919 (tt) REVERT: k 128 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8958 (mm-30) REVERT: k 129 ILE cc_start: 0.9334 (mt) cc_final: 0.8572 (pt) REVERT: k 131 LYS cc_start: 0.9505 (ttmt) cc_final: 0.9086 (ttmt) REVERT: k 136 LEU cc_start: 0.9762 (tt) cc_final: 0.9459 (mt) REVERT: k 139 ASN cc_start: 0.9109 (m-40) cc_final: 0.8887 (m110) REVERT: k 164 TYR cc_start: 0.8749 (t80) cc_final: 0.8202 (t80) REVERT: k 173 ARG cc_start: 0.8776 (ttt180) cc_final: 0.8465 (ttp80) REVERT: k 180 GLU cc_start: 0.8944 (mp0) cc_final: 0.8685 (mp0) REVERT: k 185 MET cc_start: 0.9539 (mtm) cc_final: 0.9241 (mtm) REVERT: k 215 MET cc_start: 0.8615 (mtm) cc_final: 0.8295 (mtp) outliers start: 9 outliers final: 0 residues processed: 1237 average time/residue: 0.1627 time to fit residues: 286.9015 Evaluate side-chains 837 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 833 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 5 ASN B 4 GLN B 53 ASN B 219 GLN ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN C 112 GLN D 4 GLN D 95 GLN G 4 GLN G 183 ASN H 4 GLN H 84 HIS N 219 GLN Y 74 ASN Y 95 GLN d 4 GLN d 95 GLN e 50 GLN e 53 ASN e 120 ASN e 219 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 ASN k 62 HIS k 63 GLN ** k 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 95 GLN k 112 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.089440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.067951 restraints weight = 69939.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.069974 restraints weight = 44829.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071403 restraints weight = 32644.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.072387 restraints weight = 25974.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.073043 restraints weight = 22057.649| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18834 Z= 0.205 Angle : 0.692 9.607 25587 Z= 0.364 Chirality : 0.046 0.228 2848 Planarity : 0.006 0.074 3345 Dihedral : 4.260 28.853 2500 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.71 % Favored : 98.20 % Rotamer: Outliers : 0.15 % Allowed : 5.49 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2338 helix: 0.25 (0.13), residues: 1442 sheet: -1.11 (0.69), residues: 56 loop : -0.55 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 82 TYR 0.021 0.002 TYR e 130 PHE 0.021 0.002 PHE D 161 TRP 0.033 0.002 TRP e 117 HIS 0.006 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00448 (18824) covalent geometry : angle 0.69141 (25567) SS BOND : bond 0.00554 ( 10) SS BOND : angle 1.50690 ( 20) hydrogen bonds : bond 0.04798 ( 1037) hydrogen bonds : angle 4.59423 ( 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 1000 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 997 time to evaluate : 0.760 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: A 25 LYS cc_start: 0.9603 (tttt) cc_final: 0.9200 (ttmm) REVERT: A 51 ASP cc_start: 0.8904 (m-30) cc_final: 0.8281 (m-30) REVERT: A 52 LEU cc_start: 0.9786 (mt) cc_final: 0.9521 (mt) REVERT: A 53 ASN cc_start: 0.9439 (m110) cc_final: 0.9174 (m110) REVERT: A 67 GLN cc_start: 0.9094 (tp40) cc_final: 0.8169 (tm-30) REVERT: A 68 MET cc_start: 0.9127 (mtt) cc_final: 0.7860 (mtp) REVERT: A 74 ASN cc_start: 0.9343 (m110) cc_final: 0.9118 (m110) REVERT: A 76 GLU cc_start: 0.9639 (mm-30) cc_final: 0.9153 (mm-30) REVERT: B 21 ASN cc_start: 0.9445 (m-40) cc_final: 0.9206 (m-40) REVERT: B 39 MET cc_start: 0.9123 (tpp) cc_final: 0.8861 (tpt) REVERT: B 43 LEU cc_start: 0.8750 (mt) cc_final: 0.8406 (mt) REVERT: B 50 GLN cc_start: 0.8302 (mt0) cc_final: 0.7929 (mt0) REVERT: B 74 ASN cc_start: 0.9444 (m-40) cc_final: 0.9185 (m110) REVERT: B 111 LEU cc_start: 0.9050 (tt) cc_final: 0.8821 (tt) REVERT: B 131 LYS cc_start: 0.9515 (ttmt) cc_final: 0.9257 (mttt) REVERT: B 139 ASN cc_start: 0.9694 (m-40) cc_final: 0.9352 (m110) REVERT: B 173 ARG cc_start: 0.8994 (ttt180) cc_final: 0.8627 (ptm160) REVERT: B 182 LYS cc_start: 0.9624 (mttt) cc_final: 0.9179 (mtpt) REVERT: B 205 LEU cc_start: 0.7304 (mp) cc_final: 0.6365 (mp) REVERT: C 51 ASP cc_start: 0.9108 (m-30) cc_final: 0.8892 (m-30) REVERT: C 55 MET cc_start: 0.9537 (ttm) cc_final: 0.9278 (ttp) REVERT: C 59 VAL cc_start: 0.9315 (t) cc_final: 0.9083 (p) REVERT: C 76 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8696 (mm-30) REVERT: C 103 ASP cc_start: 0.8734 (m-30) cc_final: 0.8365 (m-30) REVERT: C 131 LYS cc_start: 0.9410 (mtmt) cc_final: 0.9182 (mtmt) REVERT: C 132 ARG cc_start: 0.9208 (ttp-110) cc_final: 0.8869 (ttm110) REVERT: C 135 ILE cc_start: 0.9513 (mt) cc_final: 0.9282 (mt) REVERT: C 139 ASN cc_start: 0.9142 (m110) cc_final: 0.8845 (m-40) REVERT: C 140 LYS cc_start: 0.9633 (mttt) cc_final: 0.9430 (tptp) REVERT: C 178 SER cc_start: 0.8072 (m) cc_final: 0.7868 (t) REVERT: C 192 GLN cc_start: 0.8944 (mt0) cc_final: 0.8514 (tm-30) REVERT: C 215 MET cc_start: 0.8904 (mtm) cc_final: 0.8172 (mtm) REVERT: D 50 GLN cc_start: 0.8685 (mp10) cc_final: 0.8433 (mp10) REVERT: D 53 ASN cc_start: 0.9342 (m-40) cc_final: 0.9025 (m-40) REVERT: D 62 HIS cc_start: 0.8403 (m-70) cc_final: 0.8079 (m90) REVERT: D 114 GLN cc_start: 0.9363 (mm-40) cc_final: 0.8779 (mp10) REVERT: D 118 MET cc_start: 0.8758 (mmm) cc_final: 0.8528 (mmm) REVERT: D 143 ARG cc_start: 0.8952 (mtt90) cc_final: 0.8079 (tpt170) REVERT: D 164 TYR cc_start: 0.8009 (t80) cc_final: 0.7780 (t80) REVERT: D 167 ARG cc_start: 0.8659 (ptm160) cc_final: 0.8378 (ptm-80) REVERT: D 175 GLU cc_start: 0.7959 (tp30) cc_final: 0.7332 (tp30) REVERT: D 176 GLN cc_start: 0.8689 (pt0) cc_final: 0.8360 (tp40) REVERT: D 182 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8315 (mttm) REVERT: D 190 LEU cc_start: 0.9336 (tp) cc_final: 0.8848 (tp) REVERT: D 203 LYS cc_start: 0.8712 (ptmt) cc_final: 0.8402 (ptpp) REVERT: D 212 GLU cc_start: 0.9087 (pm20) cc_final: 0.8772 (pm20) REVERT: G 57 ASN cc_start: 0.9238 (m-40) cc_final: 0.8957 (m110) REVERT: G 182 LYS cc_start: 0.9391 (tttt) cc_final: 0.9139 (mtpp) REVERT: G 197 ASP cc_start: 0.9271 (m-30) cc_final: 0.9031 (p0) REVERT: G 205 LEU cc_start: 0.8036 (tt) cc_final: 0.7581 (tt) REVERT: H 23 TRP cc_start: 0.9026 (t-100) cc_final: 0.7947 (t-100) REVERT: H 51 ASP cc_start: 0.9013 (m-30) cc_final: 0.8579 (m-30) REVERT: H 68 MET cc_start: 0.9132 (mtp) cc_final: 0.8776 (ttm) REVERT: H 80 TRP cc_start: 0.9290 (t-100) cc_final: 0.8826 (t60) REVERT: H 102 SER cc_start: 0.8933 (m) cc_final: 0.8275 (t) REVERT: H 139 ASN cc_start: 0.9209 (m-40) cc_final: 0.8752 (m-40) REVERT: H 149 SER cc_start: 0.8614 (t) cc_final: 0.8178 (t) REVERT: J 22 PHE cc_start: 0.8578 (m-80) cc_final: 0.8004 (m-80) REVERT: J 35 ASN cc_start: 0.9404 (t0) cc_final: 0.9169 (t0) REVERT: J 100 MET cc_start: 0.9339 (mmt) cc_final: 0.9128 (tpt) REVERT: J 108 ASN cc_start: 0.8813 (m-40) cc_final: 0.8481 (m110) REVERT: J 122 LEU cc_start: 0.8937 (mt) cc_final: 0.8675 (mt) REVERT: J 123 ASP cc_start: 0.8895 (m-30) cc_final: 0.8680 (m-30) REVERT: J 138 ILE cc_start: 0.8887 (mm) cc_final: 0.8269 (mt) REVERT: J 140 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8799 (tp30) REVERT: J 142 MET cc_start: 0.8612 (mtm) cc_final: 0.8164 (mtm) REVERT: J 143 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7972 (mm-30) REVERT: J 164 LEU cc_start: 0.7986 (mt) cc_final: 0.7664 (mp) REVERT: N 163 ASP cc_start: 0.8990 (m-30) cc_final: 0.8107 (t0) REVERT: N 181 VAL cc_start: 0.9313 (p) cc_final: 0.9000 (p) REVERT: Y 49 PRO cc_start: 0.9511 (Cg_exo) cc_final: 0.9107 (Cg_endo) REVERT: Y 50 GLN cc_start: 0.9432 (tm-30) cc_final: 0.9168 (tm-30) REVERT: Y 51 ASP cc_start: 0.9138 (m-30) cc_final: 0.8563 (m-30) REVERT: Y 53 ASN cc_start: 0.9649 (m-40) cc_final: 0.9318 (m-40) REVERT: Y 57 ASN cc_start: 0.9619 (m110) cc_final: 0.9352 (m110) REVERT: Y 71 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8910 (mt-10) REVERT: Y 74 ASN cc_start: 0.9002 (m110) cc_final: 0.8656 (m110) REVERT: Y 96 MET cc_start: 0.3582 (mpp) cc_final: 0.2438 (mtp) REVERT: Y 104 ILE cc_start: 0.8646 (tt) cc_final: 0.8410 (pt) REVERT: Y 117 TRP cc_start: 0.8835 (m-10) cc_final: 0.8040 (m-90) REVERT: Y 128 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8232 (tm-30) REVERT: Y 131 LYS cc_start: 0.9142 (mtpt) cc_final: 0.8803 (mtpt) REVERT: Y 132 ARG cc_start: 0.8832 (ttp-110) cc_final: 0.8447 (ttp-110) REVERT: Y 136 LEU cc_start: 0.9624 (mt) cc_final: 0.9160 (mt) REVERT: Y 141 ILE cc_start: 0.9692 (mt) cc_final: 0.9444 (mt) REVERT: d 23 TRP cc_start: 0.9360 (t-100) cc_final: 0.9077 (t-100) REVERT: d 74 ASN cc_start: 0.9468 (m-40) cc_final: 0.9247 (m110) REVERT: d 103 ASP cc_start: 0.9015 (t0) cc_final: 0.8538 (t0) REVERT: d 118 MET cc_start: 0.9083 (mmt) cc_final: 0.8752 (mmm) REVERT: d 135 ILE cc_start: 0.9541 (mt) cc_final: 0.9291 (mt) REVERT: d 141 ILE cc_start: 0.9459 (mt) cc_final: 0.9230 (mt) REVERT: d 166 ASP cc_start: 0.8507 (t0) cc_final: 0.8084 (t0) REVERT: d 182 LYS cc_start: 0.9321 (mtpt) cc_final: 0.9103 (mttp) REVERT: d 215 MET cc_start: 0.4147 (mtp) cc_final: 0.3511 (tpt) REVERT: e 35 GLU cc_start: 0.9428 (pm20) cc_final: 0.9117 (pm20) REVERT: e 74 ASN cc_start: 0.9687 (m-40) cc_final: 0.9411 (m-40) REVERT: e 76 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8464 (mm-30) REVERT: e 96 MET cc_start: 0.6374 (mpp) cc_final: 0.5729 (tpp) REVERT: e 129 ILE cc_start: 0.9630 (mt) cc_final: 0.9362 (tp) REVERT: e 158 LYS cc_start: 0.8150 (tptt) cc_final: 0.7869 (tppt) REVERT: e 167 ARG cc_start: 0.9238 (ptm160) cc_final: 0.8940 (ptt180) REVERT: j 175 GLU cc_start: 0.8534 (pp20) cc_final: 0.8265 (pp20) REVERT: j 189 LEU cc_start: 0.8945 (tp) cc_final: 0.8680 (tp) REVERT: j 212 GLU cc_start: 0.9230 (pt0) cc_final: 0.8862 (pm20) REVERT: k 13 GLN cc_start: 0.9440 (tp40) cc_final: 0.9004 (mm110) REVERT: k 23 TRP cc_start: 0.9442 (t-100) cc_final: 0.9071 (t-100) REVERT: k 25 LYS cc_start: 0.9561 (mttt) cc_final: 0.9287 (ttpp) REVERT: k 29 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8330 (mt-10) REVERT: k 51 ASP cc_start: 0.9371 (m-30) cc_final: 0.9163 (m-30) REVERT: k 52 LEU cc_start: 0.9652 (mt) cc_final: 0.9437 (mt) REVERT: k 55 MET cc_start: 0.9217 (mtp) cc_final: 0.8569 (ttm) REVERT: k 57 ASN cc_start: 0.9418 (m-40) cc_final: 0.9133 (m110) REVERT: k 71 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8493 (mt-10) REVERT: k 72 THR cc_start: 0.9144 (m) cc_final: 0.8480 (m) REVERT: k 76 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8852 (mm-30) REVERT: k 79 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8874 (tp30) REVERT: k 131 LYS cc_start: 0.9528 (ttmt) cc_final: 0.9232 (ttmt) REVERT: k 139 ASN cc_start: 0.9425 (m-40) cc_final: 0.8969 (m110) REVERT: k 164 TYR cc_start: 0.8850 (t80) cc_final: 0.8376 (t80) REVERT: k 175 GLU cc_start: 0.8798 (tp30) cc_final: 0.8563 (tp30) REVERT: k 176 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8095 (tm-30) REVERT: k 182 LYS cc_start: 0.9298 (mttp) cc_final: 0.8713 (mttp) REVERT: k 192 GLN cc_start: 0.9141 (mt0) cc_final: 0.8933 (mt0) REVERT: k 212 GLU cc_start: 0.8249 (pm20) cc_final: 0.7863 (pm20) outliers start: 3 outliers final: 0 residues processed: 999 average time/residue: 0.1686 time to fit residues: 239.3201 Evaluate side-chains 781 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 781 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 78 optimal weight: 0.0000 chunk 19 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 116 optimal weight: 30.0000 chunk 148 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN B 4 GLN B 12 HIS B 53 ASN B 84 HIS C 53 ASN C 112 GLN G 179 GLN G 183 ASN H 84 HIS J 126 HIS Y 4 GLN Y 84 HIS e 67 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.089309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.068291 restraints weight = 70388.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.070304 restraints weight = 44920.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.071726 restraints weight = 32684.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.072725 restraints weight = 25929.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.073440 restraints weight = 21964.695| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18834 Z= 0.164 Angle : 0.666 12.714 25587 Z= 0.346 Chirality : 0.046 0.227 2848 Planarity : 0.006 0.054 3345 Dihedral : 4.339 33.584 2500 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.30 % Allowed : 3.60 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2338 helix: 0.34 (0.13), residues: 1441 sheet: -1.11 (0.66), residues: 55 loop : -0.34 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 82 TYR 0.025 0.002 TYR A 130 PHE 0.019 0.002 PHE d 40 TRP 0.015 0.001 TRP G 117 HIS 0.003 0.001 HIS Y 12 Details of bonding type rmsd covalent geometry : bond 0.00381 (18824) covalent geometry : angle 0.66524 (25567) SS BOND : bond 0.00283 ( 10) SS BOND : angle 1.21622 ( 20) hydrogen bonds : bond 0.04562 ( 1037) hydrogen bonds : angle 4.58137 ( 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 948 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 942 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.9508 (t0) cc_final: 0.8983 (t0) REVERT: A 23 TRP cc_start: 0.9336 (t-100) cc_final: 0.9072 (t-100) REVERT: A 25 LYS cc_start: 0.9694 (tttt) cc_final: 0.9217 (ttmm) REVERT: A 29 GLU cc_start: 0.9098 (pt0) cc_final: 0.8835 (pt0) REVERT: A 53 ASN cc_start: 0.9407 (m-40) cc_final: 0.9206 (m110) REVERT: A 58 THR cc_start: 0.9323 (p) cc_final: 0.9109 (p) REVERT: A 76 GLU cc_start: 0.9614 (mm-30) cc_final: 0.9190 (mm-30) REVERT: A 97 ARG cc_start: 0.7410 (ptt90) cc_final: 0.6785 (ptt90) REVERT: A 100 ARG cc_start: 0.8662 (mpp80) cc_final: 0.8409 (mtt90) REVERT: A 131 LYS cc_start: 0.9579 (mtpt) cc_final: 0.9221 (mttt) REVERT: B 18 ARG cc_start: 0.8956 (mtm-85) cc_final: 0.8703 (mtm-85) REVERT: B 21 ASN cc_start: 0.9427 (m-40) cc_final: 0.9191 (m-40) REVERT: B 28 GLU cc_start: 0.8855 (tt0) cc_final: 0.8625 (tt0) REVERT: B 39 MET cc_start: 0.9154 (tpp) cc_final: 0.8909 (tpt) REVERT: B 43 LEU cc_start: 0.8790 (mt) cc_final: 0.8428 (mt) REVERT: B 50 GLN cc_start: 0.8696 (mt0) cc_final: 0.8416 (mt0) REVERT: B 74 ASN cc_start: 0.9441 (m-40) cc_final: 0.9209 (m110) REVERT: B 96 MET cc_start: 0.7836 (mpp) cc_final: 0.7554 (mpp) REVERT: B 111 LEU cc_start: 0.9045 (tt) cc_final: 0.8677 (tt) REVERT: B 118 MET cc_start: 0.9334 (mmt) cc_final: 0.9076 (mmm) REVERT: B 139 ASN cc_start: 0.9714 (m-40) cc_final: 0.9153 (m110) REVERT: B 173 ARG cc_start: 0.9009 (ttt180) cc_final: 0.8662 (ptm160) REVERT: B 182 LYS cc_start: 0.9625 (mttt) cc_final: 0.9184 (mttt) REVERT: B 203 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7563 (mmmm) REVERT: C 51 ASP cc_start: 0.8943 (m-30) cc_final: 0.8729 (m-30) REVERT: C 76 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8679 (mm-30) REVERT: C 103 ASP cc_start: 0.8620 (m-30) cc_final: 0.8357 (m-30) REVERT: C 135 ILE cc_start: 0.9548 (mt) cc_final: 0.9315 (mt) REVERT: C 139 ASN cc_start: 0.9208 (m110) cc_final: 0.8902 (m110) REVERT: C 140 LYS cc_start: 0.9689 (mttt) cc_final: 0.9439 (tptp) REVERT: C 192 GLN cc_start: 0.8949 (mt0) cc_final: 0.8541 (tm-30) REVERT: C 215 MET cc_start: 0.8924 (mtm) cc_final: 0.8696 (tmm) REVERT: D 53 ASN cc_start: 0.9345 (m-40) cc_final: 0.9029 (m-40) REVERT: D 103 ASP cc_start: 0.8785 (t0) cc_final: 0.7515 (t0) REVERT: D 114 GLN cc_start: 0.9399 (mm-40) cc_final: 0.8777 (mp10) REVERT: D 182 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8274 (mttm) REVERT: D 203 LYS cc_start: 0.8555 (ptmt) cc_final: 0.8259 (ptpp) REVERT: G 45 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8322 (mt-10) REVERT: G 57 ASN cc_start: 0.9261 (m-40) cc_final: 0.8963 (m110) REVERT: G 79 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8926 (tm-30) REVERT: G 132 ARG cc_start: 0.9279 (mtm110) cc_final: 0.8956 (mtm110) REVERT: G 139 ASN cc_start: 0.9543 (m110) cc_final: 0.9322 (m-40) REVERT: G 179 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8872 (pp30) REVERT: G 182 LYS cc_start: 0.9393 (tttt) cc_final: 0.9129 (mtpp) REVERT: G 197 ASP cc_start: 0.9206 (m-30) cc_final: 0.8985 (p0) REVERT: H 23 TRP cc_start: 0.9143 (t-100) cc_final: 0.8231 (t-100) REVERT: H 50 GLN cc_start: 0.9336 (tt0) cc_final: 0.8788 (pt0) REVERT: H 51 ASP cc_start: 0.8631 (m-30) cc_final: 0.8319 (m-30) REVERT: H 55 MET cc_start: 0.9193 (tpp) cc_final: 0.8896 (tpp) REVERT: H 59 VAL cc_start: 0.9318 (t) cc_final: 0.8969 (p) REVERT: H 66 MET cc_start: 0.9252 (mmp) cc_final: 0.8977 (mmm) REVERT: H 102 SER cc_start: 0.8827 (m) cc_final: 0.8457 (t) REVERT: H 111 LEU cc_start: 0.9249 (tt) cc_final: 0.9038 (tp) REVERT: H 132 ARG cc_start: 0.9224 (ptp-110) cc_final: 0.8953 (mtm110) REVERT: H 149 SER cc_start: 0.8847 (t) cc_final: 0.8452 (t) REVERT: J 37 ARG cc_start: 0.9432 (ttt-90) cc_final: 0.8922 (ptm-80) REVERT: J 53 PHE cc_start: 0.9242 (m-80) cc_final: 0.8635 (m-10) REVERT: J 84 GLU cc_start: 0.8665 (pm20) cc_final: 0.8233 (pm20) REVERT: J 106 ASN cc_start: 0.8974 (m-40) cc_final: 0.8114 (t0) REVERT: J 108 ASN cc_start: 0.8772 (m-40) cc_final: 0.8381 (m110) REVERT: J 111 GLN cc_start: 0.8824 (mt0) cc_final: 0.8466 (mm-40) REVERT: J 138 ILE cc_start: 0.8931 (mm) cc_final: 0.8497 (mt) REVERT: J 139 VAL cc_start: 0.9609 (t) cc_final: 0.9365 (t) REVERT: J 140 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8775 (tp30) REVERT: J 142 MET cc_start: 0.8638 (mtm) cc_final: 0.8053 (mtm) REVERT: N 163 ASP cc_start: 0.9173 (m-30) cc_final: 0.8290 (t0) REVERT: N 181 VAL cc_start: 0.9257 (p) cc_final: 0.8922 (p) REVERT: N 183 ASN cc_start: 0.9274 (m-40) cc_final: 0.9053 (m-40) REVERT: N 203 LYS cc_start: 0.8627 (ptmt) cc_final: 0.8164 (pttp) REVERT: Y 15 ILE cc_start: 0.9111 (mm) cc_final: 0.8903 (mm) REVERT: Y 39 MET cc_start: 0.9305 (ttm) cc_final: 0.9064 (ttm) REVERT: Y 48 THR cc_start: 0.9414 (t) cc_final: 0.9131 (t) REVERT: Y 49 PRO cc_start: 0.9266 (Cg_exo) cc_final: 0.8953 (Cg_endo) REVERT: Y 51 ASP cc_start: 0.9090 (m-30) cc_final: 0.8455 (m-30) REVERT: Y 53 ASN cc_start: 0.9594 (m-40) cc_final: 0.9207 (m-40) REVERT: Y 55 MET cc_start: 0.9399 (ttp) cc_final: 0.8916 (tmm) REVERT: Y 74 ASN cc_start: 0.9003 (m110) cc_final: 0.8610 (m110) REVERT: Y 96 MET cc_start: 0.3630 (mpp) cc_final: 0.2310 (mtp) REVERT: Y 118 MET cc_start: 0.8790 (mmp) cc_final: 0.8573 (mmp) REVERT: Y 131 LYS cc_start: 0.9158 (mtpt) cc_final: 0.8789 (mtpt) REVERT: Y 139 ASN cc_start: 0.9555 (m-40) cc_final: 0.9232 (m110) REVERT: d 74 ASN cc_start: 0.9416 (m-40) cc_final: 0.9163 (m110) REVERT: d 103 ASP cc_start: 0.8960 (t0) cc_final: 0.8552 (t0) REVERT: d 130 TYR cc_start: 0.8442 (t80) cc_final: 0.8148 (t80) REVERT: d 182 LYS cc_start: 0.9312 (mtpt) cc_final: 0.9102 (mttp) REVERT: d 214 MET cc_start: 0.8880 (mtm) cc_final: 0.8612 (mpp) REVERT: d 215 MET cc_start: 0.3770 (mtp) cc_final: 0.3541 (tpt) REVERT: e 7 GLN cc_start: 0.9030 (mm110) cc_final: 0.8682 (mm110) REVERT: e 57 ASN cc_start: 0.9443 (m110) cc_final: 0.9219 (m110) REVERT: e 74 ASN cc_start: 0.9689 (m-40) cc_final: 0.9354 (m110) REVERT: e 96 MET cc_start: 0.6872 (mpp) cc_final: 0.5881 (tpp) REVERT: e 128 GLU cc_start: 0.8648 (pm20) cc_final: 0.8423 (pm20) REVERT: e 129 ILE cc_start: 0.9631 (mt) cc_final: 0.9298 (mm) REVERT: e 158 LYS cc_start: 0.8147 (tptt) cc_final: 0.7883 (tppt) REVERT: e 167 ARG cc_start: 0.9232 (ptm160) cc_final: 0.8920 (ptt180) REVERT: e 173 ARG cc_start: 0.9055 (ttt180) cc_final: 0.8336 (ttt180) REVERT: j 166 ASP cc_start: 0.8566 (m-30) cc_final: 0.8305 (m-30) REVERT: j 175 GLU cc_start: 0.8591 (pp20) cc_final: 0.8227 (pp20) REVERT: j 189 LEU cc_start: 0.8962 (tp) cc_final: 0.8743 (tp) REVERT: j 199 LYS cc_start: 0.9422 (tttt) cc_final: 0.9049 (ttmm) REVERT: k 3 VAL cc_start: 0.9172 (m) cc_final: 0.8759 (t) REVERT: k 13 GLN cc_start: 0.9455 (tp40) cc_final: 0.9204 (mp10) REVERT: k 23 TRP cc_start: 0.9459 (t-100) cc_final: 0.9076 (t-100) REVERT: k 25 LYS cc_start: 0.9556 (mttt) cc_final: 0.9224 (ttpp) REVERT: k 29 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8399 (mt-10) REVERT: k 55 MET cc_start: 0.9265 (mtp) cc_final: 0.8743 (ttm) REVERT: k 57 ASN cc_start: 0.9452 (m-40) cc_final: 0.9200 (m110) REVERT: k 63 GLN cc_start: 0.8774 (mp10) cc_final: 0.8312 (mp10) REVERT: k 71 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8656 (mt-10) REVERT: k 72 THR cc_start: 0.9177 (m) cc_final: 0.8442 (m) REVERT: k 76 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8839 (mm-30) REVERT: k 79 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8904 (tm-30) REVERT: k 111 LEU cc_start: 0.8453 (tt) cc_final: 0.8081 (tt) REVERT: k 128 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8804 (mm-30) REVERT: k 131 LYS cc_start: 0.9512 (ttmt) cc_final: 0.9172 (ttmt) REVERT: k 139 ASN cc_start: 0.9463 (m-40) cc_final: 0.8998 (m110) REVERT: k 164 TYR cc_start: 0.8955 (t80) cc_final: 0.8313 (t80) REVERT: k 176 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8395 (tm-30) REVERT: k 185 MET cc_start: 0.8958 (mtm) cc_final: 0.8719 (mtm) REVERT: k 211 LEU cc_start: 0.9288 (tp) cc_final: 0.9035 (tt) REVERT: k 212 GLU cc_start: 0.8530 (pm20) cc_final: 0.8168 (pm20) REVERT: k 213 GLU cc_start: 0.9405 (mp0) cc_final: 0.8660 (mp0) REVERT: k 214 MET cc_start: 0.9522 (mtm) cc_final: 0.9261 (mtm) REVERT: k 215 MET cc_start: 0.8761 (mtm) cc_final: 0.8530 (mtm) outliers start: 6 outliers final: 0 residues processed: 944 average time/residue: 0.1698 time to fit residues: 226.8268 Evaluate side-chains 757 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 756 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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: 9.9990 chunk 14 optimal weight: 0.4980 chunk 85 optimal weight: 8.9990 chunk 147 optimal weight: 50.0000 chunk 206 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 195 optimal weight: 0.0470 chunk 35 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 overall best weight: 2.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 4 GLN C 53 ASN C 193 ASN H 84 HIS J 35 ASN ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.089417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068564 restraints weight = 70413.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.070531 restraints weight = 44997.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.071938 restraints weight = 32775.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.072924 restraints weight = 26049.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.073576 restraints weight = 22068.942| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 18834 Z= 0.142 Angle : 0.662 13.136 25587 Z= 0.340 Chirality : 0.046 0.238 2848 Planarity : 0.006 0.068 3345 Dihedral : 4.389 24.828 2500 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2338 helix: 0.38 (0.14), residues: 1452 sheet: -1.46 (0.51), residues: 79 loop : -0.23 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 143 TYR 0.023 0.002 TYR B 145 PHE 0.016 0.002 PHE A 32 TRP 0.035 0.001 TRP G 117 HIS 0.003 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00327 (18824) covalent geometry : angle 0.66129 (25567) SS BOND : bond 0.00228 ( 10) SS BOND : angle 1.09941 ( 20) hydrogen bonds : bond 0.04246 ( 1037) hydrogen bonds : angle 4.49598 ( 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 940 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 938 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.9106 (pt0) cc_final: 0.8618 (pt0) REVERT: A 45 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8629 (tm-30) REVERT: A 53 ASN cc_start: 0.9485 (m-40) cc_final: 0.9131 (m110) REVERT: A 68 MET cc_start: 0.9334 (mtt) cc_final: 0.9103 (mtp) REVERT: A 76 GLU cc_start: 0.9612 (mm-30) cc_final: 0.9198 (mm-30) REVERT: A 97 ARG cc_start: 0.7481 (ptt90) cc_final: 0.6858 (ptt90) REVERT: A 103 ASP cc_start: 0.8091 (m-30) cc_final: 0.7872 (m-30) REVERT: A 131 LYS cc_start: 0.9586 (mtpt) cc_final: 0.9212 (mttt) REVERT: B 21 ASN cc_start: 0.9444 (m-40) cc_final: 0.9191 (m-40) REVERT: B 28 GLU cc_start: 0.8866 (tt0) cc_final: 0.8576 (tt0) REVERT: B 33 SER cc_start: 0.9102 (m) cc_final: 0.8880 (t) REVERT: B 35 GLU cc_start: 0.8972 (mp0) cc_final: 0.8332 (mp0) REVERT: B 39 MET cc_start: 0.9171 (tpp) cc_final: 0.8914 (tpt) REVERT: B 43 LEU cc_start: 0.8855 (mt) cc_final: 0.8477 (mt) REVERT: B 50 GLN cc_start: 0.8684 (mt0) cc_final: 0.8446 (mt0) REVERT: B 70 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8983 (mtmm) REVERT: B 74 ASN cc_start: 0.9462 (m-40) cc_final: 0.9208 (m110) REVERT: B 96 MET cc_start: 0.7786 (mpp) cc_final: 0.7339 (mpp) REVERT: B 111 LEU cc_start: 0.9060 (tt) cc_final: 0.8728 (tt) REVERT: B 118 MET cc_start: 0.9339 (mmt) cc_final: 0.9100 (mmm) REVERT: B 131 LYS cc_start: 0.9569 (ttmt) cc_final: 0.9367 (mttt) REVERT: B 153 ILE cc_start: 0.8915 (tp) cc_final: 0.8535 (tp) REVERT: B 173 ARG cc_start: 0.9062 (ttt180) cc_final: 0.8736 (ptm160) REVERT: B 179 GLN cc_start: 0.9119 (pp30) cc_final: 0.8885 (pp30) REVERT: B 182 LYS cc_start: 0.9627 (mttt) cc_final: 0.9227 (mttt) REVERT: B 205 LEU cc_start: 0.8002 (mp) cc_final: 0.6825 (mp) REVERT: B 213 GLU cc_start: 0.9513 (tp30) cc_final: 0.9029 (tp30) REVERT: B 215 MET cc_start: 0.8103 (mtp) cc_final: 0.7835 (mtp) REVERT: C 25 LYS cc_start: 0.9332 (ptmm) cc_final: 0.9028 (pttm) REVERT: C 76 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8676 (mm-30) REVERT: C 103 ASP cc_start: 0.8672 (m-30) cc_final: 0.8367 (m-30) REVERT: C 131 LYS cc_start: 0.9409 (mtmt) cc_final: 0.9017 (mttt) REVERT: C 135 ILE cc_start: 0.9571 (mt) cc_final: 0.9330 (mt) REVERT: C 139 ASN cc_start: 0.9226 (m110) cc_final: 0.8935 (m110) REVERT: C 144 MET cc_start: 0.8640 (ttp) cc_final: 0.8440 (ttt) REVERT: C 178 SER cc_start: 0.8500 (t) cc_final: 0.8262 (t) REVERT: D 41 SER cc_start: 0.9356 (p) cc_final: 0.9067 (p) REVERT: D 53 ASN cc_start: 0.9405 (m-40) cc_final: 0.9046 (m-40) REVERT: D 68 MET cc_start: 0.8974 (mtm) cc_final: 0.8651 (mtt) REVERT: D 103 ASP cc_start: 0.8768 (t0) cc_final: 0.8032 (t0) REVERT: D 114 GLN cc_start: 0.9386 (mm-40) cc_final: 0.8685 (mp10) REVERT: D 143 ARG cc_start: 0.8740 (mtt90) cc_final: 0.8494 (tpm170) REVERT: D 175 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6950 (mm-30) REVERT: D 182 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8228 (mttm) REVERT: D 205 LEU cc_start: 0.8669 (tt) cc_final: 0.8373 (tt) REVERT: G 45 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8368 (mt-10) REVERT: G 57 ASN cc_start: 0.9244 (m-40) cc_final: 0.8935 (m110) REVERT: G 79 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8875 (tm-30) REVERT: G 81 ASP cc_start: 0.8956 (m-30) cc_final: 0.8599 (m-30) REVERT: G 114 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8621 (mm-40) REVERT: G 139 ASN cc_start: 0.9557 (m110) cc_final: 0.9302 (m110) REVERT: G 182 LYS cc_start: 0.9379 (tttt) cc_final: 0.9077 (mtpp) REVERT: G 197 ASP cc_start: 0.9120 (m-30) cc_final: 0.8893 (p0) REVERT: H 23 TRP cc_start: 0.9168 (t-100) cc_final: 0.8000 (t-100) REVERT: H 50 GLN cc_start: 0.9320 (tt0) cc_final: 0.8881 (pt0) REVERT: H 51 ASP cc_start: 0.8542 (m-30) cc_final: 0.8291 (m-30) REVERT: H 55 MET cc_start: 0.9165 (tpp) cc_final: 0.8792 (tmm) REVERT: H 80 TRP cc_start: 0.8859 (t60) cc_final: 0.8041 (t60) REVERT: H 102 SER cc_start: 0.8773 (m) cc_final: 0.8414 (t) REVERT: H 132 ARG cc_start: 0.9170 (ptp-110) cc_final: 0.8890 (mtm110) REVERT: H 139 ASN cc_start: 0.9257 (m-40) cc_final: 0.9013 (m-40) REVERT: H 140 LYS cc_start: 0.9227 (tptp) cc_final: 0.8860 (tptp) REVERT: H 149 SER cc_start: 0.8833 (t) cc_final: 0.8412 (t) REVERT: H 152 ASP cc_start: 0.8737 (m-30) cc_final: 0.8523 (m-30) REVERT: H 167 ARG cc_start: 0.9003 (ptm160) cc_final: 0.8734 (ptm160) REVERT: H 168 PHE cc_start: 0.8722 (t80) cc_final: 0.8518 (t80) REVERT: J 37 ARG cc_start: 0.9276 (ttt-90) cc_final: 0.9021 (ptm-80) REVERT: J 39 LEU cc_start: 0.9320 (mt) cc_final: 0.9107 (mt) REVERT: J 53 PHE cc_start: 0.9145 (m-80) cc_final: 0.8679 (m-10) REVERT: J 84 GLU cc_start: 0.8724 (pm20) cc_final: 0.8521 (pm20) REVERT: J 100 MET cc_start: 0.9339 (tpt) cc_final: 0.8900 (tpt) REVERT: J 106 ASN cc_start: 0.9099 (m-40) cc_final: 0.8277 (t0) REVERT: J 111 GLN cc_start: 0.8813 (mt0) cc_final: 0.8539 (mm110) REVERT: J 138 ILE cc_start: 0.8857 (mm) cc_final: 0.8195 (mt) REVERT: J 140 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8578 (tp30) REVERT: J 142 MET cc_start: 0.8808 (mtm) cc_final: 0.8360 (mtm) REVERT: N 163 ASP cc_start: 0.9155 (m-30) cc_final: 0.8414 (t0) REVERT: N 181 VAL cc_start: 0.9230 (p) cc_final: 0.8894 (p) REVERT: N 183 ASN cc_start: 0.9248 (m-40) cc_final: 0.9033 (m-40) REVERT: N 215 MET cc_start: 0.8115 (mtp) cc_final: 0.7711 (mtp) REVERT: Y 39 MET cc_start: 0.9289 (ttm) cc_final: 0.9089 (ttm) REVERT: Y 49 PRO cc_start: 0.9301 (Cg_exo) cc_final: 0.9009 (Cg_endo) REVERT: Y 50 GLN cc_start: 0.9568 (tm-30) cc_final: 0.9361 (tm-30) REVERT: Y 51 ASP cc_start: 0.9177 (m-30) cc_final: 0.8513 (m-30) REVERT: Y 52 LEU cc_start: 0.9733 (mt) cc_final: 0.9499 (mt) REVERT: Y 53 ASN cc_start: 0.9584 (m-40) cc_final: 0.9248 (m-40) REVERT: Y 74 ASN cc_start: 0.8983 (m110) cc_final: 0.8559 (m110) REVERT: Y 96 MET cc_start: 0.3510 (mpp) cc_final: 0.2233 (mtp) REVERT: Y 113 GLU cc_start: 0.8695 (pm20) cc_final: 0.8199 (pm20) REVERT: Y 114 GLN cc_start: 0.9171 (mt0) cc_final: 0.8495 (mt0) REVERT: Y 117 TRP cc_start: 0.8860 (m-10) cc_final: 0.8296 (m-90) REVERT: Y 131 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8950 (mtpt) REVERT: Y 139 ASN cc_start: 0.9538 (m-40) cc_final: 0.9262 (m-40) REVERT: d 74 ASN cc_start: 0.9346 (m-40) cc_final: 0.9117 (m110) REVERT: d 103 ASP cc_start: 0.8943 (t0) cc_final: 0.8611 (t0) REVERT: d 114 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8224 (pt0) REVERT: d 136 LEU cc_start: 0.9427 (tt) cc_final: 0.9115 (tt) REVERT: d 139 ASN cc_start: 0.9420 (m110) cc_final: 0.9170 (m110) REVERT: d 141 ILE cc_start: 0.9497 (mt) cc_final: 0.9292 (mt) REVERT: d 182 LYS cc_start: 0.9310 (mtpt) cc_final: 0.9080 (mttp) REVERT: d 189 LEU cc_start: 0.9386 (mp) cc_final: 0.8904 (mp) REVERT: d 215 MET cc_start: 0.3618 (mtp) cc_final: 0.3269 (tpt) REVERT: e 57 ASN cc_start: 0.9407 (m110) cc_final: 0.9191 (m110) REVERT: e 74 ASN cc_start: 0.9671 (m-40) cc_final: 0.9309 (m110) REVERT: e 76 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8502 (mm-30) REVERT: e 96 MET cc_start: 0.7049 (mpp) cc_final: 0.5989 (tpp) REVERT: e 141 ILE cc_start: 0.9653 (mt) cc_final: 0.9443 (mt) REVERT: e 167 ARG cc_start: 0.9217 (ptm160) cc_final: 0.8851 (ptt180) REVERT: j 162 ARG cc_start: 0.8462 (mmm160) cc_final: 0.8162 (mmm160) REVERT: j 166 ASP cc_start: 0.8520 (m-30) cc_final: 0.8267 (m-30) REVERT: j 175 GLU cc_start: 0.8571 (pp20) cc_final: 0.8195 (pp20) REVERT: j 189 LEU cc_start: 0.8901 (tp) cc_final: 0.8671 (tp) REVERT: j 199 LYS cc_start: 0.9429 (tttt) cc_final: 0.9035 (ttmm) REVERT: k 3 VAL cc_start: 0.9166 (m) cc_final: 0.8786 (t) REVERT: k 13 GLN cc_start: 0.9441 (tp40) cc_final: 0.9215 (mp-120) REVERT: k 18 ARG cc_start: 0.8778 (ptm160) cc_final: 0.8438 (ptm160) REVERT: k 23 TRP cc_start: 0.9419 (t-100) cc_final: 0.9125 (t-100) REVERT: k 25 LYS cc_start: 0.9534 (mttt) cc_final: 0.9210 (ttpp) REVERT: k 29 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8270 (mt-10) REVERT: k 55 MET cc_start: 0.9237 (mtp) cc_final: 0.8724 (ttm) REVERT: k 71 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8344 (mt-10) REVERT: k 72 THR cc_start: 0.9224 (m) cc_final: 0.8386 (m) REVERT: k 76 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8870 (mm-30) REVERT: k 79 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8895 (tm-30) REVERT: k 111 LEU cc_start: 0.8411 (tt) cc_final: 0.8040 (tt) REVERT: k 131 LYS cc_start: 0.9508 (ttmt) cc_final: 0.9175 (ttmt) REVERT: k 139 ASN cc_start: 0.9461 (m-40) cc_final: 0.8999 (m110) REVERT: k 213 GLU cc_start: 0.9399 (mp0) cc_final: 0.8659 (mp0) REVERT: k 214 MET cc_start: 0.9486 (mtm) cc_final: 0.9250 (mtm) outliers start: 2 outliers final: 0 residues processed: 940 average time/residue: 0.1669 time to fit residues: 222.3315 Evaluate side-chains 757 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 757 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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: 50.0000 chunk 180 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 136 optimal weight: 30.0000 chunk 203 optimal weight: 40.0000 chunk 65 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN C 53 ASN C 62 HIS C 176 GLN H 84 HIS J 35 ASN N 193 ASN ** Y 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN d 192 GLN j 192 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 12 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.086309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.065553 restraints weight = 71812.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.067457 restraints weight = 46200.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.068786 restraints weight = 33930.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.069742 restraints weight = 27163.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.070383 restraints weight = 23153.874| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18834 Z= 0.212 Angle : 0.717 15.047 25587 Z= 0.372 Chirality : 0.047 0.214 2848 Planarity : 0.006 0.101 3345 Dihedral : 4.559 24.347 2500 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.20 % Allowed : 3.55 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2338 helix: 0.26 (0.13), residues: 1455 sheet: -1.16 (0.60), residues: 69 loop : -0.20 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 132 TYR 0.028 0.003 TYR A 130 PHE 0.031 0.002 PHE N 168 TRP 0.034 0.002 TRP G 23 HIS 0.007 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00470 (18824) covalent geometry : angle 0.71598 (25567) SS BOND : bond 0.01541 ( 10) SS BOND : angle 1.39892 ( 20) hydrogen bonds : bond 0.04437 ( 1037) hydrogen bonds : angle 4.71506 ( 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 890 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 886 time to evaluate : 0.729 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: A 23 TRP cc_start: 0.9284 (t-100) cc_final: 0.8873 (t-100) REVERT: A 29 GLU cc_start: 0.9138 (pt0) cc_final: 0.8650 (pt0) REVERT: A 45 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8756 (tm-30) REVERT: A 53 ASN cc_start: 0.9485 (m-40) cc_final: 0.9192 (m110) REVERT: A 55 MET cc_start: 0.9611 (ttp) cc_final: 0.9192 (tmm) REVERT: A 68 MET cc_start: 0.9313 (mtt) cc_final: 0.8916 (mtp) REVERT: A 74 ASN cc_start: 0.9272 (m110) cc_final: 0.9017 (m110) REVERT: A 76 GLU cc_start: 0.9650 (mm-30) cc_final: 0.9333 (mm-30) REVERT: A 97 ARG cc_start: 0.7912 (ptt90) cc_final: 0.7579 (ptt90) REVERT: A 131 LYS cc_start: 0.9603 (mtpt) cc_final: 0.9229 (mttt) REVERT: B 21 ASN cc_start: 0.9483 (m-40) cc_final: 0.9235 (m-40) REVERT: B 28 GLU cc_start: 0.8909 (tt0) cc_final: 0.8695 (tt0) REVERT: B 30 LYS cc_start: 0.9198 (mmtm) cc_final: 0.8861 (mmtm) REVERT: B 35 GLU cc_start: 0.8975 (mp0) cc_final: 0.8471 (mp0) REVERT: B 39 MET cc_start: 0.9161 (tpp) cc_final: 0.8900 (tpt) REVERT: B 43 LEU cc_start: 0.9020 (mt) cc_final: 0.8676 (mt) REVERT: B 50 GLN cc_start: 0.8728 (mt0) cc_final: 0.8467 (mt0) REVERT: B 70 LYS cc_start: 0.9268 (mtmt) cc_final: 0.8944 (mttp) REVERT: B 74 ASN cc_start: 0.9415 (m-40) cc_final: 0.9152 (m-40) REVERT: B 111 LEU cc_start: 0.9023 (tt) cc_final: 0.8674 (tt) REVERT: B 118 MET cc_start: 0.9403 (mmt) cc_final: 0.9172 (mmm) REVERT: B 131 LYS cc_start: 0.9548 (ttmt) cc_final: 0.9270 (tttt) REVERT: B 182 LYS cc_start: 0.9626 (mttt) cc_final: 0.9149 (mttt) REVERT: B 205 LEU cc_start: 0.8140 (mp) cc_final: 0.7092 (mp) REVERT: B 213 GLU cc_start: 0.9562 (tp30) cc_final: 0.9173 (tp30) REVERT: C 25 LYS cc_start: 0.9307 (ptmm) cc_final: 0.9049 (pttm) REVERT: C 51 ASP cc_start: 0.8887 (m-30) cc_final: 0.8670 (m-30) REVERT: C 55 MET cc_start: 0.9540 (ttm) cc_final: 0.9330 (ttp) REVERT: C 76 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8755 (mm-30) REVERT: C 103 ASP cc_start: 0.8713 (m-30) cc_final: 0.8372 (m-30) REVERT: C 131 LYS cc_start: 0.9443 (mtmt) cc_final: 0.9107 (mttt) REVERT: C 192 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8533 (tm-30) REVERT: D 53 ASN cc_start: 0.9392 (m-40) cc_final: 0.9089 (m-40) REVERT: D 103 ASP cc_start: 0.8714 (t0) cc_final: 0.7959 (t0) REVERT: D 114 GLN cc_start: 0.9506 (mm-40) cc_final: 0.8764 (mp10) REVERT: D 118 MET cc_start: 0.8940 (mmp) cc_final: 0.8669 (mmp) REVERT: D 132 ARG cc_start: 0.9451 (ptp-110) cc_final: 0.8951 (ptp-170) REVERT: D 175 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7027 (mm-30) REVERT: D 182 LYS cc_start: 0.9029 (mtpt) cc_final: 0.8292 (mttm) REVERT: D 203 LYS cc_start: 0.8572 (ptmt) cc_final: 0.8226 (pttm) REVERT: G 23 TRP cc_start: 0.9262 (t60) cc_final: 0.8824 (t60) REVERT: G 45 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8332 (mt-10) REVERT: G 57 ASN cc_start: 0.9234 (m-40) cc_final: 0.8954 (m110) REVERT: G 79 GLU cc_start: 0.9287 (tm-30) cc_final: 0.8896 (tm-30) REVERT: G 96 MET cc_start: 0.5405 (mpp) cc_final: 0.2653 (mtp) REVERT: G 132 ARG cc_start: 0.9271 (mtm110) cc_final: 0.8847 (mtm180) REVERT: G 139 ASN cc_start: 0.9594 (m110) cc_final: 0.9378 (m-40) REVERT: G 197 ASP cc_start: 0.9197 (m-30) cc_final: 0.8885 (p0) REVERT: G 215 MET cc_start: 0.7564 (ptp) cc_final: 0.7357 (ptt) REVERT: H 23 TRP cc_start: 0.9137 (t-100) cc_final: 0.8147 (t-100) REVERT: H 50 GLN cc_start: 0.9362 (tt0) cc_final: 0.9154 (pt0) REVERT: H 51 ASP cc_start: 0.8646 (m-30) cc_final: 0.8377 (m-30) REVERT: H 55 MET cc_start: 0.9151 (tpp) cc_final: 0.8845 (tpp) REVERT: H 66 MET cc_start: 0.9332 (mmp) cc_final: 0.8953 (mmm) REVERT: H 70 LYS cc_start: 0.9442 (mttt) cc_final: 0.9196 (mttt) REVERT: H 72 THR cc_start: 0.9532 (m) cc_final: 0.9163 (m) REVERT: H 80 TRP cc_start: 0.8954 (t60) cc_final: 0.8224 (t60) REVERT: H 102 SER cc_start: 0.8685 (m) cc_final: 0.8332 (p) REVERT: H 129 ILE cc_start: 0.9546 (tt) cc_final: 0.9116 (tt) REVERT: H 132 ARG cc_start: 0.9215 (ptp-110) cc_final: 0.8779 (mtm110) REVERT: H 139 ASN cc_start: 0.9325 (m-40) cc_final: 0.9089 (m-40) REVERT: H 140 LYS cc_start: 0.9180 (tptp) cc_final: 0.8952 (tptp) REVERT: H 149 SER cc_start: 0.8869 (t) cc_final: 0.8419 (t) REVERT: H 167 ARG cc_start: 0.8952 (ptm160) cc_final: 0.8685 (ptm160) REVERT: H 168 PHE cc_start: 0.8867 (t80) cc_final: 0.8618 (t80) REVERT: J 53 PHE cc_start: 0.9131 (m-80) cc_final: 0.8761 (m-10) REVERT: J 84 GLU cc_start: 0.8869 (pm20) cc_final: 0.8636 (pm20) REVERT: J 100 MET cc_start: 0.9282 (tpt) cc_final: 0.9015 (tpt) REVERT: J 106 ASN cc_start: 0.9143 (m-40) cc_final: 0.8307 (t0) REVERT: J 138 ILE cc_start: 0.8845 (mm) cc_final: 0.8359 (mm) REVERT: J 139 VAL cc_start: 0.9564 (t) cc_final: 0.9352 (t) REVERT: J 140 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8601 (tp30) REVERT: J 142 MET cc_start: 0.8884 (mtm) cc_final: 0.8536 (mtm) REVERT: N 163 ASP cc_start: 0.9226 (m-30) cc_final: 0.8376 (t0) REVERT: N 167 ARG cc_start: 0.7497 (ptt-90) cc_final: 0.7230 (ptt-90) REVERT: N 181 VAL cc_start: 0.9221 (p) cc_final: 0.8856 (p) REVERT: N 183 ASN cc_start: 0.9304 (m-40) cc_final: 0.9056 (m-40) REVERT: Y 39 MET cc_start: 0.9340 (ttm) cc_final: 0.9108 (ttm) REVERT: Y 50 GLN cc_start: 0.9596 (tm-30) cc_final: 0.9349 (tm-30) REVERT: Y 51 ASP cc_start: 0.9182 (m-30) cc_final: 0.8563 (m-30) REVERT: Y 53 ASN cc_start: 0.9586 (m-40) cc_final: 0.9171 (m-40) REVERT: Y 57 ASN cc_start: 0.9626 (m110) cc_final: 0.9342 (m110) REVERT: Y 67 GLN cc_start: 0.9289 (mt0) cc_final: 0.8604 (mt0) REVERT: Y 74 ASN cc_start: 0.9038 (m110) cc_final: 0.8589 (m110) REVERT: Y 96 MET cc_start: 0.3474 (mpp) cc_final: 0.2346 (mtp) REVERT: Y 114 GLN cc_start: 0.9233 (mt0) cc_final: 0.8751 (mt0) REVERT: Y 117 TRP cc_start: 0.8925 (m-10) cc_final: 0.8522 (m-90) REVERT: Y 131 LYS cc_start: 0.9314 (mtpt) cc_final: 0.9050 (mtpt) REVERT: Y 132 ARG cc_start: 0.9069 (ttp-110) cc_final: 0.8812 (ttm110) REVERT: Y 139 ASN cc_start: 0.9597 (m-40) cc_final: 0.9270 (m110) REVERT: Y 141 ILE cc_start: 0.9645 (mt) cc_final: 0.9420 (mt) REVERT: d 70 LYS cc_start: 0.9496 (tppp) cc_final: 0.9134 (tppp) REVERT: d 71 GLU cc_start: 0.9538 (tt0) cc_final: 0.9274 (tt0) REVERT: d 74 ASN cc_start: 0.9373 (m-40) cc_final: 0.9090 (m110) REVERT: d 97 ARG cc_start: 0.8356 (ptt90) cc_final: 0.7720 (tmm160) REVERT: d 103 ASP cc_start: 0.9042 (t0) cc_final: 0.8763 (t0) REVERT: d 132 ARG cc_start: 0.9354 (ttp-110) cc_final: 0.8748 (mtp-110) REVERT: d 133 TRP cc_start: 0.9303 (m-10) cc_final: 0.8803 (m-10) REVERT: d 139 ASN cc_start: 0.9435 (m110) cc_final: 0.9172 (m110) REVERT: d 182 LYS cc_start: 0.9385 (mtpt) cc_final: 0.9173 (mttp) REVERT: d 214 MET cc_start: 0.8807 (mtp) cc_final: 0.8484 (mpp) REVERT: d 215 MET cc_start: 0.3595 (mtp) cc_final: 0.3297 (tpt) REVERT: e 7 GLN cc_start: 0.8998 (mm110) cc_final: 0.8742 (mm110) REVERT: e 25 LYS cc_start: 0.9309 (pptt) cc_final: 0.8946 (pptt) REVERT: e 74 ASN cc_start: 0.9689 (m-40) cc_final: 0.9385 (m110) REVERT: e 76 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8461 (mm-30) REVERT: e 96 MET cc_start: 0.7146 (mpp) cc_final: 0.5992 (tpp) REVERT: e 128 GLU cc_start: 0.8877 (pm20) cc_final: 0.8378 (pm20) REVERT: e 129 ILE cc_start: 0.9602 (mm) cc_final: 0.9179 (tp) REVERT: e 167 ARG cc_start: 0.9280 (ptm160) cc_final: 0.8906 (ptt180) REVERT: e 169 TYR cc_start: 0.9012 (m-80) cc_final: 0.8326 (m-80) REVERT: e 181 VAL cc_start: 0.9685 (t) cc_final: 0.9471 (t) REVERT: j 162 ARG cc_start: 0.8396 (mmm160) cc_final: 0.8137 (mmm160) REVERT: j 166 ASP cc_start: 0.8493 (m-30) cc_final: 0.8227 (m-30) REVERT: j 175 GLU cc_start: 0.8657 (pp20) cc_final: 0.8239 (pp20) REVERT: j 180 GLU cc_start: 0.9075 (pp20) cc_final: 0.8827 (pm20) REVERT: j 181 VAL cc_start: 0.9501 (t) cc_final: 0.9285 (t) REVERT: j 199 LYS cc_start: 0.9450 (tttt) cc_final: 0.9069 (ttmm) REVERT: k 18 ARG cc_start: 0.8871 (ptm160) cc_final: 0.8564 (ptm160) REVERT: k 25 LYS cc_start: 0.9556 (mttt) cc_final: 0.9231 (ttpp) REVERT: k 29 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8387 (mt-10) REVERT: k 53 ASN cc_start: 0.9256 (m110) cc_final: 0.8910 (m110) REVERT: k 57 ASN cc_start: 0.9441 (m-40) cc_final: 0.9124 (m110) REVERT: k 71 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8638 (mt-10) REVERT: k 76 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8938 (mm-30) REVERT: k 79 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8938 (tm-30) REVERT: k 111 LEU cc_start: 0.8518 (tt) cc_final: 0.8210 (tt) REVERT: k 131 LYS cc_start: 0.9557 (ttmt) cc_final: 0.9280 (ttmt) REVERT: k 132 ARG cc_start: 0.9324 (ptp90) cc_final: 0.8518 (ptp-170) REVERT: k 135 ILE cc_start: 0.9673 (mt) cc_final: 0.9463 (mt) REVERT: k 139 ASN cc_start: 0.9486 (m-40) cc_final: 0.9027 (m110) REVERT: k 164 TYR cc_start: 0.8317 (t80) cc_final: 0.7806 (t80) REVERT: k 187 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8884 (tm-30) REVERT: k 213 GLU cc_start: 0.9171 (mp0) cc_final: 0.8596 (mp0) REVERT: k 214 MET cc_start: 0.9468 (mtm) cc_final: 0.9201 (mtm) outliers start: 4 outliers final: 0 residues processed: 887 average time/residue: 0.1751 time to fit residues: 218.8028 Evaluate side-chains 712 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 712 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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: 10.0000 chunk 233 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 138 optimal weight: 40.0000 chunk 74 optimal weight: 9.9990 chunk 131 optimal weight: 30.0000 chunk 84 optimal weight: 0.6980 chunk 210 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 4 GLN C 53 ASN C 176 GLN D 74 ASN ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN H 183 ASN J 35 ASN ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 ASN d 50 GLN ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 195 ASN j 192 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 GLN k 193 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.086409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.066263 restraints weight = 71215.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.068182 restraints weight = 45093.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.069536 restraints weight = 32654.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.070465 restraints weight = 25857.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.071143 restraints weight = 21917.242| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.6914 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= 0.176 Angle : 0.722 15.517 25587 Z= 0.374 Chirality : 0.047 0.262 2848 Planarity : 0.006 0.065 3345 Dihedral : 4.636 24.342 2500 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.20 % Allowed : 2.55 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.17), residues: 2338 helix: 0.25 (0.13), residues: 1477 sheet: -1.26 (0.58), residues: 69 loop : -0.29 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG e 154 TYR 0.019 0.002 TYR B 145 PHE 0.027 0.002 PHE N 168 TRP 0.029 0.002 TRP H 117 HIS 0.007 0.001 HIS J 54 Details of bonding type rmsd covalent geometry : bond 0.00397 (18824) covalent geometry : angle 0.72059 (25567) SS BOND : bond 0.00286 ( 10) SS BOND : angle 1.53588 ( 20) hydrogen bonds : bond 0.04383 ( 1037) hydrogen bonds : angle 4.72539 ( 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 877 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 873 time to evaluate : 0.719 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: A 21 ASN cc_start: 0.9484 (t0) cc_final: 0.9226 (t0) REVERT: A 23 TRP cc_start: 0.9374 (t-100) cc_final: 0.8927 (t-100) REVERT: A 25 LYS cc_start: 0.9684 (tttt) cc_final: 0.9128 (ttmm) REVERT: A 29 GLU cc_start: 0.9064 (pt0) cc_final: 0.8707 (pt0) REVERT: A 45 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8710 (tm-30) REVERT: A 50 GLN cc_start: 0.9115 (pm20) cc_final: 0.8847 (pm20) REVERT: A 52 LEU cc_start: 0.9850 (mt) cc_final: 0.9594 (mt) REVERT: A 53 ASN cc_start: 0.9490 (m-40) cc_final: 0.9155 (m110) REVERT: A 55 MET cc_start: 0.9617 (ttp) cc_final: 0.9305 (tmm) REVERT: A 68 MET cc_start: 0.9278 (mtt) cc_final: 0.8984 (mtp) REVERT: A 76 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9324 (mm-30) REVERT: B 18 ARG cc_start: 0.8981 (mtm-85) cc_final: 0.8679 (mtm-85) REVERT: B 21 ASN cc_start: 0.9474 (m-40) cc_final: 0.9220 (m-40) REVERT: B 30 LYS cc_start: 0.9272 (mmtm) cc_final: 0.9013 (mmtp) REVERT: B 33 SER cc_start: 0.9311 (t) cc_final: 0.9073 (t) REVERT: B 39 MET cc_start: 0.9110 (tpp) cc_final: 0.8803 (tpt) REVERT: B 43 LEU cc_start: 0.9009 (mt) cc_final: 0.8541 (mt) REVERT: B 50 GLN cc_start: 0.8791 (mt0) cc_final: 0.8455 (mt0) REVERT: B 51 ASP cc_start: 0.9027 (m-30) cc_final: 0.8809 (m-30) REVERT: B 70 LYS cc_start: 0.9251 (mtmt) cc_final: 0.8958 (mttp) REVERT: B 74 ASN cc_start: 0.9390 (m-40) cc_final: 0.9145 (m110) REVERT: B 111 LEU cc_start: 0.9071 (tt) cc_final: 0.8717 (tt) REVERT: B 131 LYS cc_start: 0.9542 (ttmt) cc_final: 0.9222 (tttt) REVERT: B 153 ILE cc_start: 0.8954 (tp) cc_final: 0.8557 (tp) REVERT: B 167 ARG cc_start: 0.9335 (mtm110) cc_final: 0.8989 (ptm-80) REVERT: B 179 GLN cc_start: 0.9133 (pp30) cc_final: 0.8862 (pp30) REVERT: B 182 LYS cc_start: 0.9661 (mttt) cc_final: 0.9173 (mttt) REVERT: B 205 LEU cc_start: 0.8214 (mp) cc_final: 0.7256 (mp) REVERT: B 213 GLU cc_start: 0.9535 (tp30) cc_final: 0.9166 (tp30) REVERT: C 25 LYS cc_start: 0.9273 (ptmm) cc_final: 0.9027 (pttm) REVERT: C 55 MET cc_start: 0.9560 (ttm) cc_final: 0.9312 (ttp) REVERT: C 103 ASP cc_start: 0.8698 (m-30) cc_final: 0.8304 (m-30) REVERT: C 131 LYS cc_start: 0.9424 (mtmt) cc_final: 0.9147 (mttt) REVERT: C 192 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8512 (tm-30) REVERT: C 219 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8529 (tm-30) REVERT: D 53 ASN cc_start: 0.9423 (m-40) cc_final: 0.9039 (m-40) REVERT: D 103 ASP cc_start: 0.8713 (t0) cc_final: 0.8007 (t0) REVERT: D 114 GLN cc_start: 0.9495 (mm-40) cc_final: 0.8717 (mp10) REVERT: D 118 MET cc_start: 0.8916 (mmp) cc_final: 0.8577 (mmp) REVERT: D 132 ARG cc_start: 0.9484 (ptp-110) cc_final: 0.9011 (ptp-170) REVERT: D 141 ILE cc_start: 0.9703 (mt) cc_final: 0.9501 (pt) REVERT: D 143 ARG cc_start: 0.7782 (tpm170) cc_final: 0.7465 (tpm170) REVERT: D 182 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8320 (mttm) REVERT: D 213 GLU cc_start: 0.9286 (mp0) cc_final: 0.9080 (mp0) REVERT: G 57 ASN cc_start: 0.9219 (m-40) cc_final: 0.8885 (m110) REVERT: G 79 GLU cc_start: 0.9292 (tm-30) cc_final: 0.8635 (tm-30) REVERT: G 96 MET cc_start: 0.5358 (mpp) cc_final: 0.2651 (mtp) REVERT: G 103 ASP cc_start: 0.9342 (m-30) cc_final: 0.9073 (m-30) REVERT: G 111 LEU cc_start: 0.9434 (tt) cc_final: 0.9117 (tt) REVERT: G 182 LYS cc_start: 0.9383 (tttt) cc_final: 0.9182 (mtpp) REVERT: G 197 ASP cc_start: 0.9163 (m-30) cc_final: 0.8863 (p0) REVERT: H 23 TRP cc_start: 0.9208 (t-100) cc_final: 0.8234 (t-100) REVERT: H 51 ASP cc_start: 0.8768 (m-30) cc_final: 0.8536 (m-30) REVERT: H 55 MET cc_start: 0.9204 (tpp) cc_final: 0.8930 (tpp) REVERT: H 80 TRP cc_start: 0.8751 (t60) cc_final: 0.8219 (t60) REVERT: H 86 VAL cc_start: 0.7334 (p) cc_final: 0.7067 (t) REVERT: H 102 SER cc_start: 0.9088 (m) cc_final: 0.8772 (t) REVERT: H 139 ASN cc_start: 0.9270 (m-40) cc_final: 0.9001 (m-40) REVERT: H 140 LYS cc_start: 0.9110 (tptp) cc_final: 0.8906 (tptp) REVERT: H 143 ARG cc_start: 0.8705 (mtm-85) cc_final: 0.8378 (mtm-85) REVERT: H 149 SER cc_start: 0.8873 (t) cc_final: 0.8414 (t) REVERT: H 167 ARG cc_start: 0.8936 (ptm160) cc_final: 0.8701 (ptm160) REVERT: J 35 ASN cc_start: 0.9667 (t0) cc_final: 0.9231 (t0) REVERT: J 36 PHE cc_start: 0.9443 (t80) cc_final: 0.9047 (t80) REVERT: J 39 LEU cc_start: 0.9396 (mt) cc_final: 0.8737 (mt) REVERT: J 53 PHE cc_start: 0.9100 (m-80) cc_final: 0.8422 (m-80) REVERT: J 106 ASN cc_start: 0.9197 (m-40) cc_final: 0.8439 (t0) REVERT: J 112 PHE cc_start: 0.9298 (p90) cc_final: 0.8996 (p90) REVERT: J 138 ILE cc_start: 0.8840 (mm) cc_final: 0.7935 (mm) REVERT: J 139 VAL cc_start: 0.9616 (t) cc_final: 0.9364 (t) REVERT: J 140 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8606 (tp30) REVERT: J 142 MET cc_start: 0.8755 (mtm) cc_final: 0.8434 (mtm) REVERT: N 163 ASP cc_start: 0.9227 (m-30) cc_final: 0.8337 (t0) REVERT: N 167 ARG cc_start: 0.7558 (ptt-90) cc_final: 0.7192 (ptt-90) REVERT: N 183 ASN cc_start: 0.9264 (m-40) cc_final: 0.8992 (m-40) REVERT: N 211 LEU cc_start: 0.8811 (tt) cc_final: 0.8581 (tt) REVERT: Y 39 MET cc_start: 0.9222 (ttm) cc_final: 0.8962 (ttm) REVERT: Y 50 GLN cc_start: 0.9617 (tm-30) cc_final: 0.9318 (tm-30) REVERT: Y 51 ASP cc_start: 0.9208 (m-30) cc_final: 0.8461 (m-30) REVERT: Y 52 LEU cc_start: 0.9710 (mt) cc_final: 0.9470 (mt) REVERT: Y 53 ASN cc_start: 0.9574 (m-40) cc_final: 0.9227 (m-40) REVERT: Y 57 ASN cc_start: 0.9628 (m110) cc_final: 0.9367 (m-40) REVERT: Y 70 LYS cc_start: 0.9408 (tptp) cc_final: 0.9088 (tppt) REVERT: Y 74 ASN cc_start: 0.8992 (m110) cc_final: 0.8547 (m110) REVERT: Y 96 MET cc_start: 0.3354 (mpp) cc_final: 0.2732 (mtp) REVERT: Y 114 GLN cc_start: 0.9242 (mt0) cc_final: 0.8780 (mt0) REVERT: Y 117 TRP cc_start: 0.8934 (m-10) cc_final: 0.8514 (m-90) REVERT: Y 139 ASN cc_start: 0.9597 (m-40) cc_final: 0.9262 (m110) REVERT: d 67 GLN cc_start: 0.9287 (mt0) cc_final: 0.8633 (mt0) REVERT: d 97 ARG cc_start: 0.8348 (ptt90) cc_final: 0.7740 (tmm160) REVERT: d 112 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8983 (mm-40) REVERT: d 128 GLU cc_start: 0.9391 (mp0) cc_final: 0.9183 (mp0) REVERT: d 132 ARG cc_start: 0.9330 (ttp-110) cc_final: 0.8683 (mtp-110) REVERT: d 133 TRP cc_start: 0.9298 (m-10) cc_final: 0.8789 (m-10) REVERT: d 136 LEU cc_start: 0.9515 (tp) cc_final: 0.9272 (tp) REVERT: d 139 ASN cc_start: 0.9465 (m110) cc_final: 0.9196 (m110) REVERT: d 167 ARG cc_start: 0.9365 (ptm160) cc_final: 0.9105 (ptm160) REVERT: d 182 LYS cc_start: 0.9399 (mtpt) cc_final: 0.9189 (mttp) REVERT: e 10 MET cc_start: 0.8529 (mmp) cc_final: 0.8152 (tpp) REVERT: e 25 LYS cc_start: 0.9353 (pptt) cc_final: 0.9121 (pptt) REVERT: e 57 ASN cc_start: 0.9420 (m110) cc_final: 0.9183 (m110) REVERT: e 76 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8688 (mm-30) REVERT: e 96 MET cc_start: 0.7101 (mpp) cc_final: 0.6055 (tpt) REVERT: e 129 ILE cc_start: 0.9455 (mm) cc_final: 0.9110 (mm) REVERT: e 167 ARG cc_start: 0.9263 (ptm160) cc_final: 0.8886 (ptt180) REVERT: e 181 VAL cc_start: 0.9648 (t) cc_final: 0.9446 (t) REVERT: j 162 ARG cc_start: 0.8293 (mmm160) cc_final: 0.8014 (mmt180) REVERT: j 166 ASP cc_start: 0.8412 (m-30) cc_final: 0.8105 (m-30) REVERT: j 181 VAL cc_start: 0.9604 (t) cc_final: 0.9279 (t) REVERT: k 18 ARG cc_start: 0.8857 (ptm-80) cc_final: 0.8641 (ptm160) REVERT: k 25 LYS cc_start: 0.9529 (mttt) cc_final: 0.9187 (ttpp) REVERT: k 29 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8312 (mt-10) REVERT: k 53 ASN cc_start: 0.9230 (m110) cc_final: 0.8859 (m110) REVERT: k 57 ASN cc_start: 0.9441 (m-40) cc_final: 0.9130 (m110) REVERT: k 71 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8586 (mt-10) REVERT: k 76 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8940 (mm-30) REVERT: k 79 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8946 (tm-30) REVERT: k 131 LYS cc_start: 0.9549 (ttmt) cc_final: 0.9266 (ttmt) REVERT: k 135 ILE cc_start: 0.9669 (mt) cc_final: 0.9451 (mt) REVERT: k 139 ASN cc_start: 0.9490 (m-40) cc_final: 0.9022 (m110) REVERT: k 164 TYR cc_start: 0.8261 (t80) cc_final: 0.7559 (t80) REVERT: k 179 GLN cc_start: 0.9057 (tp-100) cc_final: 0.8782 (tp-100) REVERT: k 213 GLU cc_start: 0.8996 (mp0) cc_final: 0.8446 (mp0) outliers start: 4 outliers final: 0 residues processed: 875 average time/residue: 0.1780 time to fit residues: 219.4631 Evaluate side-chains 715 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 715 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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: 7.9990 chunk 135 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 171 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 chunk 208 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN C 53 ASN C 176 GLN D 74 ASN ** J 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS ** Y 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 193 ASN ** k 112 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 = 0.3583 r_free = 0.3583 target = 0.086326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065832 restraints weight = 72015.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.067756 restraints weight = 46039.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.069126 restraints weight = 33528.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070068 restraints weight = 26675.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.070749 restraints weight = 22647.977| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.7161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18834 Z= 0.166 Angle : 0.733 14.806 25587 Z= 0.379 Chirality : 0.048 0.298 2848 Planarity : 0.006 0.072 3345 Dihedral : 4.650 24.105 2500 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.05 % Allowed : 1.35 % Favored : 98.60 % 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: -0.18 (0.17), residues: 2338 helix: 0.17 (0.13), residues: 1475 sheet: -1.26 (0.58), residues: 69 loop : -0.28 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 132 TYR 0.030 0.002 TYR D 169 PHE 0.023 0.002 PHE N 168 TRP 0.041 0.002 TRP G 23 HIS 0.004 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00378 (18824) covalent geometry : angle 0.73221 (25567) SS BOND : bond 0.00259 ( 10) SS BOND : angle 1.50652 ( 20) hydrogen bonds : bond 0.04528 ( 1037) hydrogen bonds : angle 4.75943 ( 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 871 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 870 time to evaluate : 0.677 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: A 23 TRP cc_start: 0.9314 (t-100) cc_final: 0.8897 (t-100) REVERT: A 29 GLU cc_start: 0.9162 (pt0) cc_final: 0.8590 (pt0) REVERT: A 45 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8682 (tm-30) REVERT: A 50 GLN cc_start: 0.9116 (pm20) cc_final: 0.8876 (pm20) REVERT: A 52 LEU cc_start: 0.9860 (mt) cc_final: 0.9614 (mt) REVERT: A 53 ASN cc_start: 0.9472 (m-40) cc_final: 0.9166 (m110) REVERT: A 55 MET cc_start: 0.9627 (ttp) cc_final: 0.9327 (tmm) REVERT: A 68 MET cc_start: 0.9272 (mtt) cc_final: 0.9027 (mtp) REVERT: A 74 ASN cc_start: 0.9310 (m110) cc_final: 0.9052 (m110) REVERT: A 76 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9198 (mm-30) REVERT: A 103 ASP cc_start: 0.8434 (m-30) cc_final: 0.8186 (m-30) REVERT: B 21 ASN cc_start: 0.9482 (m-40) cc_final: 0.9221 (m-40) REVERT: B 30 LYS cc_start: 0.9280 (mmtm) cc_final: 0.9015 (mmtp) REVERT: B 33 SER cc_start: 0.9266 (t) cc_final: 0.8984 (t) REVERT: B 39 MET cc_start: 0.9133 (tpp) cc_final: 0.8813 (tpt) REVERT: B 43 LEU cc_start: 0.9003 (mt) cc_final: 0.8490 (mt) REVERT: B 50 GLN cc_start: 0.8819 (mt0) cc_final: 0.8488 (mt0) REVERT: B 70 LYS cc_start: 0.9246 (mtmt) cc_final: 0.8879 (mttp) REVERT: B 74 ASN cc_start: 0.9356 (m-40) cc_final: 0.9110 (m110) REVERT: B 111 LEU cc_start: 0.9093 (tt) cc_final: 0.8738 (tt) REVERT: B 131 LYS cc_start: 0.9586 (ttmt) cc_final: 0.9242 (tttt) REVERT: B 139 ASN cc_start: 0.9457 (m-40) cc_final: 0.9200 (m110) REVERT: B 167 ARG cc_start: 0.9321 (mtm110) cc_final: 0.8947 (ptm-80) REVERT: B 179 GLN cc_start: 0.9130 (pp30) cc_final: 0.8851 (pp30) REVERT: B 182 LYS cc_start: 0.9654 (mttt) cc_final: 0.9244 (mttt) REVERT: B 205 LEU cc_start: 0.8246 (mp) cc_final: 0.7764 (mp) REVERT: C 25 LYS cc_start: 0.9263 (ptmm) cc_final: 0.9011 (ptpp) REVERT: C 55 MET cc_start: 0.9570 (ttm) cc_final: 0.9349 (ttp) REVERT: C 103 ASP cc_start: 0.8736 (m-30) cc_final: 0.8310 (m-30) REVERT: C 131 LYS cc_start: 0.9416 (mtmt) cc_final: 0.9126 (mttt) REVERT: C 154 ARG cc_start: 0.8858 (mmm160) cc_final: 0.8577 (mmm160) REVERT: C 219 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8531 (tm-30) REVERT: D 53 ASN cc_start: 0.9373 (m-40) cc_final: 0.9113 (m-40) REVERT: D 103 ASP cc_start: 0.8718 (t0) cc_final: 0.7807 (t0) REVERT: D 111 LEU cc_start: 0.9166 (tp) cc_final: 0.8960 (tp) REVERT: D 114 GLN cc_start: 0.9503 (mm-40) cc_final: 0.8965 (mp10) REVERT: D 132 ARG cc_start: 0.9471 (ptp-110) cc_final: 0.8984 (ptp-170) REVERT: D 141 ILE cc_start: 0.9689 (mt) cc_final: 0.9482 (pt) REVERT: D 182 LYS cc_start: 0.9068 (mtpt) cc_final: 0.8329 (mttm) REVERT: D 203 LYS cc_start: 0.8224 (ptmt) cc_final: 0.7845 (pttm) REVERT: D 214 MET cc_start: 0.8924 (mpp) cc_final: 0.8605 (mpp) REVERT: G 23 TRP cc_start: 0.9060 (t60) cc_final: 0.8841 (t60) REVERT: G 57 ASN cc_start: 0.9243 (m-40) cc_final: 0.8919 (m110) REVERT: G 79 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8716 (tm-30) REVERT: G 96 MET cc_start: 0.5393 (mpp) cc_final: 0.2709 (mtp) REVERT: G 197 ASP cc_start: 0.9117 (m-30) cc_final: 0.8885 (p0) REVERT: G 203 LYS cc_start: 0.9397 (mttp) cc_final: 0.9092 (mttp) REVERT: H 23 TRP cc_start: 0.9233 (t-100) cc_final: 0.8319 (t-100) REVERT: H 51 ASP cc_start: 0.8767 (m-30) cc_final: 0.8554 (m-30) REVERT: H 55 MET cc_start: 0.9205 (tpp) cc_final: 0.8960 (tpp) REVERT: H 66 MET cc_start: 0.9308 (mmp) cc_final: 0.8850 (mmm) REVERT: H 80 TRP cc_start: 0.8780 (t60) cc_final: 0.8315 (t60) REVERT: H 86 VAL cc_start: 0.7120 (p) cc_final: 0.6887 (t) REVERT: H 102 SER cc_start: 0.9210 (m) cc_final: 0.8728 (t) REVERT: H 139 ASN cc_start: 0.9234 (m-40) cc_final: 0.8954 (m-40) REVERT: H 149 SER cc_start: 0.8847 (t) cc_final: 0.8405 (t) REVERT: H 167 ARG cc_start: 0.8969 (ptm160) cc_final: 0.8732 (ptm160) REVERT: J 22 PHE cc_start: 0.8677 (m-10) cc_final: 0.8470 (m-10) REVERT: J 35 ASN cc_start: 0.9670 (t0) cc_final: 0.9341 (t0) REVERT: J 36 PHE cc_start: 0.9423 (t80) cc_final: 0.8960 (t80) REVERT: J 39 LEU cc_start: 0.9423 (mt) cc_final: 0.8730 (mt) REVERT: J 53 PHE cc_start: 0.9031 (m-80) cc_final: 0.8429 (m-80) REVERT: J 84 GLU cc_start: 0.8990 (pm20) cc_final: 0.8164 (pm20) REVERT: J 100 MET cc_start: 0.9226 (tpt) cc_final: 0.8946 (tpt) REVERT: J 106 ASN cc_start: 0.9215 (m-40) cc_final: 0.8495 (t0) REVERT: J 112 PHE cc_start: 0.9260 (p90) cc_final: 0.9035 (p90) REVERT: J 122 LEU cc_start: 0.9214 (mt) cc_final: 0.8998 (mt) REVERT: J 138 ILE cc_start: 0.8733 (mm) cc_final: 0.8021 (mm) REVERT: J 139 VAL cc_start: 0.9557 (t) cc_final: 0.9330 (t) REVERT: J 140 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8604 (tp30) REVERT: J 142 MET cc_start: 0.8694 (mtm) cc_final: 0.8389 (mtm) REVERT: N 163 ASP cc_start: 0.9281 (m-30) cc_final: 0.8317 (t0) REVERT: N 167 ARG cc_start: 0.7510 (ptt-90) cc_final: 0.7245 (ptt-90) REVERT: N 183 ASN cc_start: 0.9244 (m-40) cc_final: 0.8992 (m-40) REVERT: Y 25 LYS cc_start: 0.9220 (tmmt) cc_final: 0.8900 (tmmt) REVERT: Y 50 GLN cc_start: 0.9620 (tm-30) cc_final: 0.9340 (tm-30) REVERT: Y 51 ASP cc_start: 0.9209 (m-30) cc_final: 0.8564 (m-30) REVERT: Y 53 ASN cc_start: 0.9585 (m-40) cc_final: 0.9211 (m-40) REVERT: Y 57 ASN cc_start: 0.9616 (m110) cc_final: 0.9405 (m-40) REVERT: Y 67 GLN cc_start: 0.9272 (mt0) cc_final: 0.8384 (mt0) REVERT: Y 70 LYS cc_start: 0.9466 (tptp) cc_final: 0.9126 (tppt) REVERT: Y 74 ASN cc_start: 0.9047 (m110) cc_final: 0.8592 (m110) REVERT: Y 96 MET cc_start: 0.3369 (mpp) cc_final: 0.2724 (mtp) REVERT: Y 114 GLN cc_start: 0.9232 (mt0) cc_final: 0.8897 (mt0) REVERT: Y 117 TRP cc_start: 0.9011 (m-10) cc_final: 0.8568 (m-90) REVERT: Y 131 LYS cc_start: 0.9253 (mtpt) cc_final: 0.9026 (mtpt) REVERT: Y 139 ASN cc_start: 0.9597 (m-40) cc_final: 0.9278 (m110) REVERT: d 39 MET cc_start: 0.8695 (tpt) cc_final: 0.8386 (tpp) REVERT: d 57 ASN cc_start: 0.9305 (m-40) cc_final: 0.8492 (t0) REVERT: d 58 THR cc_start: 0.8692 (p) cc_final: 0.8433 (p) REVERT: d 67 GLN cc_start: 0.9373 (mt0) cc_final: 0.9136 (mt0) REVERT: d 74 ASN cc_start: 0.9309 (m-40) cc_final: 0.9060 (m110) REVERT: d 97 ARG cc_start: 0.8241 (ptt90) cc_final: 0.7701 (tmm160) REVERT: d 112 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8796 (mm-40) REVERT: d 129 ILE cc_start: 0.9217 (mt) cc_final: 0.8990 (mt) REVERT: d 132 ARG cc_start: 0.9319 (ttp-110) cc_final: 0.9055 (mtp-110) REVERT: d 136 LEU cc_start: 0.9481 (tp) cc_final: 0.9251 (tp) REVERT: d 139 ASN cc_start: 0.9446 (m110) cc_final: 0.9168 (m110) REVERT: d 167 ARG cc_start: 0.9370 (ptm160) cc_final: 0.9117 (ptt180) REVERT: d 182 LYS cc_start: 0.9428 (mtpt) cc_final: 0.9200 (mttp) REVERT: e 76 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8851 (mm-30) REVERT: e 96 MET cc_start: 0.7179 (mpp) cc_final: 0.6110 (tpt) REVERT: e 167 ARG cc_start: 0.9244 (ptm160) cc_final: 0.8868 (ptt180) REVERT: e 169 TYR cc_start: 0.8896 (m-80) cc_final: 0.8597 (m-80) REVERT: j 162 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7760 (mmm160) REVERT: j 166 ASP cc_start: 0.8457 (m-30) cc_final: 0.7973 (m-30) REVERT: j 175 GLU cc_start: 0.8763 (pp20) cc_final: 0.8518 (pp20) REVERT: j 181 VAL cc_start: 0.9726 (t) cc_final: 0.9492 (p) REVERT: j 183 ASN cc_start: 0.9669 (m110) cc_final: 0.9183 (m-40) REVERT: k 25 LYS cc_start: 0.9543 (mttt) cc_final: 0.9273 (ttpp) REVERT: k 29 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8307 (mt-10) REVERT: k 53 ASN cc_start: 0.9178 (m110) cc_final: 0.8846 (m110) REVERT: k 57 ASN cc_start: 0.9443 (m-40) cc_final: 0.9133 (m110) REVERT: k 70 LYS cc_start: 0.9417 (mtmm) cc_final: 0.9046 (mtmm) REVERT: k 71 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8474 (mt-10) REVERT: k 76 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8951 (mm-30) REVERT: k 79 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8931 (tm-30) REVERT: k 131 LYS cc_start: 0.9547 (ttmt) cc_final: 0.9231 (ttmt) REVERT: k 135 ILE cc_start: 0.9669 (mt) cc_final: 0.9450 (mt) REVERT: k 139 ASN cc_start: 0.9490 (m-40) cc_final: 0.9064 (m110) REVERT: k 159 GLU cc_start: 0.8432 (tt0) cc_final: 0.8083 (mt-10) REVERT: k 164 TYR cc_start: 0.8322 (t80) cc_final: 0.7582 (t80) REVERT: k 179 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8789 (tp-100) REVERT: k 213 GLU cc_start: 0.9005 (mp0) cc_final: 0.8531 (mp0) outliers start: 1 outliers final: 0 residues processed: 871 average time/residue: 0.1712 time to fit residues: 210.2816 Evaluate side-chains 699 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 699 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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: 0.0870 chunk 207 optimal weight: 10.0000 chunk 28 optimal weight: 0.2980 chunk 125 optimal weight: 40.0000 chunk 226 optimal weight: 0.9980 chunk 230 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 overall best weight: 1.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN B 176 GLN C 53 ASN C 176 GLN D 74 ASN H 183 ASN ** J 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 GLN ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 84 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.087785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.067171 restraints weight = 70358.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.069103 restraints weight = 45065.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.070457 restraints weight = 32841.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.071411 restraints weight = 26150.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.072095 restraints weight = 22181.555| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.7310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18834 Z= 0.143 Angle : 0.714 14.753 25587 Z= 0.367 Chirality : 0.047 0.247 2848 Planarity : 0.006 0.095 3345 Dihedral : 4.587 24.861 2500 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.05 % Allowed : 1.15 % Favored : 98.80 % 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: -0.03 (0.17), residues: 2338 helix: 0.29 (0.13), residues: 1456 sheet: -1.20 (0.56), residues: 69 loop : -0.22 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 143 TYR 0.021 0.002 TYR B 145 PHE 0.029 0.002 PHE C 168 TRP 0.025 0.001 TRP d 133 HIS 0.006 0.001 HIS e 84 Details of bonding type rmsd covalent geometry : bond 0.00322 (18824) covalent geometry : angle 0.71344 (25567) SS BOND : bond 0.00191 ( 10) SS BOND : angle 1.33259 ( 20) hydrogen bonds : bond 0.04268 ( 1037) hydrogen bonds : angle 4.66670 ( 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 878 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 877 time to evaluate : 0.694 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: A 23 TRP cc_start: 0.9312 (t-100) cc_final: 0.8950 (t-100) REVERT: A 29 GLU cc_start: 0.9128 (pt0) cc_final: 0.8480 (pt0) REVERT: A 50 GLN cc_start: 0.9188 (pm20) cc_final: 0.8870 (pm20) REVERT: A 52 LEU cc_start: 0.9858 (mt) cc_final: 0.9644 (mt) REVERT: A 53 ASN cc_start: 0.9432 (m-40) cc_final: 0.9118 (m110) REVERT: A 68 MET cc_start: 0.9211 (mtt) cc_final: 0.8918 (mtp) REVERT: A 74 ASN cc_start: 0.9293 (m110) cc_final: 0.9085 (m110) REVERT: A 76 GLU cc_start: 0.9671 (mm-30) cc_final: 0.9267 (mm-30) REVERT: A 131 LYS cc_start: 0.9624 (mtpt) cc_final: 0.9382 (mttt) REVERT: B 18 ARG cc_start: 0.8964 (mtm-85) cc_final: 0.8658 (mtm-85) REVERT: B 21 ASN cc_start: 0.9455 (m-40) cc_final: 0.9201 (m-40) REVERT: B 30 LYS cc_start: 0.9286 (mmtm) cc_final: 0.8746 (mmtm) REVERT: B 33 SER cc_start: 0.9222 (t) cc_final: 0.8837 (t) REVERT: B 35 GLU cc_start: 0.8919 (mp0) cc_final: 0.8654 (mp0) REVERT: B 39 MET cc_start: 0.9103 (tpp) cc_final: 0.8817 (tpt) REVERT: B 43 LEU cc_start: 0.8972 (mt) cc_final: 0.8438 (mt) REVERT: B 66 MET cc_start: 0.8785 (mmm) cc_final: 0.8339 (mmm) REVERT: B 70 LYS cc_start: 0.9241 (mtmt) cc_final: 0.8904 (ttmm) REVERT: B 74 ASN cc_start: 0.9341 (m-40) cc_final: 0.9093 (m110) REVERT: B 79 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8842 (mm-30) REVERT: B 111 LEU cc_start: 0.9102 (tt) cc_final: 0.8620 (tt) REVERT: B 131 LYS cc_start: 0.9587 (ttmt) cc_final: 0.9214 (tttt) REVERT: B 139 ASN cc_start: 0.9431 (m-40) cc_final: 0.9227 (m110) REVERT: B 153 ILE cc_start: 0.8975 (tp) cc_final: 0.8764 (tp) REVERT: B 154 ARG cc_start: 0.9169 (tpp80) cc_final: 0.8845 (tpp80) REVERT: B 167 ARG cc_start: 0.9337 (mtm110) cc_final: 0.8941 (ptm-80) REVERT: B 179 GLN cc_start: 0.9151 (pp30) cc_final: 0.8881 (pp30) REVERT: B 182 LYS cc_start: 0.9685 (mttt) cc_final: 0.9365 (mtpp) REVERT: B 183 ASN cc_start: 0.9461 (m-40) cc_final: 0.8822 (m110) REVERT: C 55 MET cc_start: 0.9578 (ttm) cc_final: 0.9377 (ttp) REVERT: C 103 ASP cc_start: 0.8751 (m-30) cc_final: 0.8315 (m-30) REVERT: C 131 LYS cc_start: 0.9395 (mtmt) cc_final: 0.9099 (mttt) REVERT: C 219 GLN cc_start: 0.8832 (tp-100) cc_final: 0.8498 (tm-30) REVERT: D 53 ASN cc_start: 0.9432 (m-40) cc_final: 0.8958 (m-40) REVERT: D 57 ASN cc_start: 0.9516 (m-40) cc_final: 0.9188 (m-40) REVERT: D 103 ASP cc_start: 0.8650 (t0) cc_final: 0.7663 (t0) REVERT: D 111 LEU cc_start: 0.9220 (tp) cc_final: 0.8736 (mm) REVERT: D 114 GLN cc_start: 0.9452 (mm-40) cc_final: 0.8941 (mp10) REVERT: D 132 ARG cc_start: 0.9519 (ptp-110) cc_final: 0.9057 (ptp-170) REVERT: D 141 ILE cc_start: 0.9685 (mt) cc_final: 0.9474 (pt) REVERT: D 182 LYS cc_start: 0.9095 (mtpt) cc_final: 0.8345 (mttm) REVERT: D 203 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7764 (pttm) REVERT: G 57 ASN cc_start: 0.9175 (m-40) cc_final: 0.8785 (m110) REVERT: G 79 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8900 (tm-30) REVERT: G 96 MET cc_start: 0.5313 (mpp) cc_final: 0.2413 (mtp) REVERT: G 182 LYS cc_start: 0.9424 (mtpt) cc_final: 0.8998 (mtpp) REVERT: H 23 TRP cc_start: 0.9251 (t-100) cc_final: 0.8578 (t-100) REVERT: H 51 ASP cc_start: 0.8726 (m-30) cc_final: 0.8524 (m-30) REVERT: H 55 MET cc_start: 0.9209 (tpp) cc_final: 0.9007 (tpp) REVERT: H 66 MET cc_start: 0.9351 (mmp) cc_final: 0.8829 (mmm) REVERT: H 80 TRP cc_start: 0.8699 (t60) cc_final: 0.8224 (t60) REVERT: H 102 SER cc_start: 0.9252 (m) cc_final: 0.8902 (t) REVERT: H 149 SER cc_start: 0.8810 (t) cc_final: 0.8356 (t) REVERT: H 167 ARG cc_start: 0.8938 (ptm160) cc_final: 0.8673 (ptm160) REVERT: J 39 LEU cc_start: 0.9411 (mt) cc_final: 0.9178 (mt) REVERT: J 53 PHE cc_start: 0.8951 (m-80) cc_final: 0.8573 (m-10) REVERT: J 84 GLU cc_start: 0.9042 (pm20) cc_final: 0.8117 (pm20) REVERT: J 106 ASN cc_start: 0.9277 (m-40) cc_final: 0.8466 (t0) REVERT: J 122 LEU cc_start: 0.9153 (mt) cc_final: 0.8949 (mt) REVERT: J 138 ILE cc_start: 0.8763 (mm) cc_final: 0.7991 (mm) REVERT: J 140 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8402 (tp30) REVERT: J 142 MET cc_start: 0.8621 (mtm) cc_final: 0.8311 (mtm) REVERT: N 163 ASP cc_start: 0.9262 (m-30) cc_final: 0.8369 (t0) REVERT: N 183 ASN cc_start: 0.9258 (m-40) cc_final: 0.8984 (m-40) REVERT: Y 50 GLN cc_start: 0.9607 (tm-30) cc_final: 0.9310 (tm-30) REVERT: Y 51 ASP cc_start: 0.9218 (m-30) cc_final: 0.8540 (m-30) REVERT: Y 53 ASN cc_start: 0.9550 (m-40) cc_final: 0.9119 (m-40) REVERT: Y 67 GLN cc_start: 0.9275 (mt0) cc_final: 0.8329 (mt0) REVERT: Y 70 LYS cc_start: 0.9494 (tptp) cc_final: 0.9137 (tppt) REVERT: Y 74 ASN cc_start: 0.9052 (m110) cc_final: 0.8660 (m110) REVERT: Y 75 GLU cc_start: 0.9248 (pt0) cc_final: 0.8677 (pp20) REVERT: Y 96 MET cc_start: 0.3273 (mpp) cc_final: 0.2638 (mtp) REVERT: Y 114 GLN cc_start: 0.9302 (mt0) cc_final: 0.8928 (mt0) REVERT: Y 117 TRP cc_start: 0.8945 (m-10) cc_final: 0.8495 (m-90) REVERT: Y 128 GLU cc_start: 0.9014 (pp20) cc_final: 0.8814 (pp20) REVERT: Y 131 LYS cc_start: 0.9245 (mtpt) cc_final: 0.9019 (mtpt) REVERT: Y 132 ARG cc_start: 0.9150 (ttm110) cc_final: 0.8948 (mtm-85) REVERT: Y 139 ASN cc_start: 0.9565 (m-40) cc_final: 0.9240 (m110) REVERT: d 41 SER cc_start: 0.9304 (m) cc_final: 0.8947 (p) REVERT: d 57 ASN cc_start: 0.9285 (m-40) cc_final: 0.8433 (t0) REVERT: d 58 THR cc_start: 0.8763 (p) cc_final: 0.8527 (p) REVERT: d 97 ARG cc_start: 0.8222 (ptt90) cc_final: 0.7685 (tmm160) REVERT: d 132 ARG cc_start: 0.9345 (ttp-110) cc_final: 0.8875 (mtp-110) REVERT: d 133 TRP cc_start: 0.9225 (m-10) cc_final: 0.8649 (m-10) REVERT: d 136 LEU cc_start: 0.9485 (tp) cc_final: 0.9250 (tp) REVERT: d 139 ASN cc_start: 0.9442 (m110) cc_final: 0.9125 (m-40) REVERT: d 167 ARG cc_start: 0.9343 (ptm160) cc_final: 0.9028 (ptm160) REVERT: d 215 MET cc_start: 0.2463 (mtp) cc_final: 0.2159 (mmt) REVERT: e 10 MET cc_start: 0.8406 (mmp) cc_final: 0.8153 (tpp) REVERT: e 57 ASN cc_start: 0.9397 (m110) cc_final: 0.9137 (m110) REVERT: e 66 MET cc_start: 0.8766 (ptp) cc_final: 0.8533 (mpp) REVERT: e 96 MET cc_start: 0.7190 (mpp) cc_final: 0.6044 (tpt) REVERT: e 111 LEU cc_start: 0.9210 (mt) cc_final: 0.8481 (mt) REVERT: e 118 MET cc_start: 0.9049 (mmt) cc_final: 0.8736 (mmm) REVERT: e 167 ARG cc_start: 0.9230 (ptm160) cc_final: 0.8840 (ptt180) REVERT: e 169 TYR cc_start: 0.8908 (m-80) cc_final: 0.8558 (m-80) REVERT: e 186 THR cc_start: 0.9355 (p) cc_final: 0.9100 (p) REVERT: j 162 ARG cc_start: 0.8186 (mmm160) cc_final: 0.7815 (mmt180) REVERT: j 166 ASP cc_start: 0.8331 (m-30) cc_final: 0.7924 (m-30) REVERT: j 175 GLU cc_start: 0.8669 (pp20) cc_final: 0.8457 (pp20) REVERT: j 181 VAL cc_start: 0.9696 (t) cc_final: 0.9451 (p) REVERT: j 182 LYS cc_start: 0.9044 (mtmm) cc_final: 0.8778 (ptpt) REVERT: j 183 ASN cc_start: 0.9618 (m110) cc_final: 0.9271 (m110) REVERT: j 189 LEU cc_start: 0.8914 (tp) cc_final: 0.8712 (tp) REVERT: k 25 LYS cc_start: 0.9506 (mttt) cc_final: 0.9142 (ttpp) REVERT: k 29 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8399 (mt-10) REVERT: k 70 LYS cc_start: 0.9404 (mtmm) cc_final: 0.9157 (mtmm) REVERT: k 71 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8448 (mt-10) REVERT: k 76 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8884 (mm-30) REVERT: k 121 ASN cc_start: 0.9103 (m-40) cc_final: 0.8690 (t0) REVERT: k 131 LYS cc_start: 0.9525 (ttmt) cc_final: 0.9243 (ttmt) REVERT: k 132 ARG cc_start: 0.9233 (ptp-170) cc_final: 0.8019 (ptp-170) REVERT: k 135 ILE cc_start: 0.9648 (mt) cc_final: 0.9389 (mt) REVERT: k 139 ASN cc_start: 0.9472 (m-40) cc_final: 0.9079 (m110) REVERT: k 143 ARG cc_start: 0.8541 (ttm110) cc_final: 0.7975 (ttm110) REVERT: k 159 GLU cc_start: 0.8390 (tt0) cc_final: 0.8022 (mt-10) REVERT: k 176 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8421 (tm-30) REVERT: k 213 GLU cc_start: 0.8995 (mp0) cc_final: 0.8542 (mp0) outliers start: 1 outliers final: 0 residues processed: 878 average time/residue: 0.1763 time to fit residues: 217.5632 Evaluate side-chains 705 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 705 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 108 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 45 optimal weight: 0.0870 chunk 230 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN B 67 GLN C 53 ASN C 176 GLN D 74 ASN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.085592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.065508 restraints weight = 71634.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.067418 restraints weight = 45799.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.068758 restraints weight = 33476.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.069694 restraints weight = 26603.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.070377 restraints weight = 22523.135| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.7573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18834 Z= 0.177 Angle : 0.735 10.232 25587 Z= 0.385 Chirality : 0.048 0.242 2848 Planarity : 0.006 0.086 3345 Dihedral : 4.666 25.382 2500 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.10 % Allowed : 0.85 % Favored : 99.05 % 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: -0.12 (0.17), residues: 2338 helix: 0.21 (0.13), residues: 1446 sheet: -1.27 (0.55), residues: 69 loop : -0.24 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 143 TYR 0.029 0.002 TYR D 130 PHE 0.023 0.002 PHE G 40 TRP 0.038 0.002 TRP G 23 HIS 0.004 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00394 (18824) covalent geometry : angle 0.73441 (25567) SS BOND : bond 0.00251 ( 10) SS BOND : angle 1.43885 ( 20) hydrogen bonds : bond 0.04451 ( 1037) hydrogen bonds : angle 4.83341 ( 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 853 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 851 time to evaluate : 0.881 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: A 29 GLU cc_start: 0.9154 (pt0) cc_final: 0.8493 (pt0) REVERT: A 50 GLN cc_start: 0.9248 (pm20) cc_final: 0.8969 (pm20) REVERT: A 52 LEU cc_start: 0.9870 (mt) cc_final: 0.9584 (mt) REVERT: A 53 ASN cc_start: 0.9474 (m-40) cc_final: 0.9146 (m110) REVERT: A 76 GLU cc_start: 0.9663 (mm-30) cc_final: 0.9229 (mm-30) REVERT: B 21 ASN cc_start: 0.9471 (m-40) cc_final: 0.9220 (m-40) REVERT: B 30 LYS cc_start: 0.9315 (mmtm) cc_final: 0.8796 (mmtm) REVERT: B 33 SER cc_start: 0.9229 (t) cc_final: 0.8812 (t) REVERT: B 35 GLU cc_start: 0.8915 (mp0) cc_final: 0.8631 (mp0) REVERT: B 39 MET cc_start: 0.9053 (tpp) cc_final: 0.8783 (tpt) REVERT: B 43 LEU cc_start: 0.9017 (mt) cc_final: 0.8502 (mt) REVERT: B 70 LYS cc_start: 0.9270 (mtmt) cc_final: 0.9022 (mtmm) REVERT: B 74 ASN cc_start: 0.9363 (m-40) cc_final: 0.9144 (m110) REVERT: B 111 LEU cc_start: 0.9159 (tt) cc_final: 0.8684 (tt) REVERT: B 131 LYS cc_start: 0.9541 (ttmt) cc_final: 0.9277 (tttt) REVERT: B 139 ASN cc_start: 0.9442 (m-40) cc_final: 0.9220 (m110) REVERT: B 154 ARG cc_start: 0.9202 (tpp80) cc_final: 0.8711 (tpp80) REVERT: B 167 ARG cc_start: 0.9362 (mtm110) cc_final: 0.8990 (ptm160) REVERT: B 179 GLN cc_start: 0.9210 (pp30) cc_final: 0.8946 (tm-30) REVERT: B 182 LYS cc_start: 0.9666 (mttt) cc_final: 0.9338 (mttt) REVERT: B 183 ASN cc_start: 0.9469 (m-40) cc_final: 0.9048 (m110) REVERT: C 103 ASP cc_start: 0.8793 (m-30) cc_final: 0.8346 (m-30) REVERT: C 108 THR cc_start: 0.9335 (p) cc_final: 0.9125 (p) REVERT: C 131 LYS cc_start: 0.9390 (mtmt) cc_final: 0.9119 (mttt) REVERT: C 219 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8494 (tm-30) REVERT: D 10 MET cc_start: 0.6922 (mmp) cc_final: 0.6454 (mmm) REVERT: D 53 ASN cc_start: 0.9396 (m-40) cc_final: 0.9185 (m-40) REVERT: D 103 ASP cc_start: 0.8659 (t0) cc_final: 0.8243 (t0) REVERT: D 111 LEU cc_start: 0.9180 (tp) cc_final: 0.8909 (mm) REVERT: D 132 ARG cc_start: 0.9478 (ptp-110) cc_final: 0.8969 (ptp-170) REVERT: D 172 LEU cc_start: 0.9679 (tt) cc_final: 0.9479 (tt) REVERT: D 182 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8548 (mttp) REVERT: D 203 LYS cc_start: 0.8192 (ptmt) cc_final: 0.7777 (pttm) REVERT: D 214 MET cc_start: 0.8780 (mpp) cc_final: 0.8468 (mpp) REVERT: G 52 LEU cc_start: 0.9639 (mt) cc_final: 0.9398 (mt) REVERT: G 55 MET cc_start: 0.8893 (tmm) cc_final: 0.8592 (tmm) REVERT: G 57 ASN cc_start: 0.9185 (m-40) cc_final: 0.8814 (m110) REVERT: G 79 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8725 (tm-30) REVERT: G 96 MET cc_start: 0.5621 (mpp) cc_final: 0.3085 (mtp) REVERT: G 139 ASN cc_start: 0.9604 (m110) cc_final: 0.9333 (m110) REVERT: G 182 LYS cc_start: 0.9472 (mtpt) cc_final: 0.8852 (mtpp) REVERT: G 197 ASP cc_start: 0.8631 (p0) cc_final: 0.8409 (p0) REVERT: G 203 LYS cc_start: 0.9427 (mttp) cc_final: 0.9031 (mttp) REVERT: H 23 TRP cc_start: 0.9242 (t-100) cc_final: 0.8549 (t-100) REVERT: H 70 LYS cc_start: 0.9441 (mttt) cc_final: 0.9176 (mttm) REVERT: H 80 TRP cc_start: 0.8830 (t60) cc_final: 0.8287 (t60) REVERT: H 96 MET cc_start: 0.3822 (ptp) cc_final: 0.3517 (ptp) REVERT: H 102 SER cc_start: 0.9171 (m) cc_final: 0.8906 (t) REVERT: H 149 SER cc_start: 0.8838 (t) cc_final: 0.8373 (t) REVERT: H 167 ARG cc_start: 0.8967 (ptm160) cc_final: 0.8704 (ptm160) REVERT: J 53 PHE cc_start: 0.8921 (m-80) cc_final: 0.8287 (m-80) REVERT: J 84 GLU cc_start: 0.9214 (pm20) cc_final: 0.8778 (pm20) REVERT: J 106 ASN cc_start: 0.9284 (m-40) cc_final: 0.8537 (t0) REVERT: J 138 ILE cc_start: 0.8779 (mm) cc_final: 0.8309 (mm) REVERT: N 163 ASP cc_start: 0.9318 (m-30) cc_final: 0.8638 (t0) REVERT: N 183 ASN cc_start: 0.9254 (m-40) cc_final: 0.9007 (m-40) REVERT: Y 50 GLN cc_start: 0.9620 (tm-30) cc_final: 0.9335 (tm-30) REVERT: Y 51 ASP cc_start: 0.9252 (m-30) cc_final: 0.8638 (m-30) REVERT: Y 53 ASN cc_start: 0.9573 (m-40) cc_final: 0.9213 (m-40) REVERT: Y 67 GLN cc_start: 0.9313 (mt0) cc_final: 0.8533 (mt0) REVERT: Y 70 LYS cc_start: 0.9530 (tptp) cc_final: 0.9169 (tppt) REVERT: Y 74 ASN cc_start: 0.9027 (m110) cc_final: 0.8646 (m110) REVERT: Y 96 MET cc_start: 0.3322 (mpp) cc_final: 0.2573 (mtp) REVERT: Y 114 GLN cc_start: 0.9249 (mt0) cc_final: 0.8925 (mt0) REVERT: Y 117 TRP cc_start: 0.9048 (m-10) cc_final: 0.8598 (m-90) REVERT: Y 131 LYS cc_start: 0.9286 (mtpt) cc_final: 0.9076 (mtpt) REVERT: Y 139 ASN cc_start: 0.9610 (m-40) cc_final: 0.9287 (m110) REVERT: d 41 SER cc_start: 0.9328 (m) cc_final: 0.8998 (p) REVERT: d 55 MET cc_start: 0.9282 (tpp) cc_final: 0.9061 (tpt) REVERT: d 57 ASN cc_start: 0.9384 (m-40) cc_final: 0.8495 (t0) REVERT: d 58 THR cc_start: 0.8685 (p) cc_final: 0.8331 (p) REVERT: d 97 ARG cc_start: 0.8199 (ptt90) cc_final: 0.7699 (tmm160) REVERT: d 126 VAL cc_start: 0.8209 (m) cc_final: 0.7949 (m) REVERT: d 132 ARG cc_start: 0.9317 (ttp-110) cc_final: 0.8945 (mtp-110) REVERT: d 136 LEU cc_start: 0.9482 (tp) cc_final: 0.9268 (tp) REVERT: d 139 ASN cc_start: 0.9492 (m110) cc_final: 0.9234 (m110) REVERT: d 167 ARG cc_start: 0.9351 (ptm160) cc_final: 0.9031 (ptm160) REVERT: d 179 GLN cc_start: 0.9215 (tp-100) cc_final: 0.8904 (tp-100) REVERT: d 182 LYS cc_start: 0.9283 (mttm) cc_final: 0.8933 (mttm) REVERT: d 215 MET cc_start: 0.2491 (mtp) cc_final: 0.2200 (mmt) REVERT: e 10 MET cc_start: 0.8486 (mmp) cc_final: 0.8229 (tpp) REVERT: e 57 ASN cc_start: 0.9390 (m110) cc_final: 0.9140 (m110) REVERT: e 76 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8831 (tp30) REVERT: e 96 MET cc_start: 0.7311 (mpp) cc_final: 0.6078 (tpt) REVERT: e 144 MET cc_start: 0.8786 (ptm) cc_final: 0.8169 (ttt) REVERT: e 167 ARG cc_start: 0.9260 (ptm160) cc_final: 0.8739 (ptt180) REVERT: e 169 TYR cc_start: 0.8951 (m-80) cc_final: 0.8653 (m-80) REVERT: j 162 ARG cc_start: 0.8212 (mmm160) cc_final: 0.7743 (mmt180) REVERT: j 166 ASP cc_start: 0.8359 (m-30) cc_final: 0.7994 (m-30) REVERT: j 175 GLU cc_start: 0.8762 (pp20) cc_final: 0.8245 (pp20) REVERT: j 182 LYS cc_start: 0.9062 (mtmm) cc_final: 0.8757 (ptpt) REVERT: j 183 ASN cc_start: 0.9650 (m110) cc_final: 0.9255 (m110) REVERT: k 25 LYS cc_start: 0.9516 (mttt) cc_final: 0.9221 (ttpp) REVERT: k 29 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8407 (mt-10) REVERT: k 53 ASN cc_start: 0.9245 (m110) cc_final: 0.8853 (m110) REVERT: k 57 ASN cc_start: 0.9419 (m-40) cc_final: 0.9104 (m110) REVERT: k 70 LYS cc_start: 0.9473 (mtmm) cc_final: 0.9227 (mtmm) REVERT: k 71 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8477 (mt-10) REVERT: k 121 ASN cc_start: 0.9164 (m-40) cc_final: 0.8765 (t0) REVERT: k 131 LYS cc_start: 0.9533 (ttmt) cc_final: 0.9268 (ttmt) REVERT: k 132 ARG cc_start: 0.9280 (ptp-170) cc_final: 0.8016 (ptp-170) REVERT: k 135 ILE cc_start: 0.9667 (mt) cc_final: 0.9431 (mt) REVERT: k 139 ASN cc_start: 0.9502 (m-40) cc_final: 0.9089 (m110) REVERT: k 164 TYR cc_start: 0.8235 (t80) cc_final: 0.7575 (t80) REVERT: k 179 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8796 (tp-100) REVERT: k 213 GLU cc_start: 0.8999 (mp0) cc_final: 0.8552 (mp0) outliers start: 2 outliers final: 0 residues processed: 852 average time/residue: 0.1702 time to fit residues: 205.1338 Evaluate side-chains 679 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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: 9.9990 chunk 27 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN C 176 GLN D 74 ASN ** J 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.085354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.065209 restraints weight = 71763.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067140 restraints weight = 45952.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.068497 restraints weight = 33462.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.069429 restraints weight = 26602.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.070093 restraints weight = 22516.506| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.7723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18834 Z= 0.172 Angle : 0.763 13.738 25587 Z= 0.397 Chirality : 0.048 0.235 2848 Planarity : 0.006 0.078 3345 Dihedral : 4.792 27.089 2500 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.10 % Allowed : 0.75 % Favored : 99.15 % 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: -0.18 (0.17), residues: 2338 helix: 0.16 (0.13), residues: 1445 sheet: -1.37 (0.55), residues: 73 loop : -0.24 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG k 162 TYR 0.023 0.002 TYR A 130 PHE 0.020 0.002 PHE e 40 TRP 0.034 0.002 TRP G 117 HIS 0.005 0.001 HIS J 54 Details of bonding type rmsd covalent geometry : bond 0.00388 (18824) covalent geometry : angle 0.76210 (25567) SS BOND : bond 0.00233 ( 10) SS BOND : angle 1.39639 ( 20) hydrogen bonds : bond 0.04448 ( 1037) hydrogen bonds : angle 4.86404 ( 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 864 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 862 time to evaluate : 0.743 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: A 29 GLU cc_start: 0.9153 (pt0) cc_final: 0.8518 (pt0) REVERT: A 50 GLN cc_start: 0.9251 (pm20) cc_final: 0.8965 (pm20) REVERT: A 52 LEU cc_start: 0.9879 (mt) cc_final: 0.9628 (mt) REVERT: A 53 ASN cc_start: 0.9427 (m-40) cc_final: 0.9139 (m110) REVERT: A 66 MET cc_start: 0.9343 (tpp) cc_final: 0.9122 (mmm) REVERT: A 76 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9214 (mm-30) REVERT: B 13 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8488 (tp40) REVERT: B 21 ASN cc_start: 0.9466 (m-40) cc_final: 0.9215 (m-40) REVERT: B 30 LYS cc_start: 0.9305 (mmtm) cc_final: 0.9047 (mmtp) REVERT: B 33 SER cc_start: 0.9238 (t) cc_final: 0.8941 (t) REVERT: B 39 MET cc_start: 0.9068 (tpp) cc_final: 0.8797 (tpt) REVERT: B 43 LEU cc_start: 0.9035 (mt) cc_final: 0.8501 (mt) REVERT: B 66 MET cc_start: 0.8827 (mmm) cc_final: 0.8483 (mmm) REVERT: B 70 LYS cc_start: 0.9273 (mtmt) cc_final: 0.8938 (mttp) REVERT: B 74 ASN cc_start: 0.9338 (m-40) cc_final: 0.9115 (m110) REVERT: B 111 LEU cc_start: 0.9131 (tt) cc_final: 0.8656 (tt) REVERT: B 118 MET cc_start: 0.9228 (mmt) cc_final: 0.9025 (mmt) REVERT: B 131 LYS cc_start: 0.9525 (ttmt) cc_final: 0.9229 (tttt) REVERT: B 139 ASN cc_start: 0.9470 (m-40) cc_final: 0.9249 (m110) REVERT: B 154 ARG cc_start: 0.9229 (tpp80) cc_final: 0.8776 (tpp80) REVERT: B 179 GLN cc_start: 0.9193 (pp30) cc_final: 0.8929 (pp30) REVERT: B 182 LYS cc_start: 0.9677 (mttt) cc_final: 0.9323 (mttt) REVERT: B 183 ASN cc_start: 0.9463 (m-40) cc_final: 0.9065 (m110) REVERT: B 205 LEU cc_start: 0.8371 (pp) cc_final: 0.7895 (pp) REVERT: B 213 GLU cc_start: 0.9527 (tp30) cc_final: 0.9194 (tp30) REVERT: C 55 MET cc_start: 0.9577 (ttm) cc_final: 0.9351 (ttp) REVERT: C 103 ASP cc_start: 0.8764 (m-30) cc_final: 0.8307 (m-30) REVERT: C 108 THR cc_start: 0.9376 (p) cc_final: 0.9155 (p) REVERT: C 131 LYS cc_start: 0.9405 (mtmt) cc_final: 0.9115 (mttt) REVERT: C 219 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8443 (tm-30) REVERT: D 10 MET cc_start: 0.6973 (mmp) cc_final: 0.6508 (mmm) REVERT: D 53 ASN cc_start: 0.9446 (m-40) cc_final: 0.9048 (m-40) REVERT: D 57 ASN cc_start: 0.9559 (m-40) cc_final: 0.9245 (m-40) REVERT: D 103 ASP cc_start: 0.8783 (t0) cc_final: 0.7779 (t0) REVERT: D 111 LEU cc_start: 0.9187 (tp) cc_final: 0.8613 (mm) REVERT: D 114 GLN cc_start: 0.9569 (mm-40) cc_final: 0.9074 (mp10) REVERT: D 132 ARG cc_start: 0.9482 (ptp-110) cc_final: 0.8985 (ptp-170) REVERT: D 172 LEU cc_start: 0.9687 (tt) cc_final: 0.9473 (tt) REVERT: D 182 LYS cc_start: 0.9095 (mtpt) cc_final: 0.8504 (mttp) REVERT: D 203 LYS cc_start: 0.8250 (ptmt) cc_final: 0.7845 (pttm) REVERT: D 214 MET cc_start: 0.8839 (mpp) cc_final: 0.8531 (mpp) REVERT: G 25 LYS cc_start: 0.9565 (tptt) cc_final: 0.9363 (tptp) REVERT: G 57 ASN cc_start: 0.9181 (m-40) cc_final: 0.8800 (m110) REVERT: G 79 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8882 (tm-30) REVERT: G 112 GLN cc_start: 0.9116 (pp30) cc_final: 0.8685 (pm20) REVERT: G 182 LYS cc_start: 0.9481 (mtpt) cc_final: 0.8980 (mtpp) REVERT: G 197 ASP cc_start: 0.8620 (p0) cc_final: 0.8406 (p0) REVERT: H 23 TRP cc_start: 0.9139 (t-100) cc_final: 0.8766 (t-100) REVERT: H 51 ASP cc_start: 0.8980 (m-30) cc_final: 0.8475 (m-30) REVERT: H 66 MET cc_start: 0.9318 (mmp) cc_final: 0.8854 (mmm) REVERT: H 70 LYS cc_start: 0.9435 (mttt) cc_final: 0.9231 (mttm) REVERT: H 80 TRP cc_start: 0.8886 (t60) cc_final: 0.8405 (t60) REVERT: H 96 MET cc_start: 0.3898 (ptp) cc_final: 0.3570 (ptp) REVERT: H 143 ARG cc_start: 0.8838 (mtm-85) cc_final: 0.8438 (mtm-85) REVERT: H 149 SER cc_start: 0.8917 (t) cc_final: 0.8473 (t) REVERT: H 167 ARG cc_start: 0.8957 (ptm160) cc_final: 0.8671 (ptm160) REVERT: H 168 PHE cc_start: 0.8618 (t80) cc_final: 0.8337 (t80) REVERT: J 22 PHE cc_start: 0.8803 (m-10) cc_final: 0.8595 (m-10) REVERT: J 53 PHE cc_start: 0.8925 (m-80) cc_final: 0.8552 (m-10) REVERT: J 84 GLU cc_start: 0.9194 (pm20) cc_final: 0.8740 (pm20) REVERT: J 106 ASN cc_start: 0.9320 (m-40) cc_final: 0.8598 (t0) REVERT: J 138 ILE cc_start: 0.8847 (mm) cc_final: 0.8414 (mm) REVERT: J 140 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8872 (mm-30) REVERT: N 163 ASP cc_start: 0.9271 (m-30) cc_final: 0.8581 (t0) REVERT: N 183 ASN cc_start: 0.9234 (m-40) cc_final: 0.8971 (m-40) REVERT: N 188 THR cc_start: 0.8995 (m) cc_final: 0.8381 (p) REVERT: Y 25 LYS cc_start: 0.9271 (tmmt) cc_final: 0.9041 (ttpp) REVERT: Y 50 GLN cc_start: 0.9618 (tm-30) cc_final: 0.9271 (tm-30) REVERT: Y 51 ASP cc_start: 0.9205 (m-30) cc_final: 0.8461 (m-30) REVERT: Y 52 LEU cc_start: 0.9694 (mt) cc_final: 0.9449 (mt) REVERT: Y 53 ASN cc_start: 0.9548 (m-40) cc_final: 0.9118 (m-40) REVERT: Y 67 GLN cc_start: 0.9290 (mt0) cc_final: 0.8480 (mt0) REVERT: Y 70 LYS cc_start: 0.9538 (tptp) cc_final: 0.9118 (tppt) REVERT: Y 74 ASN cc_start: 0.9005 (m110) cc_final: 0.8579 (m110) REVERT: Y 75 GLU cc_start: 0.9177 (pt0) cc_final: 0.8698 (pp20) REVERT: Y 96 MET cc_start: 0.3294 (mpp) cc_final: 0.2645 (mtp) REVERT: Y 114 GLN cc_start: 0.9255 (mt0) cc_final: 0.8890 (mt0) REVERT: Y 117 TRP cc_start: 0.9087 (m-10) cc_final: 0.8645 (m-90) REVERT: Y 131 LYS cc_start: 0.9260 (mtpt) cc_final: 0.9012 (mtpt) REVERT: Y 135 ILE cc_start: 0.9700 (mt) cc_final: 0.9467 (mt) REVERT: Y 139 ASN cc_start: 0.9623 (m-40) cc_final: 0.9330 (m110) REVERT: d 41 SER cc_start: 0.9255 (m) cc_final: 0.8976 (p) REVERT: d 55 MET cc_start: 0.9243 (tpp) cc_final: 0.8998 (tpt) REVERT: d 97 ARG cc_start: 0.8164 (ptt90) cc_final: 0.7666 (tmm160) REVERT: d 132 ARG cc_start: 0.9323 (ttp-110) cc_final: 0.8918 (mtp-110) REVERT: d 133 TRP cc_start: 0.9210 (m-10) cc_final: 0.8595 (m-10) REVERT: d 136 LEU cc_start: 0.9492 (tp) cc_final: 0.9277 (tp) REVERT: d 139 ASN cc_start: 0.9529 (m110) cc_final: 0.9281 (m110) REVERT: d 143 ARG cc_start: 0.9559 (ttm170) cc_final: 0.9265 (tpp80) REVERT: d 167 ARG cc_start: 0.9334 (ptm160) cc_final: 0.8989 (ptm160) REVERT: d 179 GLN cc_start: 0.9202 (tp-100) cc_final: 0.8867 (tp-100) REVERT: d 182 LYS cc_start: 0.9305 (mttm) cc_final: 0.8924 (mttm) REVERT: d 189 LEU cc_start: 0.9388 (mm) cc_final: 0.9185 (mm) REVERT: d 215 MET cc_start: 0.2586 (mtp) cc_final: 0.2266 (mmt) REVERT: e 25 LYS cc_start: 0.9559 (pptt) cc_final: 0.9313 (pptt) REVERT: e 57 ASN cc_start: 0.9407 (m110) cc_final: 0.9144 (m110) REVERT: e 76 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8777 (tp30) REVERT: e 96 MET cc_start: 0.7344 (mpp) cc_final: 0.6152 (tpt) REVERT: e 118 MET cc_start: 0.9076 (mmt) cc_final: 0.8808 (mmm) REVERT: e 167 ARG cc_start: 0.9195 (ptm160) cc_final: 0.8757 (ptt180) REVERT: e 169 TYR cc_start: 0.8955 (m-80) cc_final: 0.8586 (m-80) REVERT: e 214 MET cc_start: 0.8948 (ptp) cc_final: 0.8723 (mtm) REVERT: j 162 ARG cc_start: 0.8107 (mmm160) cc_final: 0.7791 (mmt180) REVERT: j 166 ASP cc_start: 0.8367 (m-30) cc_final: 0.7973 (m-30) REVERT: j 172 LEU cc_start: 0.9449 (tp) cc_final: 0.9141 (tt) REVERT: j 175 GLU cc_start: 0.8756 (pp20) cc_final: 0.8230 (pp20) REVERT: j 181 VAL cc_start: 0.9694 (t) cc_final: 0.9148 (t) REVERT: j 182 LYS cc_start: 0.9036 (mtmm) cc_final: 0.8762 (ptpt) REVERT: j 183 ASN cc_start: 0.9638 (m110) cc_final: 0.9269 (m110) REVERT: j 189 LEU cc_start: 0.9062 (tp) cc_final: 0.8854 (tp) REVERT: k 25 LYS cc_start: 0.9524 (mttt) cc_final: 0.9256 (ttpp) REVERT: k 29 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8422 (mt-10) REVERT: k 68 MET cc_start: 0.8685 (ptp) cc_final: 0.8395 (ptm) REVERT: k 70 LYS cc_start: 0.9486 (mtmm) cc_final: 0.9247 (mtmm) REVERT: k 71 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8339 (mt-10) REVERT: k 111 LEU cc_start: 0.8554 (tt) cc_final: 0.8341 (tp) REVERT: k 121 ASN cc_start: 0.9138 (m-40) cc_final: 0.8785 (t0) REVERT: k 131 LYS cc_start: 0.9521 (ttmt) cc_final: 0.9232 (ttmt) REVERT: k 132 ARG cc_start: 0.9243 (ptp-170) cc_final: 0.7971 (ptp-170) REVERT: k 135 ILE cc_start: 0.9643 (mt) cc_final: 0.9426 (mt) REVERT: k 139 ASN cc_start: 0.9496 (m-40) cc_final: 0.9126 (m110) REVERT: k 143 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8009 (ttm110) REVERT: k 176 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8479 (tm-30) REVERT: k 179 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8754 (tp-100) REVERT: k 213 GLU cc_start: 0.9069 (mp0) cc_final: 0.8637 (mp0) outliers start: 2 outliers final: 0 residues processed: 863 average time/residue: 0.1725 time to fit residues: 210.5298 Evaluate side-chains 694 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 694 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 30.0000 chunk 152 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN C 176 GLN D 74 ASN G 95 GLN ** J 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 ASN N 195 ASN d 50 GLN ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 ASN k 193 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.085550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.064833 restraints weight = 71506.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.066729 restraints weight = 46323.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.068066 restraints weight = 34063.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.068958 restraints weight = 27269.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.069648 restraints weight = 23250.161| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.7856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 18834 Z= 0.160 Angle : 0.778 13.263 25587 Z= 0.402 Chirality : 0.048 0.255 2848 Planarity : 0.006 0.089 3345 Dihedral : 4.772 32.746 2500 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.10 % Allowed : 0.30 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.22 (0.17), residues: 2338 helix: 0.15 (0.13), residues: 1438 sheet: -1.37 (0.55), residues: 73 loop : -0.30 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 132 TYR 0.027 0.002 TYR D 130 PHE 0.028 0.002 PHE C 168 TRP 0.053 0.002 TRP G 23 HIS 0.003 0.001 HIS k 62 Details of bonding type rmsd covalent geometry : bond 0.00370 (18824) covalent geometry : angle 0.77673 (25567) SS BOND : bond 0.00248 ( 10) SS BOND : angle 1.51570 ( 20) hydrogen bonds : bond 0.04475 ( 1037) hydrogen bonds : angle 4.90859 ( 3081) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4438.21 seconds wall clock time: 76 minutes 52.09 seconds (4612.09 seconds total)