Starting phenix.real_space_refine on Mon Jun 16 00:09:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y9x_10740/06_2025/6y9x_10740.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y9x_10740/06_2025/6y9x_10740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y9x_10740/06_2025/6y9x_10740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y9x_10740/06_2025/6y9x_10740.map" model { file = "/net/cci-nas-00/data/ceres_data/6y9x_10740/06_2025/6y9x_10740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y9x_10740/06_2025/6y9x_10740.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 11607 2.51 5 N 3207 2.21 5 O 3466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.63, per 1000 atoms: 0.58 Number of scatterers: 18418 At special positions: 0 Unit cell: (136.74, 179.14, 106, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 3466 8.00 N 3207 7.00 C 11607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.04 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS G 198 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS H 198 " - pdb=" SG CYS H 218 " distance=2.03 Simple disulfide: pdb=" SG CYS N 198 " - pdb=" SG CYS N 218 " distance=2.04 Simple disulfide: pdb=" SG CYS d 198 " - pdb=" SG CYS d 218 " distance=2.03 Simple disulfide: pdb=" SG CYS e 198 " - pdb=" SG CYS e 218 " distance=2.03 Simple disulfide: pdb=" SG CYS j 198 " - pdb=" SG CYS j 218 " distance=2.03 Simple disulfide: pdb=" SG CYS k 198 " - pdb=" SG CYS k 218 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.88 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.527A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.791A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.596A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.804A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 36 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 removed outlier: 4.006A pdb=" N ALA C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 160 through 174 Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.537A pdb=" N GLU C 187 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.870A pdb=" N CYS C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.675A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 83 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.700A pdb=" N GLN D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 146 removed outlier: 3.602A pdb=" N ARG D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.765A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 145 Processing helix chain 'G' and resid 160 through 175 Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.897A pdb=" N TRP G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'G' and resid 210 through 218 Processing helix chain 'H' and resid 16 through 31 Processing helix chain 'H' and resid 35 through 44 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 62 through 84 Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'H' and resid 160 through 175 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.895A pdb=" N TRP H 184 " --> pdb=" O GLU H 180 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 206 Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'J' and resid 29 through 42 Processing helix chain 'J' and resid 119 through 123 Processing helix chain 'J' and resid 135 through 144 removed outlier: 4.122A pdb=" N ARG J 144 " --> pdb=" O GLU J 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 153 removed outlier: 3.526A pdb=" N ILE N 153 " --> pdb=" O ILE N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 175 Processing helix chain 'N' and resid 178 through 190 removed outlier: 3.791A pdb=" N TRP N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N 187 " --> pdb=" O ASN N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 206 removed outlier: 3.593A pdb=" N LEU N 205 " --> pdb=" O ILE N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 removed outlier: 3.800A pdb=" N CYS N 218 " --> pdb=" O MET N 214 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 30 removed outlier: 3.675A pdb=" N LEU Y 20 " --> pdb=" O SER Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 44 Processing helix chain 'Y' and resid 48 through 58 Processing helix chain 'Y' and resid 62 through 83 Processing helix chain 'Y' and resid 100 through 105 Processing helix chain 'Y' and resid 110 through 118 removed outlier: 3.699A pdb=" N GLN Y 114 " --> pdb=" O THR Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 126 through 146 removed outlier: 3.601A pdb=" N ARG Y 132 " --> pdb=" O GLU Y 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 30 removed outlier: 3.674A pdb=" N LEU d 20 " --> pdb=" O SER d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 44 Processing helix chain 'd' and resid 48 through 58 Processing helix chain 'd' and resid 62 through 83 Processing helix chain 'd' and resid 100 through 105 Processing helix chain 'd' and resid 110 through 118 removed outlier: 3.700A pdb=" N GLN d 114 " --> pdb=" O THR d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 146 removed outlier: 3.603A pdb=" N ARG d 132 " --> pdb=" O GLU d 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 174 Processing helix chain 'd' and resid 178 through 193 removed outlier: 4.765A pdb=" N LEU d 190 " --> pdb=" O THR d 186 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 206 Processing helix chain 'd' and resid 210 through 218 Processing helix chain 'e' and resid 16 through 31 Processing helix chain 'e' and resid 35 through 44 Processing helix chain 'e' and resid 48 through 58 Processing helix chain 'e' and resid 62 through 84 Processing helix chain 'e' and resid 100 through 105 Processing helix chain 'e' and resid 110 through 120 Processing helix chain 'e' and resid 125 through 145 Processing helix chain 'e' and resid 149 through 153 Processing helix chain 'e' and resid 160 through 175 Processing helix chain 'e' and resid 178 through 189 removed outlier: 3.692A pdb=" N GLU e 187 " --> pdb=" O ASN e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 195 through 206 removed outlier: 3.906A pdb=" N ILE e 201 " --> pdb=" O ASP e 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 210 through 218 removed outlier: 3.510A pdb=" N MET e 214 " --> pdb=" O THR e 210 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 153 Processing helix chain 'j' and resid 160 through 175 Processing helix chain 'j' and resid 178 through 189 removed outlier: 3.690A pdb=" N GLU j 187 " --> pdb=" O ASN j 183 " (cutoff:3.500A) Processing helix chain 'j' and resid 195 through 206 removed outlier: 3.904A pdb=" N ILE j 201 " --> pdb=" O ASP j 197 " (cutoff:3.500A) Processing helix chain 'j' and resid 210 through 218 removed outlier: 3.511A pdb=" N MET j 214 " --> pdb=" O THR j 210 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 31 removed outlier: 3.524A pdb=" N LEU k 20 " --> pdb=" O SER k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 36 through 44 Processing helix chain 'k' and resid 48 through 58 Processing helix chain 'k' and resid 62 through 84 Processing helix chain 'k' and resid 100 through 105 Processing helix chain 'k' and resid 110 through 119 Processing helix chain 'k' and resid 125 through 145 Processing helix chain 'k' and resid 160 through 176 Processing helix chain 'k' and resid 179 through 193 removed outlier: 4.359A pdb=" N LEU k 190 " --> pdb=" O THR k 186 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL k 191 " --> pdb=" O GLU k 187 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN k 193 " --> pdb=" O LEU k 189 " (cutoff:3.500A) Processing helix chain 'k' and resid 195 through 204 Processing helix chain 'k' and resid 210 through 219 removed outlier: 3.923A pdb=" N CYS k 218 " --> pdb=" O MET k 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.668A pdb=" N VAL B 3 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 11 " --> pdb=" O VAL B 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.600A pdb=" N VAL C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 11 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'H' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'J' and resid 53 through 57 removed outlier: 4.395A pdb=" N ILE J 97 " --> pdb=" O CYS J 115 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET J 100 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL J 128 " --> pdb=" O MET J 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER J 21 " --> pdb=" O LYS J 133 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL J 12 " --> pdb=" O PRO J 16 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY J 18 " --> pdb=" O ILE J 10 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP J 160 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA J 11 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE J 158 " --> pdb=" O ALA J 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 2 through 3 removed outlier: 3.665A pdb=" N VAL e 3 " --> pdb=" O VAL e 11 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL e 11 " --> pdb=" O VAL e 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'k' and resid 3 through 4 removed outlier: 3.540A pdb=" N VAL k 3 " --> pdb=" O VAL k 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL k 11 " --> pdb=" O VAL k 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 1037 hydrogen bonds defined for protein. 3081 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.44: 7785 1.44 - 1.67: 10784 1.67 - 1.90: 252 1.90 - 2.14: 0 2.14 - 2.37: 3 Bond restraints: 18824 Sorted by residual: bond pdb=" C PRO C 147 " pdb=" N THR C 148 " ideal model delta sigma weight residual 1.331 2.237 -0.906 1.23e-02 6.61e+03 5.43e+03 bond pdb=" CA ARG C 18 " pdb=" C ARG C 18 " ideal model delta sigma weight residual 1.522 2.366 -0.844 1.37e-02 5.33e+03 3.80e+03 bond pdb=" N ARG C 18 " pdb=" CA ARG C 18 " ideal model delta sigma weight residual 1.456 2.274 -0.818 1.33e-02 5.65e+03 3.78e+03 bond pdb=" C HIS e 84 " pdb=" N PRO e 85 " ideal model delta sigma weight residual 1.330 1.514 -0.184 1.22e-02 6.72e+03 2.28e+02 bond pdb=" CD2 HIS J 54 " pdb=" NE2 HIS J 54 " ideal model delta sigma weight residual 1.374 1.296 0.078 1.10e-02 8.26e+03 5.06e+01 ... (remaining 18819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.81: 25549 9.81 - 19.63: 14 19.63 - 29.44: 3 29.44 - 39.25: 0 39.25 - 49.07: 1 Bond angle restraints: 25567 Sorted by residual: angle pdb=" N ARG C 18 " pdb=" CA ARG C 18 " pdb=" C ARG C 18 " ideal model delta sigma weight residual 113.23 64.16 49.07 1.24e+00 6.50e-01 1.57e+03 angle pdb=" CA ARG C 18 " pdb=" C ARG C 18 " pdb=" O ARG C 18 " ideal model delta sigma weight residual 119.27 92.00 27.27 1.17e+00 7.31e-01 5.43e+02 angle pdb=" CA ARG C 18 " pdb=" C ARG C 18 " pdb=" N THR C 19 " ideal model delta sigma weight residual 118.21 145.56 -27.35 1.36e+00 5.41e-01 4.04e+02 angle pdb=" O PRO C 147 " pdb=" C PRO C 147 " pdb=" N THR C 148 " ideal model delta sigma weight residual 122.30 108.80 13.50 1.36e+00 5.41e-01 9.85e+01 angle pdb=" C ARG e 97 " pdb=" CA ARG e 97 " pdb=" CB ARG e 97 " ideal model delta sigma weight residual 111.30 133.23 -21.93 2.23e+00 2.01e-01 9.67e+01 ... (remaining 25562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10634 17.94 - 35.87: 711 35.87 - 53.81: 180 53.81 - 71.75: 19 71.75 - 89.69: 13 Dihedral angle restraints: 11557 sinusoidal: 4764 harmonic: 6793 Sorted by residual: dihedral pdb=" C ARG e 97 " pdb=" N ARG e 97 " pdb=" CA ARG e 97 " pdb=" CB ARG e 97 " ideal model delta harmonic sigma weight residual -122.60 -163.07 40.47 0 2.50e+00 1.60e-01 2.62e+02 dihedral pdb=" N ARG e 97 " pdb=" C ARG e 97 " pdb=" CA ARG e 97 " pdb=" CB ARG e 97 " ideal model delta harmonic sigma weight residual 122.80 158.61 -35.81 0 2.50e+00 1.60e-01 2.05e+02 dihedral pdb=" CB CYS B 198 " pdb=" SG CYS B 198 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -134.76 48.76 1 1.00e+01 1.00e-02 3.27e+01 ... (remaining 11554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.947: 2846 0.947 - 1.893: 1 1.893 - 2.839: 0 2.839 - 3.786: 0 3.786 - 4.732: 1 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA ARG C 18 " pdb=" N ARG C 18 " pdb=" C ARG C 18 " pdb=" CB ARG C 18 " both_signs ideal model delta sigma weight residual False 2.51 7.24 -4.73 2.00e-01 2.50e+01 5.60e+02 chirality pdb=" CA ARG e 97 " pdb=" N ARG e 97 " pdb=" C ARG e 97 " pdb=" CB ARG e 97 " both_signs ideal model delta sigma weight residual False 2.51 0.89 1.62 2.00e-01 2.50e+01 6.54e+01 chirality pdb=" CA PRO J 30 " pdb=" N PRO J 30 " pdb=" C PRO J 30 " pdb=" CB PRO J 30 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 2845 not shown) Planarity restraints: 3345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 60 " 0.124 2.00e-02 2.50e+03 7.90e-02 1.09e+02 pdb=" CG PHE J 60 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE J 60 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 PHE J 60 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE J 60 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE J 60 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE J 60 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 147 " -0.064 2.00e-02 2.50e+03 9.94e-02 9.89e+01 pdb=" C PRO C 147 " 0.171 2.00e-02 2.50e+03 pdb=" O PRO C 147 " -0.068 2.00e-02 2.50e+03 pdb=" N THR C 148 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG e 97 " 0.039 2.00e-02 2.50e+03 7.89e-02 6.23e+01 pdb=" C ARG e 97 " -0.136 2.00e-02 2.50e+03 pdb=" O ARG e 97 " 0.053 2.00e-02 2.50e+03 pdb=" N GLU e 98 " 0.044 2.00e-02 2.50e+03 ... (remaining 3342 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.06: 6 2.06 - 2.77: 3418 2.77 - 3.48: 26032 3.48 - 4.19: 40619 4.19 - 4.90: 71418 Nonbonded interactions: 141493 Sorted by model distance: nonbonded pdb=" OE1 GLN G 7 " pdb=" NE2 GLN k 9 " model vdw 1.344 3.120 nonbonded pdb=" OE1 GLN D 192 " pdb=" CD1 LEU H 151 " model vdw 1.514 3.460 nonbonded pdb=" CG2 VAL G 181 " pdb=" OE1 GLU d 180 " model vdw 1.586 3.460 nonbonded pdb=" OE1 GLN G 192 " pdb=" CD1 LEU d 151 " model vdw 1.748 3.460 nonbonded pdb=" CD GLN G 7 " pdb=" NE2 GLN k 9 " model vdw 1.920 3.350 ... (remaining 141488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'Y' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'd' selection = chain 'e' selection = chain 'k' } ncs_group { reference = chain 'N' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.770 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.906 18834 Z= 0.921 Angle : 1.068 49.068 25587 Z= 0.726 Chirality : 0.108 4.732 2848 Planarity : 0.007 0.099 3345 Dihedral : 13.054 89.686 7127 Min Nonbonded Distance : 1.344 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.99 % Rotamer: Outliers : 0.45 % Allowed : 3.00 % Favored : 96.55 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (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 TRP 0.019 0.001 TRP J 121 HIS 0.009 0.001 HIS J 70 PHE 0.124 0.009 PHE J 60 TYR 0.100 0.003 TYR J 48 ARG 0.018 0.001 ARG J 37 Details of bonding type rmsd hydrogen bonds : bond 0.13584 ( 1037) hydrogen bonds : angle 5.13706 ( 3081) SS BOND : bond 0.00304 ( 10) SS BOND : angle 0.96509 ( 20) covalent geometry : bond 0.01239 (18824) covalent geometry : angle 1.06771 (25567) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1139 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.9407 (m-30) cc_final: 0.9091 (m-30) REVERT: A 56 LEU cc_start: 0.9588 (mt) cc_final: 0.9325 (mt) REVERT: A 96 MET cc_start: -0.1411 (mpp) cc_final: -0.1634 (mmt) REVERT: B 2 ILE cc_start: 0.7623 (pt) cc_final: 0.7366 (tt) REVERT: B 24 VAL cc_start: 0.9458 (t) cc_final: 0.9226 (p) REVERT: B 25 LYS cc_start: 0.9575 (mttt) cc_final: 0.9080 (ttmt) REVERT: B 35 GLU cc_start: 0.9493 (pm20) cc_final: 0.9099 (mp0) REVERT: B 39 MET cc_start: 0.9295 (tpp) cc_final: 0.9067 (tpp) REVERT: B 66 MET cc_start: 0.8800 (mmt) cc_final: 0.8172 (mmm) REVERT: B 67 GLN cc_start: 0.8821 (tp40) cc_final: 0.8398 (mm-40) REVERT: B 68 MET cc_start: 0.9518 (mtp) cc_final: 0.9023 (mtt) REVERT: B 75 GLU cc_start: 0.9166 (tt0) cc_final: 0.8956 (tt0) REVERT: B 114 GLN cc_start: 0.8780 (mt0) cc_final: 0.8516 (mt0) REVERT: B 118 MET cc_start: 0.8863 (mtm) cc_final: 0.8467 (ptp) REVERT: B 131 LYS cc_start: 0.9563 (ttmt) cc_final: 0.9147 (mmmt) REVERT: C 113 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8806 (tt0) REVERT: C 129 ILE cc_start: 0.9095 (mt) cc_final: 0.8043 (mt) REVERT: C 131 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8117 (mtpt) REVERT: C 187 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8897 (mp0) REVERT: C 189 LEU cc_start: 0.9100 (mm) cc_final: 0.8739 (mp) REVERT: D 27 VAL cc_start: 0.9377 (p) cc_final: 0.8620 (m) REVERT: D 35 GLU cc_start: 0.9093 (pm20) cc_final: 0.8539 (pm20) REVERT: D 55 MET cc_start: 0.9194 (mtp) cc_final: 0.8977 (ttm) REVERT: D 56 LEU cc_start: 0.9715 (mt) cc_final: 0.9316 (mt) REVERT: D 118 MET cc_start: 0.9032 (mtm) cc_final: 0.8543 (ppp) REVERT: D 130 TYR cc_start: 0.9155 (t80) cc_final: 0.8813 (t80) REVERT: D 140 LYS cc_start: 0.9600 (mttt) cc_final: 0.9301 (tptp) REVERT: D 141 ILE cc_start: 0.9212 (mt) cc_final: 0.8795 (mt) REVERT: G 23 TRP cc_start: 0.9468 (t-100) cc_final: 0.8839 (t-100) REVERT: G 35 GLU cc_start: 0.9512 (pm20) cc_final: 0.9205 (pm20) REVERT: G 39 MET cc_start: 0.9541 (ttm) cc_final: 0.9291 (ttm) REVERT: G 57 ASN cc_start: 0.9590 (m-40) cc_final: 0.9367 (m110) REVERT: G 58 THR cc_start: 0.9434 (p) cc_final: 0.9125 (p) REVERT: G 96 MET cc_start: 0.0872 (mpp) cc_final: -0.1168 (mtt) REVERT: G 111 LEU cc_start: 0.8486 (tp) cc_final: 0.8217 (mp) REVERT: G 141 ILE cc_start: 0.9550 (mt) cc_final: 0.9316 (mt) REVERT: G 152 ASP cc_start: 0.8923 (m-30) cc_final: 0.8632 (p0) REVERT: G 186 THR cc_start: 0.7960 (t) cc_final: 0.7708 (t) REVERT: G 199 LYS cc_start: 0.8953 (tttp) cc_final: 0.8696 (ttmt) REVERT: G 214 MET cc_start: 0.9364 (mtm) cc_final: 0.8335 (tpt) REVERT: H 39 MET cc_start: 0.8553 (ttm) cc_final: 0.8118 (tpt) REVERT: H 70 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8591 (ptpp) REVERT: H 135 ILE cc_start: 0.9569 (mt) cc_final: 0.9140 (pt) REVERT: H 139 ASN cc_start: 0.9158 (m-40) cc_final: 0.8824 (m-40) REVERT: J 34 GLU cc_start: 0.9506 (tp30) cc_final: 0.9115 (tp30) REVERT: J 115 CYS cc_start: 0.8642 (m) cc_final: 0.8037 (m) REVERT: J 120 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8737 (pm20) REVERT: J 129 PHE cc_start: 0.7261 (p90) cc_final: 0.5511 (p90) REVERT: J 161 CYS cc_start: 0.5318 (p) cc_final: 0.4957 (p) REVERT: N 189 LEU cc_start: 0.8913 (mm) cc_final: 0.8712 (mm) REVERT: Y 13 GLN cc_start: 0.8983 (tt0) cc_final: 0.8733 (pm20) REVERT: Y 21 ASN cc_start: 0.9541 (t0) cc_final: 0.9122 (t0) REVERT: Y 25 LYS cc_start: 0.9585 (tttt) cc_final: 0.9328 (mtpp) REVERT: Y 49 PRO cc_start: 0.9450 (Cg_exo) cc_final: 0.9213 (Cg_endo) REVERT: Y 52 LEU cc_start: 0.9691 (mt) cc_final: 0.9263 (mp) REVERT: Y 104 ILE cc_start: 0.7685 (tt) cc_final: 0.7202 (pt) REVERT: Y 110 THR cc_start: 0.9234 (t) cc_final: 0.8948 (t) REVERT: Y 114 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8663 (mm-40) REVERT: Y 117 TRP cc_start: 0.7666 (m-10) cc_final: 0.6995 (m-10) REVERT: Y 131 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8727 (tptt) REVERT: Y 139 ASN cc_start: 0.9600 (m-40) cc_final: 0.9222 (m110) REVERT: d 39 MET cc_start: 0.7384 (ttm) cc_final: 0.7071 (tpt) REVERT: d 67 GLN cc_start: 0.9152 (tp-100) cc_final: 0.8875 (mt0) REVERT: d 68 MET cc_start: 0.8221 (mtp) cc_final: 0.8001 (mtp) REVERT: d 130 TYR cc_start: 0.6904 (t80) cc_final: 0.6532 (t80) REVERT: d 139 ASN cc_start: 0.9541 (m-40) cc_final: 0.9254 (m-40) REVERT: d 140 LYS cc_start: 0.9348 (mttt) cc_final: 0.9100 (tptp) REVERT: d 162 ARG cc_start: 0.8611 (mtt180) cc_final: 0.8375 (tpt-90) REVERT: d 163 ASP cc_start: 0.8555 (m-30) cc_final: 0.8347 (t0) REVERT: e 35 GLU cc_start: 0.9478 (pm20) cc_final: 0.8983 (pp20) REVERT: e 39 MET cc_start: 0.9551 (tpp) cc_final: 0.9287 (tpp) REVERT: e 51 ASP cc_start: 0.9267 (m-30) cc_final: 0.8866 (m-30) REVERT: e 66 MET cc_start: 0.8748 (mmm) cc_final: 0.8494 (mmm) REVERT: e 74 ASN cc_start: 0.9583 (m-40) cc_final: 0.9269 (m110) REVERT: e 79 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8492 (pp20) REVERT: e 104 ILE cc_start: 0.8898 (mt) cc_final: 0.8620 (mt) REVERT: e 114 GLN cc_start: 0.8259 (mt0) cc_final: 0.8051 (mt0) REVERT: e 173 ARG cc_start: 0.8552 (ttt180) cc_final: 0.8320 (tpm170) REVERT: e 178 SER cc_start: 0.8082 (p) cc_final: 0.6969 (t) REVERT: j 213 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9179 (mt-10) REVERT: k 21 ASN cc_start: 0.9536 (m110) cc_final: 0.9325 (t0) REVERT: k 52 LEU cc_start: 0.9680 (mt) cc_final: 0.9367 (mt) REVERT: k 67 GLN cc_start: 0.9276 (tp40) cc_final: 0.9035 (tp-100) REVERT: k 68 MET cc_start: 0.9334 (mtp) cc_final: 0.9133 (mtt) REVERT: k 83 VAL cc_start: 0.9195 (p) cc_final: 0.8798 (p) REVERT: k 96 MET cc_start: 0.5134 (ttm) cc_final: 0.4393 (ptp) REVERT: k 129 ILE cc_start: 0.9525 (mt) cc_final: 0.8870 (tt) REVERT: k 159 GLU cc_start: 0.8064 (tt0) cc_final: 0.7829 (tt0) REVERT: k 173 ARG cc_start: 0.9376 (ttt180) cc_final: 0.8935 (ttm170) outliers start: 9 outliers final: 2 residues processed: 1144 average time/residue: 0.3834 time to fit residues: 620.4165 Evaluate side-chains 699 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 696 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 1.9990 chunk 177 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 183 optimal weight: 30.0000 chunk 70 optimal weight: 20.0000 chunk 111 optimal weight: 50.0000 chunk 136 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN B 53 ASN B 179 GLN B 183 ASN B 219 GLN C 53 ASN C 219 GLN D 4 GLN D 95 GLN D 179 GLN G 4 GLN H 4 GLN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN J 108 ASN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 GLN Y 4 GLN Y 67 GLN d 4 GLN d 95 GLN e 53 ASN j 219 GLN k 9 GLN k 21 ASN ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.107841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.082968 restraints weight = 70972.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.085196 restraints weight = 51127.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.086852 restraints weight = 39780.491| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18834 Z= 0.182 Angle : 0.682 7.674 25587 Z= 0.358 Chirality : 0.046 0.231 2848 Planarity : 0.006 0.089 3345 Dihedral : 4.171 26.138 2500 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.30 % Allowed : 5.59 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2338 helix: 0.31 (0.13), residues: 1443 sheet: -1.19 (0.68), residues: 59 loop : -0.62 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 23 HIS 0.006 0.001 HIS k 62 PHE 0.028 0.002 PHE B 161 TYR 0.015 0.002 TYR D 169 ARG 0.008 0.001 ARG J 37 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 1037) hydrogen bonds : angle 4.53645 ( 3081) SS BOND : bond 0.00257 ( 10) SS BOND : angle 1.15188 ( 20) covalent geometry : bond 0.00392 (18824) covalent geometry : angle 0.68157 (25567) *********************** 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 878 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 872 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.9436 (t-100) cc_final: 0.9210 (t-100) REVERT: A 40 PHE cc_start: 0.9602 (t80) cc_final: 0.9234 (t80) REVERT: A 41 SER cc_start: 0.9524 (m) cc_final: 0.9137 (t) REVERT: A 50 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 51 ASP cc_start: 0.9275 (m-30) cc_final: 0.9019 (m-30) REVERT: A 57 ASN cc_start: 0.9654 (m110) cc_final: 0.9453 (m110) REVERT: A 71 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8832 (tm-30) REVERT: A 113 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8813 (mt-10) REVERT: A 128 GLU cc_start: 0.9279 (mm-30) cc_final: 0.9050 (tm-30) REVERT: B 21 ASN cc_start: 0.9542 (t0) cc_final: 0.9332 (t0) REVERT: B 24 VAL cc_start: 0.9594 (t) cc_final: 0.9103 (p) REVERT: B 25 LYS cc_start: 0.9608 (mttt) cc_final: 0.9183 (ttmt) REVERT: B 74 ASN cc_start: 0.9361 (m-40) cc_final: 0.9079 (m110) REVERT: B 104 ILE cc_start: 0.9185 (mt) cc_final: 0.8969 (mt) REVERT: B 114 GLN cc_start: 0.9009 (mt0) cc_final: 0.8786 (mt0) REVERT: B 118 MET cc_start: 0.8826 (mtm) cc_final: 0.8536 (ptp) REVERT: B 129 ILE cc_start: 0.9414 (pt) cc_final: 0.8614 (pt) REVERT: B 131 LYS cc_start: 0.9516 (ttmt) cc_final: 0.9136 (mmmt) REVERT: C 53 ASN cc_start: 0.9307 (m-40) cc_final: 0.8940 (m110) REVERT: C 62 HIS cc_start: 0.8920 (m-70) cc_final: 0.8551 (m90) REVERT: C 131 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8221 (mtpt) REVERT: C 187 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8946 (mp0) REVERT: C 189 LEU cc_start: 0.9167 (mm) cc_final: 0.8898 (mp) REVERT: C 215 MET cc_start: 0.8790 (mtm) cc_final: 0.8512 (mtm) REVERT: D 56 LEU cc_start: 0.9550 (mt) cc_final: 0.9305 (mt) REVERT: D 117 TRP cc_start: 0.8241 (m-10) cc_final: 0.7988 (m-10) REVERT: D 130 TYR cc_start: 0.9114 (t80) cc_final: 0.8897 (t80) REVERT: D 131 LYS cc_start: 0.8995 (tttt) cc_final: 0.8592 (tttt) REVERT: D 140 LYS cc_start: 0.9541 (mttt) cc_final: 0.9321 (tptp) REVERT: D 163 ASP cc_start: 0.8619 (m-30) cc_final: 0.8396 (m-30) REVERT: D 164 TYR cc_start: 0.7945 (t80) cc_final: 0.7664 (t80) REVERT: D 193 ASN cc_start: 0.9259 (m-40) cc_final: 0.7982 (p0) REVERT: D 215 MET cc_start: 0.7870 (ttt) cc_final: 0.7480 (ttm) REVERT: G 23 TRP cc_start: 0.9394 (t-100) cc_final: 0.9175 (t-100) REVERT: G 39 MET cc_start: 0.9516 (ttm) cc_final: 0.9297 (ttm) REVERT: G 57 ASN cc_start: 0.9573 (m-40) cc_final: 0.9337 (m110) REVERT: G 96 MET cc_start: 0.1456 (mpp) cc_final: -0.0740 (mtt) REVERT: G 131 LYS cc_start: 0.9441 (ttmt) cc_final: 0.9155 (mttt) REVERT: G 152 ASP cc_start: 0.8860 (m-30) cc_final: 0.8520 (p0) REVERT: G 161 PHE cc_start: 0.7970 (t80) cc_final: 0.7557 (t80) REVERT: G 215 MET cc_start: 0.8876 (mmt) cc_final: 0.8412 (mmm) REVERT: H 30 LYS cc_start: 0.6734 (tptt) cc_final: 0.6446 (mttt) REVERT: H 129 ILE cc_start: 0.8886 (tt) cc_final: 0.8241 (tt) REVERT: H 133 TRP cc_start: 0.8625 (m-10) cc_final: 0.7979 (m-10) REVERT: H 135 ILE cc_start: 0.9520 (mt) cc_final: 0.9299 (mt) REVERT: H 161 PHE cc_start: 0.7830 (t80) cc_final: 0.7402 (t80) REVERT: J 10 ILE cc_start: 0.9169 (tp) cc_final: 0.8533 (tp) REVERT: J 24 LEU cc_start: 0.8697 (mp) cc_final: 0.8152 (mm) REVERT: J 36 PHE cc_start: 0.8334 (t80) cc_final: 0.8084 (t80) REVERT: J 48 TYR cc_start: 0.8442 (m-10) cc_final: 0.7728 (m-10) REVERT: J 100 MET cc_start: 0.5770 (mmm) cc_final: 0.4659 (tpt) REVERT: J 122 LEU cc_start: 0.8237 (mt) cc_final: 0.7885 (mp) REVERT: J 129 PHE cc_start: 0.7470 (p90) cc_final: 0.6539 (p90) REVERT: J 157 THR cc_start: 0.9434 (t) cc_final: 0.9213 (m) REVERT: J 158 ILE cc_start: 0.8852 (mp) cc_final: 0.8641 (tt) REVERT: J 161 CYS cc_start: 0.3870 (p) cc_final: 0.3400 (p) REVERT: N 150 ILE cc_start: 0.7768 (tp) cc_final: 0.7472 (tp) REVERT: Y 20 LEU cc_start: 0.9582 (pp) cc_final: 0.9239 (pp) REVERT: Y 45 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8450 (mm-30) REVERT: Y 49 PRO cc_start: 0.9431 (Cg_exo) cc_final: 0.9025 (Cg_endo) REVERT: Y 55 MET cc_start: 0.9454 (ttm) cc_final: 0.9117 (ttm) REVERT: Y 56 LEU cc_start: 0.9445 (mt) cc_final: 0.9146 (mt) REVERT: Y 63 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8731 (mm-40) REVERT: Y 110 THR cc_start: 0.9423 (t) cc_final: 0.9184 (t) REVERT: Y 112 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8922 (pm20) REVERT: Y 131 LYS cc_start: 0.9063 (ttmt) cc_final: 0.8527 (mmmt) REVERT: Y 139 ASN cc_start: 0.9547 (m-40) cc_final: 0.9249 (m110) REVERT: d 63 GLN cc_start: 0.6558 (tt0) cc_final: 0.5575 (tt0) REVERT: d 114 GLN cc_start: 0.8775 (mp-120) cc_final: 0.8511 (mp10) REVERT: d 130 TYR cc_start: 0.7335 (t80) cc_final: 0.6464 (t80) REVERT: d 133 TRP cc_start: 0.8523 (m-10) cc_final: 0.7708 (m-10) REVERT: d 139 ASN cc_start: 0.9553 (m-40) cc_final: 0.9270 (m-40) REVERT: d 140 LYS cc_start: 0.9453 (mttt) cc_final: 0.9095 (tptp) REVERT: d 144 MET cc_start: 0.8445 (tmm) cc_final: 0.8143 (tmm) REVERT: d 203 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8681 (mttm) REVERT: e 10 MET cc_start: 0.7903 (mmp) cc_final: 0.7668 (mmp) REVERT: e 35 GLU cc_start: 0.9489 (pm20) cc_final: 0.9215 (pm20) REVERT: e 39 MET cc_start: 0.9442 (tpp) cc_final: 0.9061 (tpp) REVERT: e 55 MET cc_start: 0.8827 (ttt) cc_final: 0.8594 (ttt) REVERT: e 57 ASN cc_start: 0.9371 (m-40) cc_final: 0.9053 (m110) REVERT: e 66 MET cc_start: 0.9009 (mmm) cc_final: 0.8667 (mmm) REVERT: e 74 ASN cc_start: 0.9605 (m-40) cc_final: 0.9320 (m110) REVERT: e 79 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8518 (pp20) REVERT: e 104 ILE cc_start: 0.9125 (mt) cc_final: 0.8915 (mt) REVERT: e 118 MET cc_start: 0.8596 (mtt) cc_final: 0.8333 (mtt) REVERT: e 138 LEU cc_start: 0.9596 (mt) cc_final: 0.9383 (mt) REVERT: e 141 ILE cc_start: 0.9585 (mt) cc_final: 0.9322 (mt) REVERT: j 155 GLN cc_start: 0.5830 (mt0) cc_final: 0.5507 (pm20) REVERT: k 25 LYS cc_start: 0.9689 (ptmt) cc_final: 0.9380 (ptmm) REVERT: k 57 ASN cc_start: 0.9567 (m-40) cc_final: 0.9322 (m110) REVERT: k 96 MET cc_start: 0.5032 (ttm) cc_final: 0.4443 (ptp) REVERT: k 173 ARG cc_start: 0.8895 (ttt180) cc_final: 0.8598 (ttp80) outliers start: 6 outliers final: 2 residues processed: 876 average time/residue: 0.3441 time to fit residues: 432.4264 Evaluate side-chains 652 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 650 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 122 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 136 optimal weight: 40.0000 chunk 180 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 150 optimal weight: 0.0020 chunk 72 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 overall best weight: 3.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN C 84 HIS G 114 GLN J 92 HIS ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 GLN ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 GLN k 53 ASN ** k 95 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 = 0.3887 r_free = 0.3887 target = 0.106304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.081607 restraints weight = 71920.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.083863 restraints weight = 51073.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.085518 restraints weight = 39512.654| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18834 Z= 0.151 Angle : 0.665 10.292 25587 Z= 0.345 Chirality : 0.046 0.193 2848 Planarity : 0.005 0.059 3345 Dihedral : 4.348 29.181 2500 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.05 % Allowed : 4.80 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2338 helix: 0.40 (0.13), residues: 1439 sheet: -1.56 (0.59), residues: 68 loop : -0.40 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 184 HIS 0.003 0.001 HIS k 62 PHE 0.015 0.002 PHE J 7 TYR 0.027 0.002 TYR G 164 ARG 0.010 0.001 ARG e 132 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 1037) hydrogen bonds : angle 4.40396 ( 3081) SS BOND : bond 0.00292 ( 10) SS BOND : angle 1.08707 ( 20) covalent geometry : bond 0.00330 (18824) covalent geometry : angle 0.66482 (25567) *********************** 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 843 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 842 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.9622 (t80) cc_final: 0.8824 (t80) REVERT: A 41 SER cc_start: 0.9493 (m) cc_final: 0.9184 (t) REVERT: A 50 GLN cc_start: 0.9199 (tm-30) cc_final: 0.8905 (tm-30) REVERT: A 51 ASP cc_start: 0.9334 (m-30) cc_final: 0.8980 (m-30) REVERT: A 52 LEU cc_start: 0.9794 (mm) cc_final: 0.9547 (mm) REVERT: A 55 MET cc_start: 0.9390 (ttt) cc_final: 0.9050 (tmm) REVERT: A 56 LEU cc_start: 0.9528 (mt) cc_final: 0.9291 (mt) REVERT: A 57 ASN cc_start: 0.9664 (m110) cc_final: 0.9430 (m110) REVERT: A 70 LYS cc_start: 0.9422 (mtmm) cc_final: 0.8979 (mttt) REVERT: A 71 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8762 (tm-30) REVERT: A 113 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8810 (mt-10) REVERT: A 114 GLN cc_start: 0.9108 (pt0) cc_final: 0.8835 (pt0) REVERT: A 128 GLU cc_start: 0.9400 (mm-30) cc_final: 0.8734 (tp30) REVERT: B 21 ASN cc_start: 0.9583 (t0) cc_final: 0.8992 (t0) REVERT: B 25 LYS cc_start: 0.9668 (mttt) cc_final: 0.9270 (mtmm) REVERT: B 30 LYS cc_start: 0.9120 (mmpt) cc_final: 0.8824 (mmmt) REVERT: B 50 GLN cc_start: 0.9222 (mt0) cc_final: 0.8933 (mt0) REVERT: B 74 ASN cc_start: 0.9364 (m-40) cc_final: 0.9103 (m110) REVERT: B 114 GLN cc_start: 0.9131 (mt0) cc_final: 0.8658 (mt0) REVERT: B 118 MET cc_start: 0.8979 (mtm) cc_final: 0.8640 (ptp) REVERT: B 131 LYS cc_start: 0.9560 (ttmt) cc_final: 0.9246 (tttt) REVERT: B 132 ARG cc_start: 0.9226 (ttm110) cc_final: 0.8833 (ttm110) REVERT: C 53 ASN cc_start: 0.9369 (m-40) cc_final: 0.9095 (m110) REVERT: C 62 HIS cc_start: 0.8708 (m-70) cc_final: 0.8317 (m170) REVERT: C 74 ASN cc_start: 0.9383 (m110) cc_final: 0.9153 (m110) REVERT: C 100 ARG cc_start: 0.8204 (mpp-170) cc_final: 0.7802 (mpp-170) REVERT: C 128 GLU cc_start: 0.9106 (mp0) cc_final: 0.8771 (mp0) REVERT: C 131 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8154 (mtpt) REVERT: C 187 GLU cc_start: 0.9240 (mt-10) cc_final: 0.9001 (mp0) REVERT: C 189 LEU cc_start: 0.9193 (mm) cc_final: 0.8945 (mp) REVERT: C 215 MET cc_start: 0.8923 (mtm) cc_final: 0.8660 (mtp) REVERT: D 56 LEU cc_start: 0.9686 (mt) cc_final: 0.9319 (mt) REVERT: D 57 ASN cc_start: 0.9624 (m110) cc_final: 0.9353 (m110) REVERT: D 117 TRP cc_start: 0.8158 (m-10) cc_final: 0.7943 (m-10) REVERT: D 130 TYR cc_start: 0.9164 (t80) cc_final: 0.8941 (t80) REVERT: D 131 LYS cc_start: 0.8976 (tttt) cc_final: 0.8756 (tttt) REVERT: D 141 ILE cc_start: 0.8994 (mt) cc_final: 0.8744 (mt) REVERT: D 193 ASN cc_start: 0.9285 (m-40) cc_final: 0.8226 (m-40) REVERT: D 203 LYS cc_start: 0.9124 (mptt) cc_final: 0.8756 (mmtp) REVERT: D 215 MET cc_start: 0.7681 (ttt) cc_final: 0.7253 (ttm) REVERT: G 23 TRP cc_start: 0.9314 (t-100) cc_final: 0.8840 (t-100) REVERT: G 57 ASN cc_start: 0.9557 (m-40) cc_final: 0.9324 (m110) REVERT: G 96 MET cc_start: 0.1275 (mpp) cc_final: -0.0714 (mtt) REVERT: G 139 ASN cc_start: 0.9602 (m110) cc_final: 0.9382 (m110) REVERT: G 152 ASP cc_start: 0.8916 (m-30) cc_final: 0.8448 (p0) REVERT: G 161 PHE cc_start: 0.8007 (t80) cc_final: 0.7452 (t80) REVERT: G 185 MET cc_start: 0.9050 (mtt) cc_final: 0.8334 (mtt) REVERT: G 214 MET cc_start: 0.9182 (mtm) cc_final: 0.8962 (ptp) REVERT: G 215 MET cc_start: 0.8715 (mmt) cc_final: 0.8478 (mmm) REVERT: H 132 ARG cc_start: 0.9197 (mmp80) cc_final: 0.8978 (mmm160) REVERT: H 215 MET cc_start: 0.8994 (tpt) cc_final: 0.8647 (mmm) REVERT: J 10 ILE cc_start: 0.9226 (tp) cc_final: 0.8844 (tp) REVERT: J 24 LEU cc_start: 0.8831 (mp) cc_final: 0.8358 (mm) REVERT: J 25 PHE cc_start: 0.8477 (m-80) cc_final: 0.7862 (m-80) REVERT: J 36 PHE cc_start: 0.8435 (t80) cc_final: 0.8138 (t80) REVERT: J 48 TYR cc_start: 0.8554 (m-10) cc_final: 0.7887 (m-10) REVERT: J 100 MET cc_start: 0.5918 (mmm) cc_final: 0.5254 (tpp) REVERT: J 161 CYS cc_start: 0.4053 (p) cc_final: 0.3672 (p) REVERT: N 185 MET cc_start: 0.8694 (ptp) cc_final: 0.8289 (ptp) REVERT: N 215 MET cc_start: 0.8454 (mtp) cc_final: 0.8090 (mtp) REVERT: Y 20 LEU cc_start: 0.9612 (pp) cc_final: 0.9293 (pp) REVERT: Y 56 LEU cc_start: 0.9489 (mt) cc_final: 0.9205 (mt) REVERT: Y 63 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8683 (mm-40) REVERT: Y 96 MET cc_start: 0.1531 (mtt) cc_final: 0.1115 (mtp) REVERT: Y 103 ASP cc_start: 0.7628 (t70) cc_final: 0.7297 (t70) REVERT: Y 110 THR cc_start: 0.9496 (t) cc_final: 0.9179 (t) REVERT: Y 112 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8958 (pm20) REVERT: Y 113 GLU cc_start: 0.8125 (pm20) cc_final: 0.7463 (pm20) REVERT: Y 139 ASN cc_start: 0.9502 (m-40) cc_final: 0.9194 (m110) REVERT: d 39 MET cc_start: 0.7259 (tpp) cc_final: 0.7041 (tpp) REVERT: d 63 GLN cc_start: 0.6060 (tt0) cc_final: 0.5199 (tt0) REVERT: d 129 ILE cc_start: 0.9587 (tp) cc_final: 0.9258 (tp) REVERT: d 130 TYR cc_start: 0.7306 (t80) cc_final: 0.6463 (t80) REVERT: d 133 TRP cc_start: 0.8502 (m-10) cc_final: 0.7537 (m-10) REVERT: d 139 ASN cc_start: 0.9556 (m-40) cc_final: 0.9282 (m-40) REVERT: d 140 LYS cc_start: 0.9448 (mttt) cc_final: 0.9073 (tptp) REVERT: d 144 MET cc_start: 0.8833 (tmm) cc_final: 0.8517 (tmm) REVERT: e 10 MET cc_start: 0.8231 (mmp) cc_final: 0.8012 (mmp) REVERT: e 39 MET cc_start: 0.9425 (tpp) cc_final: 0.9103 (tpp) REVERT: e 51 ASP cc_start: 0.9438 (m-30) cc_final: 0.9187 (m-30) REVERT: e 55 MET cc_start: 0.8888 (ttt) cc_final: 0.8641 (ttt) REVERT: e 57 ASN cc_start: 0.9342 (m-40) cc_final: 0.9028 (m110) REVERT: e 66 MET cc_start: 0.8927 (mmm) cc_final: 0.8692 (mmm) REVERT: e 70 LYS cc_start: 0.9181 (ptpp) cc_final: 0.8963 (ptpt) REVERT: e 74 ASN cc_start: 0.9609 (m-40) cc_final: 0.9280 (m110) REVERT: e 79 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8535 (pp20) REVERT: e 82 ARG cc_start: 0.8994 (tmm160) cc_final: 0.8752 (ttp80) REVERT: e 100 ARG cc_start: 0.6946 (mmm160) cc_final: 0.6483 (mmm160) REVERT: e 111 LEU cc_start: 0.9235 (pt) cc_final: 0.8581 (pt) REVERT: e 138 LEU cc_start: 0.9657 (mt) cc_final: 0.9456 (mt) REVERT: e 168 PHE cc_start: 0.9464 (t80) cc_final: 0.9158 (t80) REVERT: e 185 MET cc_start: 0.9063 (mtm) cc_final: 0.8828 (mtp) REVERT: e 215 MET cc_start: 0.8161 (ptm) cc_final: 0.7934 (ptp) REVERT: j 155 GLN cc_start: 0.5827 (mt0) cc_final: 0.5527 (pm20) REVERT: j 181 VAL cc_start: 0.8998 (t) cc_final: 0.8740 (t) REVERT: k 21 ASN cc_start: 0.9334 (t0) cc_final: 0.9076 (t0) REVERT: k 25 LYS cc_start: 0.9646 (ptmt) cc_final: 0.9342 (ptmm) REVERT: k 57 ASN cc_start: 0.9542 (m-40) cc_final: 0.9283 (m110) REVERT: k 96 MET cc_start: 0.4722 (ttm) cc_final: 0.4005 (ptp) REVERT: k 104 ILE cc_start: 0.8417 (mm) cc_final: 0.7958 (mm) REVERT: k 118 MET cc_start: 0.8840 (mmm) cc_final: 0.8617 (mmm) REVERT: k 153 ILE cc_start: 0.9279 (mm) cc_final: 0.8932 (tt) REVERT: k 173 ARG cc_start: 0.8929 (ttt180) cc_final: 0.8530 (ttp80) outliers start: 1 outliers final: 0 residues processed: 842 average time/residue: 0.3393 time to fit residues: 410.5318 Evaluate side-chains 654 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 654 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 85 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 157 optimal weight: 0.0040 chunk 133 optimal weight: 40.0000 chunk 231 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 165 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 0.0370 overall best weight: 2.8076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN J 163 GLN Y 114 GLN ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 12 HIS k 53 ASN ** k 95 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 = 0.3884 r_free = 0.3884 target = 0.106325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.081649 restraints weight = 71988.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.083857 restraints weight = 51032.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.085508 restraints weight = 39439.827| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18834 Z= 0.140 Angle : 0.659 11.817 25587 Z= 0.339 Chirality : 0.046 0.284 2848 Planarity : 0.005 0.071 3345 Dihedral : 4.387 30.226 2500 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2338 helix: 0.55 (0.14), residues: 1433 sheet: -1.58 (0.53), residues: 77 loop : -0.23 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 184 HIS 0.005 0.001 HIS C 84 PHE 0.019 0.001 PHE N 161 TYR 0.028 0.002 TYR D 164 ARG 0.008 0.001 ARG J 148 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 1037) hydrogen bonds : angle 4.46103 ( 3081) SS BOND : bond 0.00240 ( 10) SS BOND : angle 1.01917 ( 20) covalent geometry : bond 0.00309 (18824) covalent geometry : angle 0.65864 (25567) *********************** 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 824 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 823 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.9618 (t80) cc_final: 0.8820 (t80) REVERT: A 52 LEU cc_start: 0.9784 (mm) cc_final: 0.9527 (mm) REVERT: A 55 MET cc_start: 0.9281 (ttt) cc_final: 0.8995 (tmm) REVERT: A 56 LEU cc_start: 0.9494 (mt) cc_final: 0.9251 (mt) REVERT: A 70 LYS cc_start: 0.9412 (mtmm) cc_final: 0.8976 (mttt) REVERT: A 71 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8818 (tm-30) REVERT: A 86 VAL cc_start: 0.6990 (t) cc_final: 0.6784 (t) REVERT: A 113 GLU cc_start: 0.9363 (mt-10) cc_final: 0.8846 (mt-10) REVERT: A 128 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8863 (tp30) REVERT: B 21 ASN cc_start: 0.9534 (t0) cc_final: 0.9328 (t0) REVERT: B 30 LYS cc_start: 0.9142 (mmpt) cc_final: 0.8749 (mmmt) REVERT: B 50 GLN cc_start: 0.9236 (mt0) cc_final: 0.8937 (mt0) REVERT: B 68 MET cc_start: 0.9188 (mtt) cc_final: 0.8955 (mtt) REVERT: B 74 ASN cc_start: 0.9351 (m-40) cc_final: 0.8934 (m110) REVERT: B 114 GLN cc_start: 0.9161 (mt0) cc_final: 0.8755 (mt0) REVERT: B 118 MET cc_start: 0.8999 (mtm) cc_final: 0.8656 (ptp) REVERT: B 131 LYS cc_start: 0.9551 (ttmt) cc_final: 0.9221 (tttt) REVERT: B 134 ILE cc_start: 0.9603 (mm) cc_final: 0.9292 (mm) REVERT: B 211 LEU cc_start: 0.8334 (tt) cc_final: 0.8119 (tt) REVERT: C 53 ASN cc_start: 0.9401 (m-40) cc_final: 0.9166 (m110) REVERT: C 55 MET cc_start: 0.8800 (ttt) cc_final: 0.8488 (ttp) REVERT: C 62 HIS cc_start: 0.8517 (m-70) cc_final: 0.8305 (m170) REVERT: C 74 ASN cc_start: 0.9443 (m110) cc_final: 0.9188 (m110) REVERT: C 128 GLU cc_start: 0.9103 (mp0) cc_final: 0.8822 (mp0) REVERT: C 131 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8239 (mtpt) REVERT: C 181 VAL cc_start: 0.8805 (p) cc_final: 0.8506 (p) REVERT: C 187 GLU cc_start: 0.9279 (mt-10) cc_final: 0.9040 (mp0) REVERT: C 189 LEU cc_start: 0.9220 (mm) cc_final: 0.8906 (mp) REVERT: D 45 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7669 (mm-30) REVERT: D 56 LEU cc_start: 0.9623 (mt) cc_final: 0.9351 (mt) REVERT: D 57 ASN cc_start: 0.9631 (m110) cc_final: 0.9353 (m110) REVERT: D 130 TYR cc_start: 0.9212 (t80) cc_final: 0.8955 (t80) REVERT: D 131 LYS cc_start: 0.9148 (tttt) cc_final: 0.8781 (tttt) REVERT: D 141 ILE cc_start: 0.8973 (mt) cc_final: 0.8758 (mt) REVERT: D 163 ASP cc_start: 0.8607 (m-30) cc_final: 0.8370 (m-30) REVERT: D 215 MET cc_start: 0.7910 (ttt) cc_final: 0.7207 (ptm) REVERT: G 13 GLN cc_start: 0.9388 (mm-40) cc_final: 0.9186 (mp10) REVERT: G 23 TRP cc_start: 0.9258 (t-100) cc_final: 0.8401 (t-100) REVERT: G 52 LEU cc_start: 0.9773 (mt) cc_final: 0.9488 (mt) REVERT: G 55 MET cc_start: 0.9291 (ttt) cc_final: 0.8783 (tmm) REVERT: G 56 LEU cc_start: 0.9578 (mt) cc_final: 0.9151 (mt) REVERT: G 58 THR cc_start: 0.9537 (p) cc_final: 0.9205 (p) REVERT: G 96 MET cc_start: 0.1743 (mpp) cc_final: -0.0110 (mtp) REVERT: G 114 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8422 (mm110) REVERT: G 139 ASN cc_start: 0.9615 (m110) cc_final: 0.9326 (m110) REVERT: G 152 ASP cc_start: 0.8933 (m-30) cc_final: 0.8409 (p0) REVERT: G 181 VAL cc_start: 0.9124 (t) cc_final: 0.8804 (p) REVERT: G 185 MET cc_start: 0.8997 (mtt) cc_final: 0.8245 (mtt) REVERT: G 214 MET cc_start: 0.9235 (mtm) cc_final: 0.8995 (ptp) REVERT: H 130 TYR cc_start: 0.5760 (t80) cc_final: 0.5126 (t80) REVERT: H 167 ARG cc_start: 0.9072 (mmm160) cc_final: 0.8384 (mmm160) REVERT: H 215 MET cc_start: 0.8987 (tpt) cc_final: 0.8616 (mmm) REVERT: J 10 ILE cc_start: 0.9205 (tp) cc_final: 0.8653 (tp) REVERT: J 24 LEU cc_start: 0.8922 (mp) cc_final: 0.8404 (mm) REVERT: J 25 PHE cc_start: 0.8536 (m-80) cc_final: 0.7972 (m-80) REVERT: J 32 THR cc_start: 0.9090 (t) cc_final: 0.8746 (t) REVERT: J 36 PHE cc_start: 0.8478 (t80) cc_final: 0.8189 (t80) REVERT: J 43 GLU cc_start: 0.8434 (pp20) cc_final: 0.8231 (pp20) REVERT: J 48 TYR cc_start: 0.8578 (m-10) cc_final: 0.7970 (m-10) REVERT: J 76 LYS cc_start: 0.6057 (mmtp) cc_final: 0.5753 (mmmm) REVERT: J 100 MET cc_start: 0.6115 (mmm) cc_final: 0.5389 (tpp) REVERT: J 129 PHE cc_start: 0.7743 (p90) cc_final: 0.7364 (p90) REVERT: N 179 GLN cc_start: 0.9078 (pp30) cc_final: 0.8365 (pm20) REVERT: N 185 MET cc_start: 0.8681 (ptp) cc_final: 0.8192 (ptp) REVERT: Y 5 ASN cc_start: 0.8156 (t0) cc_final: 0.7706 (t0) REVERT: Y 20 LEU cc_start: 0.9626 (pp) cc_final: 0.9255 (pp) REVERT: Y 52 LEU cc_start: 0.9737 (mm) cc_final: 0.9430 (mp) REVERT: Y 56 LEU cc_start: 0.9459 (mt) cc_final: 0.9186 (mt) REVERT: Y 63 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8778 (mm110) REVERT: Y 97 ARG cc_start: 0.6851 (pmt-80) cc_final: 0.6587 (pmt-80) REVERT: Y 110 THR cc_start: 0.9286 (t) cc_final: 0.9026 (t) REVERT: Y 139 ASN cc_start: 0.9509 (m-40) cc_final: 0.9204 (m110) REVERT: d 39 MET cc_start: 0.7534 (tpp) cc_final: 0.6975 (tpt) REVERT: d 129 ILE cc_start: 0.9563 (tp) cc_final: 0.8696 (tp) REVERT: d 133 TRP cc_start: 0.8524 (m-10) cc_final: 0.6956 (m-10) REVERT: d 139 ASN cc_start: 0.9583 (m-40) cc_final: 0.9325 (m-40) REVERT: d 140 LYS cc_start: 0.9487 (mttt) cc_final: 0.9048 (tptp) REVERT: d 167 ARG cc_start: 0.8481 (mmp-170) cc_final: 0.8058 (mmp80) REVERT: e 10 MET cc_start: 0.8295 (mmp) cc_final: 0.8047 (mmp) REVERT: e 39 MET cc_start: 0.9404 (tpp) cc_final: 0.9101 (tpp) REVERT: e 57 ASN cc_start: 0.9387 (m-40) cc_final: 0.9111 (m110) REVERT: e 66 MET cc_start: 0.8910 (mmm) cc_final: 0.8699 (mmm) REVERT: e 70 LYS cc_start: 0.9208 (ptpp) cc_final: 0.8996 (ptpt) REVERT: e 79 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8527 (pp20) REVERT: e 82 ARG cc_start: 0.9006 (tmm160) cc_final: 0.8778 (ttp80) REVERT: e 100 ARG cc_start: 0.6968 (mmm160) cc_final: 0.6664 (mmm-85) REVERT: e 118 MET cc_start: 0.8756 (mtt) cc_final: 0.8465 (mtt) REVERT: e 141 ILE cc_start: 0.9523 (mt) cc_final: 0.9245 (mt) REVERT: e 185 MET cc_start: 0.9060 (mtm) cc_final: 0.8824 (mtp) REVERT: e 214 MET cc_start: 0.9201 (ptp) cc_final: 0.8512 (tpt) REVERT: e 215 MET cc_start: 0.8154 (ptm) cc_final: 0.7812 (ptm) REVERT: j 155 GLN cc_start: 0.6147 (mt0) cc_final: 0.5911 (pm20) REVERT: k 25 LYS cc_start: 0.9524 (ptmt) cc_final: 0.9272 (pttm) REVERT: k 96 MET cc_start: 0.4951 (ttm) cc_final: 0.3810 (mpp) REVERT: k 104 ILE cc_start: 0.8464 (mm) cc_final: 0.8007 (mm) REVERT: k 153 ILE cc_start: 0.9317 (mm) cc_final: 0.9106 (tp) REVERT: k 173 ARG cc_start: 0.8938 (ttt180) cc_final: 0.8681 (ttm170) outliers start: 1 outliers final: 0 residues processed: 823 average time/residue: 0.3640 time to fit residues: 437.7781 Evaluate side-chains 635 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 635 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 80 optimal weight: 40.0000 chunk 37 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN B 176 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN G 193 ASN J 92 HIS J 108 ASN J 163 GLN ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 53 ASN k 74 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.103521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.079528 restraints weight = 74227.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.081672 restraints weight = 52325.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.083255 restraints weight = 40326.408| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 18834 Z= 0.175 Angle : 0.679 10.882 25587 Z= 0.350 Chirality : 0.046 0.197 2848 Planarity : 0.005 0.076 3345 Dihedral : 4.518 33.705 2500 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2338 helix: 0.55 (0.13), residues: 1440 sheet: -1.34 (0.61), residues: 66 loop : -0.16 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 184 HIS 0.007 0.001 HIS C 62 PHE 0.022 0.002 PHE Y 40 TYR 0.021 0.002 TYR C 130 ARG 0.015 0.001 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 1037) hydrogen bonds : angle 4.57164 ( 3081) SS BOND : bond 0.00300 ( 10) SS BOND : angle 1.00969 ( 20) covalent geometry : bond 0.00369 (18824) covalent geometry : angle 0.67830 (25567) *********************** 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 810 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 809 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.9596 (t80) cc_final: 0.9167 (t80) REVERT: A 52 LEU cc_start: 0.9782 (mm) cc_final: 0.9560 (mm) REVERT: A 57 ASN cc_start: 0.9680 (m110) cc_final: 0.9442 (m110) REVERT: A 71 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8816 (tm-30) REVERT: A 86 VAL cc_start: 0.7116 (t) cc_final: 0.6895 (t) REVERT: A 113 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8812 (mt-10) REVERT: A 128 GLU cc_start: 0.9281 (mm-30) cc_final: 0.9059 (tm-30) REVERT: B 21 ASN cc_start: 0.9524 (t0) cc_final: 0.9196 (t0) REVERT: B 30 LYS cc_start: 0.9037 (mmpt) cc_final: 0.8605 (mmmt) REVERT: B 50 GLN cc_start: 0.9295 (mt0) cc_final: 0.8973 (mt0) REVERT: B 55 MET cc_start: 0.9469 (ttt) cc_final: 0.9129 (tpp) REVERT: B 68 MET cc_start: 0.9253 (mtt) cc_final: 0.8816 (mtt) REVERT: B 74 ASN cc_start: 0.9350 (m-40) cc_final: 0.8985 (m110) REVERT: B 114 GLN cc_start: 0.9299 (mt0) cc_final: 0.8865 (mt0) REVERT: B 118 MET cc_start: 0.9117 (mtm) cc_final: 0.8760 (ptp) REVERT: B 131 LYS cc_start: 0.9548 (ttmt) cc_final: 0.9320 (tttt) REVERT: C 18 ARG cc_start: 0.9143 (mtm-85) cc_final: 0.8912 (mtt90) REVERT: C 53 ASN cc_start: 0.9413 (m-40) cc_final: 0.9140 (m110) REVERT: C 55 MET cc_start: 0.8799 (ttt) cc_final: 0.8590 (ttp) REVERT: C 68 MET cc_start: 0.9258 (mtt) cc_final: 0.8992 (mtt) REVERT: C 74 ASN cc_start: 0.9424 (m110) cc_final: 0.9180 (m110) REVERT: C 79 GLU cc_start: 0.9307 (tp30) cc_final: 0.8983 (tp30) REVERT: C 128 GLU cc_start: 0.9148 (mp0) cc_final: 0.8886 (mp0) REVERT: C 187 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8991 (mm-30) REVERT: C 189 LEU cc_start: 0.9288 (mm) cc_final: 0.8997 (mp) REVERT: D 15 ILE cc_start: 0.8670 (mm) cc_final: 0.8446 (mm) REVERT: D 56 LEU cc_start: 0.9728 (mt) cc_final: 0.9384 (mt) REVERT: D 130 TYR cc_start: 0.9270 (t80) cc_final: 0.9057 (t80) REVERT: D 131 LYS cc_start: 0.9222 (tttt) cc_final: 0.8716 (tttt) REVERT: D 141 ILE cc_start: 0.8943 (mt) cc_final: 0.8727 (mt) REVERT: D 143 ARG cc_start: 0.8624 (mmm160) cc_final: 0.8290 (mmm160) REVERT: D 163 ASP cc_start: 0.8689 (m-30) cc_final: 0.8454 (m-30) REVERT: D 172 LEU cc_start: 0.9013 (tt) cc_final: 0.8668 (tt) REVERT: D 184 TRP cc_start: 0.8482 (t60) cc_final: 0.8187 (t60) REVERT: D 215 MET cc_start: 0.7851 (ttt) cc_final: 0.7239 (ptm) REVERT: G 23 TRP cc_start: 0.9328 (t-100) cc_final: 0.8485 (t-100) REVERT: G 39 MET cc_start: 0.9402 (ttp) cc_final: 0.8848 (tmm) REVERT: G 40 PHE cc_start: 0.9231 (t80) cc_final: 0.8709 (t80) REVERT: G 43 LEU cc_start: 0.9769 (mm) cc_final: 0.9345 (mm) REVERT: G 52 LEU cc_start: 0.9804 (mt) cc_final: 0.9587 (mt) REVERT: G 55 MET cc_start: 0.9307 (ttt) cc_final: 0.8852 (tmm) REVERT: G 56 LEU cc_start: 0.9567 (mt) cc_final: 0.9133 (mt) REVERT: G 57 ASN cc_start: 0.9518 (m-40) cc_final: 0.9282 (m110) REVERT: G 96 MET cc_start: 0.2122 (mpp) cc_final: 0.0669 (mmm) REVERT: G 128 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8207 (tm-30) REVERT: G 139 ASN cc_start: 0.9618 (m110) cc_final: 0.9302 (m110) REVERT: G 152 ASP cc_start: 0.9023 (m-30) cc_final: 0.8461 (p0) REVERT: G 170 LYS cc_start: 0.9403 (mtpt) cc_final: 0.8464 (mmtm) REVERT: G 181 VAL cc_start: 0.9223 (t) cc_final: 0.9002 (p) REVERT: G 185 MET cc_start: 0.9067 (mtt) cc_final: 0.8365 (mtt) REVERT: G 211 LEU cc_start: 0.9124 (tp) cc_final: 0.8705 (tp) REVERT: H 10 MET cc_start: 0.4826 (ttt) cc_final: 0.4358 (ttt) REVERT: H 215 MET cc_start: 0.9020 (tpt) cc_final: 0.8671 (mmm) REVERT: J 10 ILE cc_start: 0.9171 (tp) cc_final: 0.8648 (tp) REVERT: J 24 LEU cc_start: 0.9099 (mp) cc_final: 0.8532 (mm) REVERT: J 25 PHE cc_start: 0.8499 (m-80) cc_final: 0.7841 (m-80) REVERT: J 32 THR cc_start: 0.8856 (t) cc_final: 0.8574 (t) REVERT: J 34 GLU cc_start: 0.9499 (tp30) cc_final: 0.9217 (tp30) REVERT: J 35 ASN cc_start: 0.8834 (m110) cc_final: 0.7862 (m110) REVERT: J 76 LYS cc_start: 0.7858 (mmtp) cc_final: 0.7643 (mmmm) REVERT: J 100 MET cc_start: 0.5789 (mmm) cc_final: 0.5218 (tpp) REVERT: J 111 GLN cc_start: 0.9143 (mp-120) cc_final: 0.8715 (mm-40) REVERT: J 129 PHE cc_start: 0.7645 (p90) cc_final: 0.7385 (p90) REVERT: J 136 MET cc_start: 0.6595 (mpp) cc_final: 0.6391 (mpp) REVERT: N 179 GLN cc_start: 0.9134 (pp30) cc_final: 0.8602 (pm20) REVERT: N 181 VAL cc_start: 0.9121 (p) cc_final: 0.8700 (p) REVERT: N 185 MET cc_start: 0.8646 (ptp) cc_final: 0.8081 (ptp) REVERT: Y 5 ASN cc_start: 0.8173 (t0) cc_final: 0.7943 (t0) REVERT: Y 20 LEU cc_start: 0.9616 (pp) cc_final: 0.9311 (pp) REVERT: Y 55 MET cc_start: 0.9449 (ttm) cc_final: 0.9173 (ttm) REVERT: Y 56 LEU cc_start: 0.9511 (mt) cc_final: 0.9229 (mt) REVERT: Y 63 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8621 (mm-40) REVERT: Y 113 GLU cc_start: 0.9081 (pm20) cc_final: 0.8798 (pm20) REVERT: Y 117 TRP cc_start: 0.7930 (m-10) cc_final: 0.6766 (m-90) REVERT: Y 131 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8177 (tptt) REVERT: Y 139 ASN cc_start: 0.9487 (m-40) cc_final: 0.9180 (m110) REVERT: d 23 TRP cc_start: 0.8438 (t-100) cc_final: 0.8196 (t-100) REVERT: d 39 MET cc_start: 0.7694 (tpp) cc_final: 0.7445 (tpp) REVERT: d 66 MET cc_start: 0.9203 (mtm) cc_final: 0.8989 (mtp) REVERT: d 133 TRP cc_start: 0.7805 (m-10) cc_final: 0.7162 (m-10) REVERT: d 139 ASN cc_start: 0.9601 (m-40) cc_final: 0.9333 (m-40) REVERT: d 140 LYS cc_start: 0.9500 (mttt) cc_final: 0.9140 (tptp) REVERT: d 167 ARG cc_start: 0.8525 (mmp-170) cc_final: 0.8087 (mmp80) REVERT: e 39 MET cc_start: 0.9384 (tpp) cc_final: 0.9128 (tpp) REVERT: e 66 MET cc_start: 0.8948 (mmm) cc_final: 0.8736 (mmm) REVERT: e 70 LYS cc_start: 0.9224 (ptpp) cc_final: 0.9000 (ptpt) REVERT: e 79 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8603 (pp20) REVERT: e 82 ARG cc_start: 0.9027 (tmm160) cc_final: 0.8770 (ttp80) REVERT: e 96 MET cc_start: 0.6988 (mtp) cc_final: 0.6578 (mmm) REVERT: e 104 ILE cc_start: 0.8865 (mp) cc_final: 0.8595 (mp) REVERT: e 117 TRP cc_start: 0.8483 (m-10) cc_final: 0.8130 (m100) REVERT: e 118 MET cc_start: 0.8866 (mtt) cc_final: 0.8646 (mtt) REVERT: e 139 ASN cc_start: 0.9501 (m-40) cc_final: 0.9134 (m110) REVERT: e 185 MET cc_start: 0.9072 (mtm) cc_final: 0.8859 (mtp) REVERT: j 155 GLN cc_start: 0.6444 (mt0) cc_final: 0.5975 (pm20) REVERT: k 21 ASN cc_start: 0.9313 (t0) cc_final: 0.9052 (t0) REVERT: k 25 LYS cc_start: 0.9710 (ptmt) cc_final: 0.9401 (ptmm) REVERT: k 55 MET cc_start: 0.9519 (ttm) cc_final: 0.9283 (ttm) REVERT: k 68 MET cc_start: 0.9408 (mtp) cc_final: 0.8997 (mtt) REVERT: k 76 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9153 (mm-30) REVERT: k 96 MET cc_start: 0.4844 (ttm) cc_final: 0.3744 (mpp) REVERT: k 104 ILE cc_start: 0.8422 (mm) cc_final: 0.8006 (mm) REVERT: k 115 ILE cc_start: 0.9014 (pt) cc_final: 0.8227 (pt) REVERT: k 118 MET cc_start: 0.8491 (mmp) cc_final: 0.7969 (mtp) outliers start: 1 outliers final: 0 residues processed: 809 average time/residue: 0.3331 time to fit residues: 388.8448 Evaluate side-chains 626 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 626 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 180 optimal weight: 20.0000 chunk 138 optimal weight: 0.0770 chunk 200 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 33 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 116 optimal weight: 40.0000 chunk 191 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 overall best weight: 7.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 114 GLN J 92 HIS J 163 GLN Y 95 GLN j 195 ASN k 74 ASN ** k 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.100913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.077016 restraints weight = 74804.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.079182 restraints weight = 52516.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.080779 restraints weight = 40186.090| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.7214 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= 0.184 Angle : 0.698 12.041 25587 Z= 0.363 Chirality : 0.046 0.267 2848 Planarity : 0.005 0.066 3345 Dihedral : 4.644 39.664 2500 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.05 % Allowed : 2.55 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2338 helix: 0.49 (0.13), residues: 1439 sheet: -0.76 (0.65), residues: 61 loop : -0.22 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 23 HIS 0.007 0.001 HIS C 84 PHE 0.029 0.002 PHE H 161 TYR 0.018 0.002 TYR e 130 ARG 0.010 0.001 ARG d 82 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 1037) hydrogen bonds : angle 4.72184 ( 3081) SS BOND : bond 0.00521 ( 10) SS BOND : angle 1.51009 ( 20) covalent geometry : bond 0.00393 (18824) covalent geometry : angle 0.69729 (25567) *********************** 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 781 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 780 time to evaluate : 2.652 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: A 25 LYS cc_start: 0.9715 (ptmm) cc_final: 0.9467 (ptmm) REVERT: A 33 SER cc_start: 0.8565 (t) cc_final: 0.8272 (p) REVERT: A 50 GLN cc_start: 0.9249 (tm-30) cc_final: 0.9043 (tm-30) REVERT: A 51 ASP cc_start: 0.9333 (m-30) cc_final: 0.9047 (m-30) REVERT: A 52 LEU cc_start: 0.9786 (mm) cc_final: 0.9565 (mm) REVERT: A 57 ASN cc_start: 0.9686 (m110) cc_final: 0.9423 (m110) REVERT: A 71 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8841 (tm-30) REVERT: A 113 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8836 (mt-10) REVERT: A 128 GLU cc_start: 0.9293 (mm-30) cc_final: 0.9008 (tm-30) REVERT: A 144 MET cc_start: 0.8856 (ttt) cc_final: 0.8652 (ttt) REVERT: B 21 ASN cc_start: 0.9461 (t0) cc_final: 0.9244 (t0) REVERT: B 30 LYS cc_start: 0.9060 (mmpt) cc_final: 0.8591 (mmmt) REVERT: B 32 PHE cc_start: 0.8618 (m-80) cc_final: 0.8347 (m-80) REVERT: B 50 GLN cc_start: 0.9359 (mt0) cc_final: 0.9040 (mt0) REVERT: B 55 MET cc_start: 0.9580 (ttt) cc_final: 0.9160 (tpp) REVERT: B 68 MET cc_start: 0.9330 (mtt) cc_final: 0.8826 (mtt) REVERT: B 70 LYS cc_start: 0.9751 (ptmm) cc_final: 0.9545 (ptmm) REVERT: B 74 ASN cc_start: 0.9425 (m-40) cc_final: 0.8983 (m110) REVERT: B 114 GLN cc_start: 0.9423 (mt0) cc_final: 0.8984 (mt0) REVERT: B 118 MET cc_start: 0.9221 (mtm) cc_final: 0.8859 (ptp) REVERT: B 131 LYS cc_start: 0.9575 (ttmt) cc_final: 0.9286 (tttt) REVERT: B 144 MET cc_start: 0.9269 (ttt) cc_final: 0.8968 (ttt) REVERT: C 18 ARG cc_start: 0.9184 (mtm-85) cc_final: 0.8944 (mtt90) REVERT: C 53 ASN cc_start: 0.9477 (m-40) cc_final: 0.9160 (m110) REVERT: C 55 MET cc_start: 0.8935 (ttt) cc_final: 0.8376 (tmm) REVERT: C 67 GLN cc_start: 0.8267 (pm20) cc_final: 0.8007 (pm20) REVERT: C 128 GLU cc_start: 0.9193 (mp0) cc_final: 0.8872 (mp0) REVERT: C 131 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8467 (mtpt) REVERT: C 187 GLU cc_start: 0.9273 (mt-10) cc_final: 0.9045 (mm-30) REVERT: C 189 LEU cc_start: 0.9297 (mm) cc_final: 0.9052 (mp) REVERT: D 40 PHE cc_start: 0.9462 (t80) cc_final: 0.9240 (t80) REVERT: D 56 LEU cc_start: 0.9742 (mt) cc_final: 0.9390 (mt) REVERT: D 130 TYR cc_start: 0.9304 (t80) cc_final: 0.9072 (t80) REVERT: D 131 LYS cc_start: 0.9240 (tttt) cc_final: 0.8834 (mttt) REVERT: D 134 ILE cc_start: 0.9660 (mt) cc_final: 0.9424 (mt) REVERT: D 141 ILE cc_start: 0.8981 (mt) cc_final: 0.8424 (mt) REVERT: D 143 ARG cc_start: 0.8688 (mmm160) cc_final: 0.8215 (mmm160) REVERT: D 163 ASP cc_start: 0.8720 (m-30) cc_final: 0.8490 (m-30) REVERT: D 215 MET cc_start: 0.7846 (ttt) cc_final: 0.7439 (ttm) REVERT: G 23 TRP cc_start: 0.9306 (t-100) cc_final: 0.8893 (t-100) REVERT: G 45 GLU cc_start: 0.8855 (pm20) cc_final: 0.8640 (pm20) REVERT: G 57 ASN cc_start: 0.9477 (m-40) cc_final: 0.9233 (m110) REVERT: G 58 THR cc_start: 0.9533 (p) cc_final: 0.9258 (p) REVERT: G 96 MET cc_start: 0.2335 (mpp) cc_final: 0.0763 (mmm) REVERT: G 114 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8497 (mm110) REVERT: G 125 PRO cc_start: 0.8945 (Cg_exo) cc_final: 0.8670 (Cg_endo) REVERT: G 131 LYS cc_start: 0.9436 (ttmt) cc_final: 0.9178 (mttt) REVERT: G 139 ASN cc_start: 0.9655 (m110) cc_final: 0.9338 (m110) REVERT: G 152 ASP cc_start: 0.9078 (m-30) cc_final: 0.8483 (p0) REVERT: G 181 VAL cc_start: 0.9246 (t) cc_final: 0.9031 (p) REVERT: G 185 MET cc_start: 0.9077 (mtt) cc_final: 0.8418 (mtt) REVERT: G 211 LEU cc_start: 0.9204 (tp) cc_final: 0.8974 (tp) REVERT: H 10 MET cc_start: 0.4768 (ttt) cc_final: 0.4392 (ttt) REVERT: H 129 ILE cc_start: 0.8830 (tt) cc_final: 0.8314 (tt) REVERT: H 130 TYR cc_start: 0.5951 (t80) cc_final: 0.5534 (t80) REVERT: H 133 TRP cc_start: 0.8804 (m-10) cc_final: 0.7503 (m-10) REVERT: H 215 MET cc_start: 0.8930 (tpt) cc_final: 0.8479 (mmm) REVERT: J 6 VAL cc_start: 0.9096 (t) cc_final: 0.8512 (p) REVERT: J 10 ILE cc_start: 0.9181 (tp) cc_final: 0.8904 (tp) REVERT: J 24 LEU cc_start: 0.9107 (mp) cc_final: 0.8464 (mm) REVERT: J 25 PHE cc_start: 0.8551 (m-80) cc_final: 0.7862 (m-80) REVERT: J 32 THR cc_start: 0.8889 (t) cc_final: 0.8623 (t) REVERT: J 35 ASN cc_start: 0.8781 (m110) cc_final: 0.7431 (m110) REVERT: J 43 GLU cc_start: 0.8464 (pp20) cc_final: 0.8214 (pp20) REVERT: J 76 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7647 (mmmm) REVERT: J 78 ILE cc_start: 0.8673 (pt) cc_final: 0.8453 (pt) REVERT: J 88 PHE cc_start: 0.7757 (m-80) cc_final: 0.7140 (m-80) REVERT: J 100 MET cc_start: 0.5690 (mmm) cc_final: 0.5056 (tpp) REVERT: J 111 GLN cc_start: 0.9180 (mp-120) cc_final: 0.8764 (mm-40) REVERT: N 179 GLN cc_start: 0.8997 (pp30) cc_final: 0.8549 (pm20) REVERT: N 181 VAL cc_start: 0.8968 (p) cc_final: 0.8736 (p) REVERT: N 185 MET cc_start: 0.8639 (ptp) cc_final: 0.8139 (ptp) REVERT: Y 5 ASN cc_start: 0.8208 (t0) cc_final: 0.7951 (t0) REVERT: Y 13 GLN cc_start: 0.9248 (tt0) cc_final: 0.8935 (pm20) REVERT: Y 20 LEU cc_start: 0.9592 (pp) cc_final: 0.9295 (pp) REVERT: Y 56 LEU cc_start: 0.9524 (mt) cc_final: 0.9265 (mt) REVERT: Y 63 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8829 (mm110) REVERT: Y 79 GLU cc_start: 0.8873 (tp30) cc_final: 0.8108 (tp30) REVERT: Y 112 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8857 (tm-30) REVERT: Y 131 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8301 (tptt) REVERT: Y 139 ASN cc_start: 0.9456 (m-40) cc_final: 0.9134 (m110) REVERT: d 10 MET cc_start: 0.0796 (tmm) cc_final: 0.0465 (tmm) REVERT: d 23 TRP cc_start: 0.8522 (t-100) cc_final: 0.8243 (t-100) REVERT: d 139 ASN cc_start: 0.9634 (m-40) cc_final: 0.9073 (m-40) REVERT: d 140 LYS cc_start: 0.9526 (mttt) cc_final: 0.9195 (tptp) REVERT: d 143 ARG cc_start: 0.9150 (mtt180) cc_final: 0.8939 (mtt-85) REVERT: d 152 ASP cc_start: 0.8219 (m-30) cc_final: 0.7959 (m-30) REVERT: d 167 ARG cc_start: 0.8561 (mmp-170) cc_final: 0.8097 (mmp80) REVERT: e 39 MET cc_start: 0.9355 (tpp) cc_final: 0.9127 (tpp) REVERT: e 57 ASN cc_start: 0.9353 (m110) cc_final: 0.9065 (m110) REVERT: e 66 MET cc_start: 0.9077 (mmm) cc_final: 0.8761 (mmm) REVERT: e 70 LYS cc_start: 0.9262 (ptpp) cc_final: 0.9003 (ptpt) REVERT: e 79 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8723 (pp20) REVERT: e 82 ARG cc_start: 0.9068 (tmm160) cc_final: 0.8799 (ttp80) REVERT: e 96 MET cc_start: 0.7413 (mtp) cc_final: 0.6937 (tpp) REVERT: e 100 ARG cc_start: 0.7652 (mmm160) cc_final: 0.7356 (mmm-85) REVERT: e 104 ILE cc_start: 0.8765 (mp) cc_final: 0.8553 (mp) REVERT: e 112 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8975 (tm-30) REVERT: e 117 TRP cc_start: 0.8642 (m-10) cc_final: 0.8171 (m-10) REVERT: e 128 GLU cc_start: 0.9272 (pm20) cc_final: 0.8535 (pm20) REVERT: e 132 ARG cc_start: 0.9325 (ptp-170) cc_final: 0.8714 (ptp-170) REVERT: e 139 ASN cc_start: 0.9531 (m-40) cc_final: 0.9081 (m-40) REVERT: e 185 MET cc_start: 0.9091 (mtm) cc_final: 0.8886 (mtp) REVERT: j 185 MET cc_start: 0.9456 (ppp) cc_final: 0.9064 (ppp) REVERT: j 213 GLU cc_start: 0.9561 (mp0) cc_final: 0.9305 (pm20) REVERT: j 215 MET cc_start: 0.8512 (ppp) cc_final: 0.8231 (ppp) REVERT: k 25 LYS cc_start: 0.9702 (ptmt) cc_final: 0.9386 (ptmm) REVERT: k 44 SER cc_start: 0.9474 (p) cc_final: 0.8670 (p) REVERT: k 55 MET cc_start: 0.9512 (ttm) cc_final: 0.9263 (ttm) REVERT: k 68 MET cc_start: 0.9418 (mtp) cc_final: 0.9118 (mtp) REVERT: k 76 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9150 (mm-30) REVERT: k 96 MET cc_start: 0.4971 (ttm) cc_final: 0.3966 (mpp) REVERT: k 104 ILE cc_start: 0.8542 (mm) cc_final: 0.8257 (mm) REVERT: k 115 ILE cc_start: 0.9031 (pt) cc_final: 0.8263 (pt) REVERT: k 118 MET cc_start: 0.8542 (mmp) cc_final: 0.8068 (mtp) REVERT: k 131 LYS cc_start: 0.9403 (ttmt) cc_final: 0.9026 (tttt) REVERT: k 173 ARG cc_start: 0.9120 (ttm-80) cc_final: 0.8917 (tmm-80) outliers start: 1 outliers final: 0 residues processed: 781 average time/residue: 0.3394 time to fit residues: 382.2859 Evaluate side-chains 609 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 609 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 201 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 109 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 189 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN J 92 HIS J 163 GLN ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 ASN ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.100263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.076503 restraints weight = 74341.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.078609 restraints weight = 52139.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.080141 restraints weight = 40093.908| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.7596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18834 Z= 0.183 Angle : 0.708 11.285 25587 Z= 0.370 Chirality : 0.047 0.294 2848 Planarity : 0.005 0.072 3345 Dihedral : 4.689 39.589 2500 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2338 helix: 0.36 (0.13), residues: 1448 sheet: -0.71 (0.65), residues: 61 loop : -0.23 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP Y 117 HIS 0.004 0.001 HIS C 12 PHE 0.017 0.002 PHE H 161 TYR 0.019 0.002 TYR e 130 ARG 0.015 0.001 ARG G 132 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 1037) hydrogen bonds : angle 4.82131 ( 3081) SS BOND : bond 0.00284 ( 10) SS BOND : angle 1.81516 ( 20) covalent geometry : bond 0.00394 (18824) covalent geometry : angle 0.70611 (25567) *********************** 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 755 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 755 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.9716 (ptmm) cc_final: 0.9467 (ptmm) REVERT: A 50 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8957 (tm-30) REVERT: A 51 ASP cc_start: 0.9347 (m-30) cc_final: 0.9029 (m-30) REVERT: A 52 LEU cc_start: 0.9778 (mm) cc_final: 0.9557 (mm) REVERT: A 57 ASN cc_start: 0.9674 (m110) cc_final: 0.9391 (m110) REVERT: A 71 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8815 (tm-30) REVERT: A 113 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8807 (mt-10) REVERT: A 128 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8768 (tp30) REVERT: B 21 ASN cc_start: 0.9502 (t0) cc_final: 0.9193 (t0) REVERT: B 30 LYS cc_start: 0.9027 (mmpt) cc_final: 0.8593 (mmmm) REVERT: B 32 PHE cc_start: 0.8603 (m-80) cc_final: 0.8300 (m-80) REVERT: B 50 GLN cc_start: 0.9371 (mt0) cc_final: 0.9018 (mt0) REVERT: B 51 ASP cc_start: 0.9330 (m-30) cc_final: 0.9089 (m-30) REVERT: B 55 MET cc_start: 0.9559 (ttt) cc_final: 0.9209 (tpp) REVERT: B 66 MET cc_start: 0.8892 (mmm) cc_final: 0.8649 (mmm) REVERT: B 70 LYS cc_start: 0.9689 (ptmm) cc_final: 0.9480 (ptpt) REVERT: B 74 ASN cc_start: 0.9440 (m-40) cc_final: 0.9120 (m110) REVERT: B 114 GLN cc_start: 0.9394 (mt0) cc_final: 0.8977 (mt0) REVERT: B 118 MET cc_start: 0.9241 (mtm) cc_final: 0.8871 (ptp) REVERT: B 129 ILE cc_start: 0.9316 (pt) cc_final: 0.8715 (pt) REVERT: B 131 LYS cc_start: 0.9563 (ttmt) cc_final: 0.9259 (mtpt) REVERT: B 132 ARG cc_start: 0.9225 (ttp-110) cc_final: 0.9010 (mtm110) REVERT: B 144 MET cc_start: 0.9220 (ttt) cc_final: 0.8985 (ttm) REVERT: B 167 ARG cc_start: 0.9357 (ptp-170) cc_final: 0.8737 (ptt180) REVERT: C 53 ASN cc_start: 0.9432 (m-40) cc_final: 0.9141 (m110) REVERT: C 128 GLU cc_start: 0.9201 (mp0) cc_final: 0.8936 (mp0) REVERT: C 182 LYS cc_start: 0.9610 (mtmm) cc_final: 0.9370 (mttm) REVERT: C 189 LEU cc_start: 0.9289 (mm) cc_final: 0.9034 (mp) REVERT: D 56 LEU cc_start: 0.9766 (mt) cc_final: 0.9434 (mt) REVERT: D 57 ASN cc_start: 0.9635 (m110) cc_final: 0.9388 (m-40) REVERT: D 68 MET cc_start: 0.7379 (mtt) cc_final: 0.7073 (mtt) REVERT: D 130 TYR cc_start: 0.9306 (t80) cc_final: 0.9075 (t80) REVERT: D 131 LYS cc_start: 0.9290 (tttt) cc_final: 0.8932 (mtpt) REVERT: D 134 ILE cc_start: 0.9695 (mt) cc_final: 0.9448 (mt) REVERT: D 163 ASP cc_start: 0.8693 (m-30) cc_final: 0.8451 (m-30) REVERT: D 166 ASP cc_start: 0.8859 (m-30) cc_final: 0.8417 (m-30) REVERT: D 215 MET cc_start: 0.7833 (ttt) cc_final: 0.7435 (ttm) REVERT: G 23 TRP cc_start: 0.9295 (t-100) cc_final: 0.8637 (t-100) REVERT: G 39 MET cc_start: 0.9336 (ttp) cc_final: 0.8947 (tmm) REVERT: G 43 LEU cc_start: 0.9694 (mm) cc_final: 0.9331 (mm) REVERT: G 45 GLU cc_start: 0.8907 (pm20) cc_final: 0.8696 (pm20) REVERT: G 52 LEU cc_start: 0.9813 (mt) cc_final: 0.9603 (mt) REVERT: G 55 MET cc_start: 0.9332 (ttt) cc_final: 0.8879 (tmm) REVERT: G 56 LEU cc_start: 0.9574 (mt) cc_final: 0.9152 (mt) REVERT: G 57 ASN cc_start: 0.9467 (m-40) cc_final: 0.9238 (m110) REVERT: G 58 THR cc_start: 0.9534 (p) cc_final: 0.9254 (p) REVERT: G 70 LYS cc_start: 0.9778 (pttm) cc_final: 0.9540 (pttm) REVERT: G 96 MET cc_start: 0.2060 (mpp) cc_final: 0.0673 (mmm) REVERT: G 125 PRO cc_start: 0.8998 (Cg_exo) cc_final: 0.8795 (Cg_endo) REVERT: G 131 LYS cc_start: 0.9502 (ttmt) cc_final: 0.9271 (mttt) REVERT: G 139 ASN cc_start: 0.9652 (m110) cc_final: 0.9357 (m110) REVERT: G 152 ASP cc_start: 0.9110 (m-30) cc_final: 0.8522 (p0) REVERT: G 181 VAL cc_start: 0.9252 (t) cc_final: 0.9034 (p) REVERT: G 185 MET cc_start: 0.9018 (mtt) cc_final: 0.8372 (mtt) REVERT: G 211 LEU cc_start: 0.9216 (tp) cc_final: 0.8913 (tp) REVERT: H 10 MET cc_start: 0.5025 (ttt) cc_final: 0.4621 (ttt) REVERT: H 55 MET cc_start: 0.9292 (mmp) cc_final: 0.8943 (mmt) REVERT: H 130 TYR cc_start: 0.5830 (t80) cc_final: 0.5216 (t80) REVERT: H 215 MET cc_start: 0.8982 (tpt) cc_final: 0.8557 (mmm) REVERT: J 6 VAL cc_start: 0.9190 (t) cc_final: 0.8636 (p) REVERT: J 10 ILE cc_start: 0.9154 (tp) cc_final: 0.8779 (tp) REVERT: J 24 LEU cc_start: 0.9098 (mp) cc_final: 0.8661 (mm) REVERT: J 25 PHE cc_start: 0.8532 (m-80) cc_final: 0.7878 (m-80) REVERT: J 32 THR cc_start: 0.8902 (t) cc_final: 0.8667 (t) REVERT: J 35 ASN cc_start: 0.8711 (m110) cc_final: 0.7494 (m110) REVERT: J 43 GLU cc_start: 0.8503 (pp20) cc_final: 0.8230 (pp20) REVERT: J 76 LYS cc_start: 0.7783 (mmtp) cc_final: 0.7581 (mmmm) REVERT: J 78 ILE cc_start: 0.8710 (pt) cc_final: 0.8420 (pt) REVERT: J 100 MET cc_start: 0.5644 (mmm) cc_final: 0.5435 (tpt) REVERT: J 123 ASP cc_start: 0.9013 (m-30) cc_final: 0.8726 (m-30) REVERT: J 142 MET cc_start: 0.7418 (ttt) cc_final: 0.7129 (tpt) REVERT: N 179 GLN cc_start: 0.9073 (pp30) cc_final: 0.8599 (pm20) REVERT: N 181 VAL cc_start: 0.8956 (p) cc_final: 0.8731 (p) REVERT: N 185 MET cc_start: 0.8643 (ptp) cc_final: 0.8253 (ptp) REVERT: Y 5 ASN cc_start: 0.8348 (t0) cc_final: 0.8041 (t0) REVERT: Y 20 LEU cc_start: 0.9611 (pp) cc_final: 0.9393 (pp) REVERT: Y 56 LEU cc_start: 0.9544 (mt) cc_final: 0.9264 (mt) REVERT: Y 63 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8698 (mm-40) REVERT: Y 113 GLU cc_start: 0.8917 (pm20) cc_final: 0.8626 (pm20) REVERT: Y 131 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8317 (tptt) REVERT: Y 139 ASN cc_start: 0.9501 (m-40) cc_final: 0.9183 (m110) REVERT: d 23 TRP cc_start: 0.8526 (t-100) cc_final: 0.8282 (t-100) REVERT: d 129 ILE cc_start: 0.9545 (tp) cc_final: 0.9248 (tp) REVERT: d 130 TYR cc_start: 0.7555 (t80) cc_final: 0.6871 (t80) REVERT: d 139 ASN cc_start: 0.9694 (m-40) cc_final: 0.9462 (m-40) REVERT: d 140 LYS cc_start: 0.9519 (mttt) cc_final: 0.9160 (tptp) REVERT: d 152 ASP cc_start: 0.8188 (m-30) cc_final: 0.7950 (m-30) REVERT: e 39 MET cc_start: 0.9381 (tpp) cc_final: 0.9162 (tpp) REVERT: e 57 ASN cc_start: 0.9384 (m110) cc_final: 0.9110 (m110) REVERT: e 66 MET cc_start: 0.9168 (mmm) cc_final: 0.8852 (mmm) REVERT: e 79 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8760 (pp20) REVERT: e 82 ARG cc_start: 0.9099 (tmm160) cc_final: 0.8806 (ttp80) REVERT: e 96 MET cc_start: 0.7261 (mtp) cc_final: 0.6975 (tpp) REVERT: e 100 ARG cc_start: 0.7802 (mmm160) cc_final: 0.7555 (mmm-85) REVERT: e 114 GLN cc_start: 0.9064 (mt0) cc_final: 0.8459 (tt0) REVERT: e 117 TRP cc_start: 0.8769 (m-10) cc_final: 0.8217 (m-10) REVERT: e 128 GLU cc_start: 0.9332 (pm20) cc_final: 0.9046 (pm20) REVERT: e 185 MET cc_start: 0.9091 (mtm) cc_final: 0.8826 (mtp) REVERT: e 215 MET cc_start: 0.7538 (ptt) cc_final: 0.7277 (ptm) REVERT: j 167 ARG cc_start: 0.8334 (mmm160) cc_final: 0.7357 (mmm160) REVERT: j 170 LYS cc_start: 0.8649 (tmtt) cc_final: 0.8305 (tmtt) REVERT: j 185 MET cc_start: 0.9407 (ppp) cc_final: 0.9004 (ppp) REVERT: j 213 GLU cc_start: 0.9559 (mp0) cc_final: 0.9270 (pm20) REVERT: j 215 MET cc_start: 0.8270 (ppp) cc_final: 0.8021 (ppp) REVERT: k 44 SER cc_start: 0.9454 (p) cc_final: 0.8759 (p) REVERT: k 68 MET cc_start: 0.9404 (mtp) cc_final: 0.9145 (mtp) REVERT: k 76 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9127 (mm-30) REVERT: k 96 MET cc_start: 0.5215 (ttm) cc_final: 0.4575 (ptp) REVERT: k 104 ILE cc_start: 0.8554 (mm) cc_final: 0.8305 (mm) REVERT: k 115 ILE cc_start: 0.9057 (pt) cc_final: 0.8553 (pt) REVERT: k 118 MET cc_start: 0.8482 (mmp) cc_final: 0.8051 (mtp) REVERT: k 131 LYS cc_start: 0.9386 (ttmt) cc_final: 0.8998 (tttt) REVERT: k 173 ARG cc_start: 0.9103 (ttm-80) cc_final: 0.8827 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 755 average time/residue: 0.3389 time to fit residues: 369.3261 Evaluate side-chains 581 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 581 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.4648 > 50: distance: 29 - 52: 23.163 distance: 47 - 52: 21.457 distance: 52 - 53: 11.524 distance: 53 - 54: 10.848 distance: 53 - 56: 3.850 distance: 54 - 55: 24.833 distance: 54 - 60: 18.759 distance: 56 - 57: 8.721 distance: 57 - 59: 10.207 distance: 60 - 61: 7.813 distance: 61 - 62: 12.801 distance: 61 - 64: 4.668 distance: 62 - 63: 12.627 distance: 62 - 68: 16.147 distance: 64 - 65: 11.663 distance: 65 - 66: 13.630 distance: 65 - 67: 22.097 distance: 68 - 69: 21.734 distance: 68 - 74: 30.228 distance: 69 - 70: 17.690 distance: 69 - 72: 39.858 distance: 70 - 71: 40.726 distance: 70 - 75: 47.239 distance: 72 - 73: 13.020 distance: 73 - 74: 24.112 distance: 75 - 76: 16.063 distance: 75 - 81: 26.960 distance: 76 - 77: 14.220 distance: 76 - 79: 27.303 distance: 77 - 78: 14.797 distance: 77 - 82: 22.682 distance: 79 - 80: 37.658 distance: 80 - 81: 25.811 distance: 82 - 83: 8.869 distance: 83 - 84: 32.596 distance: 83 - 86: 30.275 distance: 84 - 85: 12.408 distance: 84 - 90: 4.901 distance: 86 - 87: 10.241 distance: 86 - 88: 42.093 distance: 87 - 89: 7.151 distance: 90 - 91: 8.308 distance: 90 - 96: 13.720 distance: 91 - 92: 19.340 distance: 91 - 94: 16.116 distance: 92 - 93: 27.435 distance: 92 - 97: 16.137 distance: 93 - 117: 36.845 distance: 94 - 95: 9.678 distance: 95 - 96: 27.047 distance: 97 - 98: 33.908 distance: 98 - 99: 9.901 distance: 98 - 101: 7.610 distance: 99 - 100: 5.530 distance: 99 - 104: 44.670 distance: 100 - 125: 33.401 distance: 101 - 102: 29.579 distance: 101 - 103: 29.184 distance: 104 - 105: 33.441 distance: 105 - 106: 25.404 distance: 106 - 107: 24.050 distance: 106 - 108: 15.252 distance: 107 - 131: 36.071 distance: 109 - 110: 20.078 distance: 109 - 112: 12.012 distance: 110 - 111: 12.212 distance: 110 - 117: 5.598 distance: 111 - 137: 20.958 distance: 112 - 113: 8.538 distance: 113 - 114: 14.303 distance: 114 - 115: 6.392 distance: 114 - 116: 5.996 distance: 117 - 118: 18.264 distance: 118 - 119: 12.885 distance: 118 - 121: 6.940 distance: 119 - 120: 6.506 distance: 119 - 125: 28.729 distance: 120 - 148: 31.459 distance: 121 - 122: 32.400 distance: 121 - 123: 46.529 distance: 122 - 124: 15.842