Starting phenix.real_space_refine on Mon May 12 10:15:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfl_45550/05_2025/9cfl_45550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfl_45550/05_2025/9cfl_45550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cfl_45550/05_2025/9cfl_45550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfl_45550/05_2025/9cfl_45550.map" model { file = "/net/cci-nas-00/data/ceres_data/9cfl_45550/05_2025/9cfl_45550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfl_45550/05_2025/9cfl_45550.cif" } resolution = 2.3 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= 0.080 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 5863 2.51 5 N 1414 2.21 5 O 1588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8925 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2229 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain: "B" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2094 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 257} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'AV0': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Restraints were copied for chains: C, D Time building chain proxies: 6.94, per 1000 atoms: 0.78 Number of scatterers: 8925 At special positions: 0 Unit cell: (86.6214, 93.0378, 108.009, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 6 15.00 Mg 2 11.99 O 1588 8.00 N 1414 7.00 C 5863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 966.4 milliseconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 66.2% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 14 through 30 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 38 through 56 Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 69 through 79 removed outlier: 3.511A pdb=" N SER A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 removed outlier: 4.132A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 137 removed outlier: 3.824A pdb=" N ARG A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.514A pdb=" N ILE A 146 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 147 " --> pdb=" O ILE A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 147' Processing helix chain 'A' and resid 148 through 174 Proline residue: A 154 - end of helix removed outlier: 3.880A pdb=" N THR A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 removed outlier: 4.445A pdb=" N GLN A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA A 183 " --> pdb=" O MET A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.922A pdb=" N PHE A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 263 Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.608A pdb=" N PHE A 269 " --> pdb=" O GLN A 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 29 removed outlier: 3.535A pdb=" N ARG B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.585A pdb=" N GLU B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 Proline residue: B 125 - end of helix Processing helix chain 'B' and resid 133 through 139 removed outlier: 3.703A pdb=" N ILE B 137 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 138 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 145 through 158 Processing helix chain 'B' and resid 175 through 192 removed outlier: 4.468A pdb=" N GLN B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 192 " --> pdb=" O GLU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 210 Processing helix chain 'B' and resid 227 through 243 Proline residue: B 232 - end of helix removed outlier: 3.616A pdb=" N LYS B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 260 removed outlier: 3.970A pdb=" N SER B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 14 through 30 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 56 Proline residue: C 44 - end of helix Processing helix chain 'C' and resid 69 through 79 removed outlier: 3.511A pdb=" N SER C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 removed outlier: 4.132A pdb=" N LYS C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 99 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.823A pdb=" N ARG C 120 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C 137 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 147 removed outlier: 3.514A pdb=" N ILE C 146 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 147 " --> pdb=" O ILE C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 147' Processing helix chain 'C' and resid 148 through 174 Proline residue: C 154 - end of helix removed outlier: 3.881A pdb=" N THR C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 191 removed outlier: 4.446A pdb=" N GLN C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA C 183 " --> pdb=" O MET C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 214 through 228 removed outlier: 3.922A pdb=" N PHE C 218 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 263 Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.608A pdb=" N PHE C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 29 removed outlier: 3.535A pdb=" N ARG D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 Processing helix chain 'D' and resid 101 through 114 removed outlier: 3.585A pdb=" N GLU D 107 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 132 Proline residue: D 125 - end of helix Processing helix chain 'D' and resid 133 through 139 removed outlier: 3.703A pdb=" N ILE D 137 " --> pdb=" O GLY D 134 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 138 " --> pdb=" O GLU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 145 through 158 Processing helix chain 'D' and resid 175 through 192 removed outlier: 4.468A pdb=" N GLN D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS D 182 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 210 Processing helix chain 'D' and resid 227 through 243 Proline residue: D 232 - end of helix removed outlier: 3.616A pdb=" N LYS D 242 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS D 243 " --> pdb=" O ASN D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 260 removed outlier: 3.970A pdb=" N SER D 259 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 78 through 83 removed outlier: 6.548A pdb=" N VAL B 78 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL B 10 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE B 43 " --> pdb=" O ASN B 9 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR B 11 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASP B 41 " --> pdb=" O THR B 11 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLU B 13 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA B 39 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARG B 15 " --> pdb=" O PHE B 37 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE B 37 " --> pdb=" O ARG B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.995A pdb=" N ASP B 168 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 52 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA B 214 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY B 54 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE B 216 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 56 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU B 217 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 78 through 83 removed outlier: 6.548A pdb=" N VAL D 78 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL D 10 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE D 43 " --> pdb=" O ASN D 9 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR D 11 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP D 41 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLU D 13 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA D 39 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ARG D 15 " --> pdb=" O PHE D 37 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE D 37 " --> pdb=" O ARG D 15 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 87 through 90 removed outlier: 3.996A pdb=" N ASP D 168 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL D 52 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA D 214 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY D 54 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE D 216 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL D 56 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU D 217 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1413 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 2598 1.34 - 1.49: 2566 1.49 - 1.64: 3884 1.64 - 1.79: 28 1.79 - 1.94: 64 Bond restraints: 9140 Sorted by residual: bond pdb=" N ILE D 29 " pdb=" CA ILE D 29 " ideal model delta sigma weight residual 1.456 1.498 -0.042 8.70e-03 1.32e+04 2.33e+01 bond pdb=" N ILE B 29 " pdb=" CA ILE B 29 " ideal model delta sigma weight residual 1.456 1.498 -0.041 8.70e-03 1.32e+04 2.27e+01 bond pdb=" N LEU D 96 " pdb=" CA LEU D 96 " ideal model delta sigma weight residual 1.456 1.508 -0.052 1.25e-02 6.40e+03 1.74e+01 bond pdb=" N LEU B 96 " pdb=" CA LEU B 96 " ideal model delta sigma weight residual 1.456 1.508 -0.052 1.25e-02 6.40e+03 1.74e+01 bond pdb=" C VAL A 174 " pdb=" O VAL A 174 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.09e-02 8.42e+03 1.72e+01 ... (remaining 9135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 11545 2.39 - 4.77: 685 4.77 - 7.16: 105 7.16 - 9.54: 18 9.54 - 11.93: 1 Bond angle restraints: 12354 Sorted by residual: angle pdb=" CA GLY D 85 " pdb=" C GLY D 85 " pdb=" O GLY D 85 " ideal model delta sigma weight residual 122.37 117.94 4.43 7.30e-01 1.88e+00 3.68e+01 angle pdb=" CA GLY B 85 " pdb=" C GLY B 85 " pdb=" O GLY B 85 " ideal model delta sigma weight residual 122.37 117.95 4.42 7.30e-01 1.88e+00 3.66e+01 angle pdb=" N GLN A 265 " pdb=" CA GLN A 265 " pdb=" CB GLN A 265 " ideal model delta sigma weight residual 110.56 103.06 7.50 1.46e+00 4.69e-01 2.64e+01 angle pdb=" N GLN C 265 " pdb=" CA GLN C 265 " pdb=" CB GLN C 265 " ideal model delta sigma weight residual 110.56 103.09 7.47 1.46e+00 4.69e-01 2.62e+01 angle pdb=" C ARG B 15 " pdb=" CA ARG B 15 " pdb=" CB ARG B 15 " ideal model delta sigma weight residual 109.65 118.21 -8.56 1.71e+00 3.42e-01 2.50e+01 ... (remaining 12349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 5197 33.80 - 67.59: 344 67.59 - 101.38: 52 101.38 - 135.18: 48 135.18 - 168.97: 3 Dihedral angle restraints: 5644 sinusoidal: 2542 harmonic: 3102 Sorted by residual: dihedral pdb=" CD ARG B 23 " pdb=" NE ARG B 23 " pdb=" CZ ARG B 23 " pdb=" NH1 ARG B 23 " ideal model delta sinusoidal sigma weight residual 0.00 -53.59 53.59 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CD ARG D 23 " pdb=" NE ARG D 23 " pdb=" CZ ARG D 23 " pdb=" NH1 ARG D 23 " ideal model delta sinusoidal sigma weight residual 0.00 -53.54 53.54 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CD ARG D 15 " pdb=" NE ARG D 15 " pdb=" CZ ARG D 15 " pdb=" NH1 ARG D 15 " ideal model delta sinusoidal sigma weight residual 0.00 44.93 -44.93 1 1.00e+01 1.00e-02 2.80e+01 ... (remaining 5641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1001 0.063 - 0.126: 272 0.126 - 0.188: 91 0.188 - 0.251: 26 0.251 - 0.314: 10 Chirality restraints: 1400 Sorted by residual: chirality pdb=" C5 AV0 A 302 " pdb=" C4 AV0 A 302 " pdb=" C6 AV0 A 302 " pdb=" O5 AV0 A 302 " both_signs ideal model delta sigma weight residual False -2.50 -2.19 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ARG D 15 " pdb=" N ARG D 15 " pdb=" C ARG D 15 " pdb=" CB ARG D 15 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ARG B 15 " pdb=" N ARG B 15 " pdb=" C ARG B 15 " pdb=" CB ARG B 15 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1397 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 23 " -0.887 9.50e-02 1.11e+02 3.98e-01 9.62e+01 pdb=" NE ARG D 23 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG D 23 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG D 23 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 23 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 23 " -0.887 9.50e-02 1.11e+02 3.98e-01 9.62e+01 pdb=" NE ARG B 23 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG B 23 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 23 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 23 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 15 " 0.786 9.50e-02 1.11e+02 3.52e-01 7.54e+01 pdb=" NE ARG D 15 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG D 15 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 15 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 15 " 0.024 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 30 2.49 - 3.09: 5599 3.09 - 3.69: 13856 3.69 - 4.30: 21498 4.30 - 4.90: 34678 Nonbonded interactions: 75661 Sorted by model distance: nonbonded pdb=" O2G AGS D 301 " pdb="MG MG D 302 " model vdw 1.887 2.170 nonbonded pdb=" O2G AGS B 301 " pdb="MG MG B 302 " model vdw 1.887 2.170 nonbonded pdb=" O THR C 160 " pdb=" OG1 THR C 164 " model vdw 2.282 3.040 nonbonded pdb=" O THR A 160 " pdb=" OG1 THR A 164 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 190 " pdb=" OH TYR C 190 " model vdw 2.302 3.040 ... (remaining 75656 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' and (resid 1 through 270 or resid 301)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 individual isotropic 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.020 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:10.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 : 0.008 0.063 9140 Z= 0.506 Angle : 1.205 11.928 12354 Z= 0.791 Chirality : 0.071 0.314 1400 Planarity : 0.022 0.398 1478 Dihedral : 25.652 168.973 3656 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.83 % Allowed : 22.34 % Favored : 73.83 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.09 (0.25), residues: 1060 helix: 0.05 (0.19), residues: 608 sheet: 1.51 (0.65), residues: 76 loop : -0.35 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 81 HIS 0.005 0.001 HIS A 259 PHE 0.016 0.002 PHE C 155 TYR 0.023 0.002 TYR A 115 ARG 0.005 0.001 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.16380 ( 479) hydrogen bonds : angle 6.70363 ( 1413) covalent geometry : bond 0.00762 ( 9140) covalent geometry : angle 1.20507 (12354) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.941 Fit side-chains REVERT: A 13 LYS cc_start: 0.7897 (pttp) cc_final: 0.7309 (ptmm) REVERT: B 240 ASP cc_start: 0.7171 (m-30) cc_final: 0.6848 (t0) REVERT: C 13 LYS cc_start: 0.7940 (pttp) cc_final: 0.7330 (ptmm) REVERT: D 240 ASP cc_start: 0.7238 (m-30) cc_final: 0.6885 (t0) outliers start: 36 outliers final: 16 residues processed: 179 average time/residue: 1.4419 time to fit residues: 272.4009 Evaluate side-chains 156 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 200 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 265 GLN B 32 HIS B 34 ASN B 59 ASN B 157 ASN C 265 GLN D 32 HIS D 34 ASN D 59 ASN D 157 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110122 restraints weight = 8307.826| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.67 r_work: 0.3154 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9140 Z= 0.132 Angle : 0.652 9.147 12354 Z= 0.308 Chirality : 0.048 0.274 1400 Planarity : 0.004 0.044 1478 Dihedral : 22.483 153.997 1594 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.09 % Allowed : 22.87 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.90 (0.26), residues: 1060 helix: 1.11 (0.21), residues: 610 sheet: 0.74 (0.58), residues: 76 loop : -0.15 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 81 HIS 0.003 0.001 HIS D 201 PHE 0.014 0.001 PHE A 155 TYR 0.016 0.001 TYR A 115 ARG 0.003 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.05366 ( 479) hydrogen bonds : angle 4.87527 ( 1413) covalent geometry : bond 0.00271 ( 9140) covalent geometry : angle 0.65250 (12354) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.023 Fit side-chains REVERT: A 13 LYS cc_start: 0.8063 (pttp) cc_final: 0.7562 (pptt) REVERT: C 13 LYS cc_start: 0.8157 (pttp) cc_final: 0.7693 (pptt) REVERT: D 126 LYS cc_start: 0.7831 (mtmm) cc_final: 0.7506 (mtmm) REVERT: D 129 GLU cc_start: 0.6676 (tm-30) cc_final: 0.6324 (pp20) REVERT: D 149 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.6977 (ttt180) REVERT: D 240 ASP cc_start: 0.7138 (m-30) cc_final: 0.6912 (m-30) outliers start: 29 outliers final: 21 residues processed: 174 average time/residue: 1.4382 time to fit residues: 263.9070 Evaluate side-chains 172 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 259 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 6 optimal weight: 0.0020 chunk 61 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN D 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111450 restraints weight = 8440.814| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.70 r_work: 0.3175 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9140 Z= 0.113 Angle : 0.594 10.335 12354 Z= 0.276 Chirality : 0.047 0.378 1400 Planarity : 0.004 0.034 1478 Dihedral : 18.296 139.477 1578 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.47 % Allowed : 20.11 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.23 (0.26), residues: 1060 helix: 1.52 (0.21), residues: 610 sheet: 0.21 (0.56), residues: 76 loop : -0.10 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 81 HIS 0.002 0.000 HIS C 124 PHE 0.012 0.001 PHE C 155 TYR 0.017 0.001 TYR C 115 ARG 0.003 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 479) hydrogen bonds : angle 4.55018 ( 1413) covalent geometry : bond 0.00234 ( 9140) covalent geometry : angle 0.59373 (12354) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 1.014 Fit side-chains REVERT: A 1 MET cc_start: 0.4941 (pmm) cc_final: 0.4451 (pmm) REVERT: A 13 LYS cc_start: 0.8018 (pttp) cc_final: 0.7754 (pptt) REVERT: A 80 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7899 (pmm) REVERT: B 49 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7567 (mt-10) REVERT: C 80 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7907 (pmm) REVERT: D 49 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7517 (mt-10) outliers start: 42 outliers final: 15 residues processed: 175 average time/residue: 1.4594 time to fit residues: 269.9815 Evaluate side-chains 172 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 259 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN B 157 ASN B 239 ASN C 47 GLN C 182 GLN D 157 ASN D 192 GLN D 239 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.104659 restraints weight = 8398.731| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.69 r_work: 0.3083 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9140 Z= 0.209 Angle : 0.702 8.277 12354 Z= 0.334 Chirality : 0.052 0.342 1400 Planarity : 0.004 0.036 1478 Dihedral : 18.031 145.484 1572 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.40 % Allowed : 20.96 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.17 (0.26), residues: 1060 helix: 1.44 (0.21), residues: 610 sheet: 0.01 (0.54), residues: 76 loop : -0.04 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 81 HIS 0.004 0.001 HIS A 11 PHE 0.020 0.002 PHE A 155 TYR 0.018 0.002 TYR A 115 ARG 0.003 0.001 ARG B 253 Details of bonding type rmsd hydrogen bonds : bond 0.06593 ( 479) hydrogen bonds : angle 4.82982 ( 1413) covalent geometry : bond 0.00501 ( 9140) covalent geometry : angle 0.70239 (12354) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.959 Fit side-chains REVERT: A 1 MET cc_start: 0.5083 (pmm) cc_final: 0.4661 (pmm) REVERT: A 13 LYS cc_start: 0.8137 (pttp) cc_final: 0.7795 (pptt) REVERT: A 41 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7857 (tp) REVERT: A 151 ILE cc_start: 0.8369 (mm) cc_final: 0.8072 (mp) REVERT: A 186 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7678 (mmt90) REVERT: A 196 TRP cc_start: 0.8909 (OUTLIER) cc_final: 0.8290 (p90) REVERT: B 49 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7616 (mt-10) REVERT: C 41 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7851 (tp) REVERT: C 151 ILE cc_start: 0.8366 (mm) cc_final: 0.8066 (mp) REVERT: C 186 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7738 (mmt90) REVERT: C 196 TRP cc_start: 0.8909 (OUTLIER) cc_final: 0.8272 (p90) REVERT: D 49 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7599 (mt-10) outliers start: 32 outliers final: 11 residues processed: 161 average time/residue: 1.4890 time to fit residues: 252.6763 Evaluate side-chains 160 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 259 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN B 157 ASN B 239 ASN C 182 GLN D 157 ASN D 192 GLN D 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.104088 restraints weight = 8290.116| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.69 r_work: 0.3079 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9140 Z= 0.185 Angle : 0.659 8.203 12354 Z= 0.317 Chirality : 0.052 0.368 1400 Planarity : 0.004 0.038 1478 Dihedral : 17.245 146.681 1572 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.04 % Allowed : 20.11 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.10 (0.26), residues: 1060 helix: 1.38 (0.21), residues: 610 sheet: -0.21 (0.55), residues: 76 loop : -0.01 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 81 HIS 0.003 0.001 HIS A 124 PHE 0.017 0.002 PHE A 155 TYR 0.017 0.002 TYR C 115 ARG 0.002 0.000 ARG D 253 Details of bonding type rmsd hydrogen bonds : bond 0.06268 ( 479) hydrogen bonds : angle 4.80112 ( 1413) covalent geometry : bond 0.00435 ( 9140) covalent geometry : angle 0.65872 (12354) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.901 Fit side-chains REVERT: A 1 MET cc_start: 0.4979 (pmm) cc_final: 0.4592 (pmm) REVERT: A 13 LYS cc_start: 0.8117 (pttp) cc_final: 0.7642 (pptt) REVERT: A 41 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7906 (tp) REVERT: A 151 ILE cc_start: 0.8378 (mm) cc_final: 0.8090 (mp) REVERT: A 186 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7742 (mmt90) REVERT: A 196 TRP cc_start: 0.8893 (OUTLIER) cc_final: 0.8366 (p90) REVERT: A 210 MET cc_start: 0.6681 (mmp) cc_final: 0.6279 (mmt) REVERT: A 265 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7410 (mp-120) REVERT: B 126 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7224 (mmpt) REVERT: C 13 LYS cc_start: 0.8107 (pttp) cc_final: 0.7588 (pptt) REVERT: C 41 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7901 (tp) REVERT: C 151 ILE cc_start: 0.8373 (mm) cc_final: 0.8079 (mp) REVERT: C 186 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7721 (mmt90) REVERT: C 196 TRP cc_start: 0.8900 (OUTLIER) cc_final: 0.8366 (p90) REVERT: C 210 MET cc_start: 0.6721 (mmp) cc_final: 0.6331 (mmt) REVERT: C 265 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7406 (mp-120) outliers start: 38 outliers final: 14 residues processed: 172 average time/residue: 1.4842 time to fit residues: 268.4465 Evaluate side-chains 165 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 259 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 103 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN B 157 ASN B 239 ASN C 182 GLN D 157 ASN D 192 GLN D 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.130044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103857 restraints weight = 8327.331| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.63 r_work: 0.3089 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9140 Z= 0.192 Angle : 0.664 8.477 12354 Z= 0.321 Chirality : 0.052 0.419 1400 Planarity : 0.004 0.039 1478 Dihedral : 16.841 147.986 1572 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.30 % Allowed : 20.74 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.09 (0.26), residues: 1060 helix: 1.35 (0.21), residues: 610 sheet: -0.30 (0.55), residues: 76 loop : 0.04 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 81 HIS 0.003 0.001 HIS C 11 PHE 0.018 0.002 PHE A 155 TYR 0.016 0.002 TYR C 115 ARG 0.003 0.000 ARG D 253 Details of bonding type rmsd hydrogen bonds : bond 0.06423 ( 479) hydrogen bonds : angle 4.82606 ( 1413) covalent geometry : bond 0.00455 ( 9140) covalent geometry : angle 0.66402 (12354) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.028 Fit side-chains REVERT: A 1 MET cc_start: 0.5024 (pmm) cc_final: 0.4687 (pmm) REVERT: A 13 LYS cc_start: 0.8104 (pttp) cc_final: 0.7701 (pptt) REVERT: A 41 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7995 (tp) REVERT: A 151 ILE cc_start: 0.8422 (mm) cc_final: 0.8146 (mp) REVERT: A 186 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7815 (mmt90) REVERT: A 210 MET cc_start: 0.6751 (mmp) cc_final: 0.6469 (mmt) REVERT: A 265 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7445 (mp-120) REVERT: B 242 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.6730 (mmtp) REVERT: C 13 LYS cc_start: 0.8074 (pttp) cc_final: 0.7692 (pptt) REVERT: C 41 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7989 (tp) REVERT: C 186 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7815 (mmt90) REVERT: C 196 TRP cc_start: 0.8944 (OUTLIER) cc_final: 0.8399 (p90) REVERT: C 210 MET cc_start: 0.6666 (mmp) cc_final: 0.6400 (mmt) REVERT: C 265 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7441 (mp-120) outliers start: 31 outliers final: 12 residues processed: 162 average time/residue: 1.5649 time to fit residues: 266.5700 Evaluate side-chains 162 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 259 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN B 157 ASN B 192 GLN B 239 ASN C 182 GLN D 157 ASN D 192 GLN D 239 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105158 restraints weight = 8351.619| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.64 r_work: 0.3111 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9140 Z= 0.151 Angle : 0.615 8.202 12354 Z= 0.298 Chirality : 0.050 0.407 1400 Planarity : 0.004 0.039 1478 Dihedral : 16.411 146.817 1570 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.51 % Allowed : 21.60 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.16 (0.26), residues: 1060 helix: 1.41 (0.21), residues: 612 sheet: -0.37 (0.55), residues: 76 loop : 0.10 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 81 HIS 0.003 0.001 HIS C 124 PHE 0.014 0.001 PHE A 155 TYR 0.015 0.001 TYR C 115 ARG 0.002 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.05721 ( 479) hydrogen bonds : angle 4.71960 ( 1413) covalent geometry : bond 0.00342 ( 9140) covalent geometry : angle 0.61497 (12354) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.040 Fit side-chains REVERT: A 13 LYS cc_start: 0.8101 (pttp) cc_final: 0.7687 (pptt) REVERT: A 41 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7979 (tp) REVERT: A 151 ILE cc_start: 0.8411 (mm) cc_final: 0.8127 (mp) REVERT: A 186 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7776 (mmt90) REVERT: A 196 TRP cc_start: 0.8937 (OUTLIER) cc_final: 0.8387 (p90) REVERT: A 210 MET cc_start: 0.6755 (mmp) cc_final: 0.6481 (mmt) REVERT: A 265 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7407 (mp-120) REVERT: B 49 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: C 13 LYS cc_start: 0.8114 (pttp) cc_final: 0.7774 (pptt) REVERT: C 41 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7955 (tp) REVERT: C 151 ILE cc_start: 0.8412 (mm) cc_final: 0.8129 (mp) REVERT: C 186 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7770 (mmt90) REVERT: C 210 MET cc_start: 0.6732 (mmp) cc_final: 0.6474 (mmt) REVERT: C 265 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7446 (mp-120) REVERT: D 126 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7282 (mmpt) outliers start: 33 outliers final: 15 residues processed: 159 average time/residue: 1.5493 time to fit residues: 259.0753 Evaluate side-chains 164 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 259 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN B 192 GLN B 239 ASN C 182 GLN D 157 ASN D 192 GLN D 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108277 restraints weight = 8413.159| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.65 r_work: 0.3157 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9140 Z= 0.121 Angle : 0.553 7.274 12354 Z= 0.271 Chirality : 0.048 0.379 1400 Planarity : 0.004 0.038 1478 Dihedral : 15.203 144.733 1570 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.98 % Allowed : 22.34 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.33 (0.26), residues: 1060 helix: 1.57 (0.21), residues: 612 sheet: -0.41 (0.54), residues: 76 loop : 0.14 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 81 HIS 0.002 0.001 HIS A 259 PHE 0.011 0.001 PHE A 155 TYR 0.014 0.001 TYR C 115 ARG 0.002 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 479) hydrogen bonds : angle 4.54313 ( 1413) covalent geometry : bond 0.00264 ( 9140) covalent geometry : angle 0.55338 (12354) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.004 Fit side-chains REVERT: A 13 LYS cc_start: 0.8243 (pttp) cc_final: 0.7726 (pptt) REVERT: A 41 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7914 (tp) REVERT: A 90 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: A 186 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7637 (mmt90) REVERT: A 210 MET cc_start: 0.6777 (mmp) cc_final: 0.6513 (mmt) REVERT: A 265 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7324 (mp-120) REVERT: B 49 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: B 126 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7349 (mmpt) REVERT: C 13 LYS cc_start: 0.8139 (pttp) cc_final: 0.7763 (pptt) REVERT: C 41 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7923 (tp) REVERT: C 90 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: C 186 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7643 (mmt90) REVERT: C 210 MET cc_start: 0.6713 (mmp) cc_final: 0.6379 (mmt) REVERT: C 265 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7324 (mp-120) REVERT: D 49 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: D 255 LYS cc_start: 0.7587 (ttpp) cc_final: 0.7325 (tmmt) outliers start: 28 outliers final: 9 residues processed: 166 average time/residue: 1.5099 time to fit residues: 264.1905 Evaluate side-chains 163 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 259 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 0.0370 chunk 105 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 94 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN B 239 ASN C 182 GLN D 157 ASN D 192 GLN D 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110553 restraints weight = 8355.992| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.65 r_work: 0.3187 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9140 Z= 0.111 Angle : 0.538 10.790 12354 Z= 0.262 Chirality : 0.046 0.370 1400 Planarity : 0.004 0.038 1478 Dihedral : 13.785 143.091 1570 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.66 % Allowed : 22.98 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.49 (0.26), residues: 1060 helix: 1.75 (0.21), residues: 610 sheet: -0.47 (0.53), residues: 76 loop : 0.17 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 81 HIS 0.002 0.001 HIS A 259 PHE 0.010 0.001 PHE A 155 TYR 0.014 0.001 TYR A 115 ARG 0.002 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 479) hydrogen bonds : angle 4.47944 ( 1413) covalent geometry : bond 0.00238 ( 9140) covalent geometry : angle 0.53764 (12354) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.974 Fit side-chains REVERT: A 13 LYS cc_start: 0.7985 (pttp) cc_final: 0.7591 (pptt) REVERT: A 186 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7647 (mmt90) REVERT: A 210 MET cc_start: 0.6686 (mmp) cc_final: 0.6433 (mmt) REVERT: A 235 MET cc_start: 0.8791 (mmm) cc_final: 0.8583 (mmm) REVERT: A 265 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7281 (mp-120) REVERT: B 49 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7605 (mt-10) REVERT: C 13 LYS cc_start: 0.8231 (pttp) cc_final: 0.7811 (pptt) REVERT: C 41 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7895 (tp) REVERT: C 186 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7649 (mmt90) REVERT: C 210 MET cc_start: 0.6639 (mmp) cc_final: 0.6272 (mmt) REVERT: C 265 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7276 (mp-120) REVERT: D 49 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7605 (mt-10) REVERT: D 255 LYS cc_start: 0.7592 (ttpp) cc_final: 0.7336 (tmmt) outliers start: 25 outliers final: 8 residues processed: 160 average time/residue: 1.5678 time to fit residues: 263.8373 Evaluate side-chains 155 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN B 239 ASN D 157 ASN D 192 GLN D 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.106241 restraints weight = 8363.926| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.64 r_work: 0.3123 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9140 Z= 0.152 Angle : 0.590 6.593 12354 Z= 0.290 Chirality : 0.048 0.378 1400 Planarity : 0.004 0.038 1478 Dihedral : 13.634 145.987 1570 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.13 % Allowed : 23.40 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.37 (0.26), residues: 1060 helix: 1.60 (0.21), residues: 612 sheet: -0.38 (0.53), residues: 76 loop : 0.17 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 39 HIS 0.003 0.001 HIS C 11 PHE 0.015 0.002 PHE A 155 TYR 0.016 0.002 TYR C 115 ARG 0.004 0.000 ARG C 224 Details of bonding type rmsd hydrogen bonds : bond 0.05565 ( 479) hydrogen bonds : angle 4.65200 ( 1413) covalent geometry : bond 0.00350 ( 9140) covalent geometry : angle 0.59025 (12354) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.963 Fit side-chains REVERT: A 13 LYS cc_start: 0.7949 (pttp) cc_final: 0.7646 (pptt) REVERT: A 186 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7701 (mmt90) REVERT: A 210 MET cc_start: 0.6671 (mmp) cc_final: 0.6413 (mmt) REVERT: A 265 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7333 (mp-120) REVERT: B 49 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7588 (mt-10) REVERT: C 13 LYS cc_start: 0.8162 (pttp) cc_final: 0.7733 (pptt) REVERT: C 41 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7946 (tp) REVERT: C 186 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7710 (mmt90) REVERT: C 210 MET cc_start: 0.6633 (mmp) cc_final: 0.6382 (mmt) REVERT: C 212 LYS cc_start: 0.7931 (mptm) cc_final: 0.7725 (mptp) REVERT: C 265 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7336 (mp-120) REVERT: D 49 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7582 (mt-10) REVERT: D 255 LYS cc_start: 0.7637 (ttpp) cc_final: 0.7354 (tmmt) outliers start: 20 outliers final: 7 residues processed: 156 average time/residue: 1.5885 time to fit residues: 260.3805 Evaluate side-chains 155 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN B 239 ASN D 157 ASN D 192 GLN D 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103495 restraints weight = 8451.283| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.65 r_work: 0.3082 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9140 Z= 0.216 Angle : 0.681 11.830 12354 Z= 0.333 Chirality : 0.052 0.397 1400 Planarity : 0.004 0.038 1478 Dihedral : 13.966 149.457 1570 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.91 % Allowed : 23.51 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.17 (0.26), residues: 1060 helix: 1.41 (0.21), residues: 612 sheet: -0.28 (0.54), residues: 76 loop : 0.08 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 39 HIS 0.004 0.001 HIS A 11 PHE 0.020 0.002 PHE A 155 TYR 0.019 0.002 TYR C 115 ARG 0.003 0.001 ARG D 253 Details of bonding type rmsd hydrogen bonds : bond 0.06635 ( 479) hydrogen bonds : angle 4.88455 ( 1413) covalent geometry : bond 0.00517 ( 9140) covalent geometry : angle 0.68127 (12354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7800.96 seconds wall clock time: 134 minutes 57.32 seconds (8097.32 seconds total)