Starting phenix.real_space_refine on Wed Sep 17 13:35:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfl_45550/09_2025/9cfl_45550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfl_45550/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cfl_45550/09_2025/9cfl_45550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfl_45550/09_2025/9cfl_45550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cfl_45550/09_2025/9cfl_45550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfl_45550/09_2025/9cfl_45550.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.080 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.61, per 1000 atoms: 0.29 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: 0.90 Conformation dependent library (CDL) restraints added in 268.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.31 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: 1.54 Time building geometry restraints manager: 1.10 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 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: 1.700 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.800 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:8.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.540 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG D 23 TYR 0.023 0.002 TYR A 115 PHE 0.016 0.002 PHE C 155 TRP 0.025 0.003 TRP A 81 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00762 ( 9140) covalent geometry : angle 1.20507 (12354) hydrogen bonds : bond 0.16380 ( 479) hydrogen bonds : angle 6.70363 ( 1413) *********************** 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 : 0.379 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: 0.7450 time to fit residues: 140.1240 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 : 0.352 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 47 GLN C 265 GLN D 32 HIS D 34 ASN D 59 ASN D 157 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.135383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109858 restraints weight = 8371.785| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.68 r_work: 0.3158 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1033 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= 0.133 Angle : 0.651 9.281 12354 Z= 0.307 Chirality : 0.048 0.264 1400 Planarity : 0.004 0.048 1478 Dihedral : 22.679 154.698 1594 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.09 % Allowed : 22.77 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.26), residues: 1060 helix: 1.14 (0.21), residues: 610 sheet: 0.72 (0.58), residues: 76 loop : -0.15 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 23 TYR 0.016 0.001 TYR C 115 PHE 0.014 0.001 PHE A 155 TRP 0.014 0.002 TRP A 81 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9140) covalent geometry : angle 0.65121 (12354) hydrogen bonds : bond 0.05360 ( 479) hydrogen bonds : angle 4.88286 ( 1413) *********************** 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 : 0.366 Fit side-chains REVERT: A 13 LYS cc_start: 0.8065 (pttp) cc_final: 0.7553 (pptt) REVERT: C 13 LYS cc_start: 0.8161 (pttp) cc_final: 0.7685 (pptt) REVERT: D 149 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.6957 (ttt180) REVERT: D 240 ASP cc_start: 0.7114 (m-30) cc_final: 0.6900 (m-30) outliers start: 29 outliers final: 19 residues processed: 174 average time/residue: 0.7612 time to fit residues: 139.0731 Evaluate side-chains 169 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 101 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.135535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109823 restraints weight = 8374.198| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.69 r_work: 0.3155 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9140 Z= 0.120 Angle : 0.603 10.308 12354 Z= 0.282 Chirality : 0.048 0.378 1400 Planarity : 0.004 0.034 1478 Dihedral : 18.577 140.517 1578 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.36 % Allowed : 20.32 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.26), residues: 1060 helix: 1.48 (0.21), residues: 610 sheet: 0.24 (0.56), residues: 76 loop : -0.09 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 15 TYR 0.017 0.001 TYR C 115 PHE 0.013 0.001 PHE A 155 TRP 0.013 0.002 TRP A 81 HIS 0.002 0.001 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9140) covalent geometry : angle 0.60326 (12354) hydrogen bonds : bond 0.04910 ( 479) hydrogen bonds : angle 4.60236 ( 1413) *********************** 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 199 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.278 Fit side-chains REVERT: A 1 MET cc_start: 0.5008 (pmm) cc_final: 0.4530 (pmm) REVERT: A 13 LYS cc_start: 0.8035 (pttp) cc_final: 0.7771 (pptt) REVERT: A 80 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7909 (pmm) REVERT: A 186 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7392 (mmt90) REVERT: B 49 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7571 (mt-10) REVERT: C 80 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7927 (pmm) REVERT: C 186 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7397 (mmt90) REVERT: D 49 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7552 (mt-10) REVERT: D 126 LYS cc_start: 0.7848 (mtmm) cc_final: 0.6945 (mmpt) outliers start: 41 outliers final: 15 residues processed: 174 average time/residue: 0.7060 time to fit residues: 129.1753 Evaluate side-chains 170 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 186 ARG 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 186 ARG 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 7 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 93 optimal weight: 0.0870 chunk 70 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3560 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.132585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.106523 restraints weight = 8473.802| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.70 r_work: 0.3107 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1506 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= 0.154 Angle : 0.639 8.279 12354 Z= 0.302 Chirality : 0.050 0.379 1400 Planarity : 0.004 0.035 1478 Dihedral : 17.217 142.466 1572 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.62 % Allowed : 20.85 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.26), residues: 1060 helix: 1.53 (0.21), residues: 610 sheet: 0.01 (0.55), residues: 76 loop : -0.04 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 60 TYR 0.017 0.002 TYR A 115 PHE 0.017 0.002 PHE A 155 TRP 0.014 0.002 TRP C 81 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9140) covalent geometry : angle 0.63894 (12354) hydrogen bonds : bond 0.05759 ( 479) hydrogen bonds : angle 4.70539 ( 1413) *********************** 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 184 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.349 Fit side-chains REVERT: A 1 MET cc_start: 0.5055 (pmm) cc_final: 0.4647 (pmm) REVERT: A 13 LYS cc_start: 0.8134 (pttp) cc_final: 0.7782 (pptt) REVERT: A 41 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7853 (tp) REVERT: A 151 ILE cc_start: 0.8411 (mm) cc_final: 0.8115 (mp) REVERT: A 196 TRP cc_start: 0.8896 (OUTLIER) cc_final: 0.8354 (p90) REVERT: B 15 ARG cc_start: 0.8753 (mmm160) cc_final: 0.8511 (mmm-85) REVERT: B 49 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 126 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7189 (mmpt) REVERT: C 41 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7855 (tp) REVERT: C 151 ILE cc_start: 0.8390 (mm) cc_final: 0.8092 (mp) REVERT: C 196 TRP cc_start: 0.8894 (OUTLIER) cc_final: 0.8322 (p90) REVERT: D 15 ARG cc_start: 0.8750 (mmm160) cc_final: 0.8521 (mmm-85) REVERT: D 49 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7590 (mt-10) outliers start: 34 outliers final: 13 residues processed: 166 average time/residue: 0.7545 time to fit residues: 131.6113 Evaluate side-chains 163 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 105 MET 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 71 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 93 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.132530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107218 restraints weight = 8531.763| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.61 r_work: 0.3114 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9140 Z= 0.161 Angle : 0.623 8.597 12354 Z= 0.300 Chirality : 0.051 0.425 1400 Planarity : 0.004 0.036 1478 Dihedral : 16.606 145.382 1572 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.30 % Allowed : 20.96 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.26), residues: 1060 helix: 1.48 (0.21), residues: 610 sheet: -0.15 (0.55), residues: 76 loop : 0.01 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 253 TYR 0.017 0.002 TYR C 115 PHE 0.016 0.002 PHE A 155 TRP 0.015 0.002 TRP C 81 HIS 0.003 0.001 HIS C 11 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9140) covalent geometry : angle 0.62348 (12354) hydrogen bonds : bond 0.05798 ( 479) hydrogen bonds : angle 4.71329 ( 1413) *********************** 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 181 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.363 Fit side-chains REVERT: A 1 MET cc_start: 0.5121 (pmm) cc_final: 0.4783 (pmm) REVERT: A 13 LYS cc_start: 0.8162 (pttp) cc_final: 0.7704 (pptt) REVERT: A 41 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7996 (tp) REVERT: A 151 ILE cc_start: 0.8436 (mm) cc_final: 0.8158 (mp) REVERT: A 186 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7808 (mmt90) REVERT: A 196 TRP cc_start: 0.8952 (OUTLIER) cc_final: 0.8411 (p90) REVERT: A 210 MET cc_start: 0.6846 (mmp) cc_final: 0.6447 (mmt) REVERT: A 265 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7468 (mp-120) REVERT: C 13 LYS cc_start: 0.8127 (pttp) cc_final: 0.7640 (pptt) REVERT: C 41 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7982 (tp) REVERT: C 151 ILE cc_start: 0.8428 (mm) cc_final: 0.8142 (mp) REVERT: C 186 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7817 (mmt90) REVERT: C 196 TRP cc_start: 0.8956 (OUTLIER) cc_final: 0.8401 (p90) REVERT: C 210 MET cc_start: 0.6820 (mmt) cc_final: 0.6429 (mmt) outliers start: 31 outliers final: 10 residues processed: 165 average time/residue: 0.7606 time to fit residues: 131.7635 Evaluate side-chains 167 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 186 ARG Chi-restraints excluded: chain C residue 196 TRP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.132652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106308 restraints weight = 8387.442| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.69 r_work: 0.3109 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9140 Z= 0.143 Angle : 0.594 8.100 12354 Z= 0.287 Chirality : 0.050 0.420 1400 Planarity : 0.004 0.036 1478 Dihedral : 16.006 145.232 1570 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.51 % Allowed : 21.38 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.26), residues: 1060 helix: 1.53 (0.21), residues: 610 sheet: -0.24 (0.55), residues: 76 loop : 0.01 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 224 TYR 0.015 0.001 TYR C 115 PHE 0.014 0.001 PHE A 155 TRP 0.014 0.002 TRP C 81 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9140) covalent geometry : angle 0.59372 (12354) hydrogen bonds : bond 0.05434 ( 479) hydrogen bonds : angle 4.64959 ( 1413) *********************** 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 182 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.350 Fit side-chains REVERT: A 13 LYS cc_start: 0.8136 (pttp) cc_final: 0.7737 (pptt) REVERT: A 41 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7906 (tp) REVERT: A 151 ILE cc_start: 0.8375 (mm) cc_final: 0.8092 (mp) REVERT: A 186 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7611 (mmt90) REVERT: A 210 MET cc_start: 0.6739 (mmp) cc_final: 0.6346 (mmt) REVERT: A 265 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7309 (mp-120) REVERT: C 13 LYS cc_start: 0.8048 (pttp) cc_final: 0.7657 (pptt) REVERT: C 41 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7894 (tp) REVERT: C 151 ILE cc_start: 0.8380 (mm) cc_final: 0.8092 (mp) REVERT: C 186 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7625 (mmt90) REVERT: C 210 MET cc_start: 0.6715 (mmp) cc_final: 0.6328 (mmt) REVERT: C 265 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7351 (mp-120) outliers start: 33 outliers final: 12 residues processed: 166 average time/residue: 0.7775 time to fit residues: 135.4126 Evaluate side-chains 161 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 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 186 ARG Chi-restraints excluded: chain C residue 196 TRP 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 43 optimal weight: 0.0870 chunk 50 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.135051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109101 restraints weight = 8452.132| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.67 r_work: 0.3169 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1719 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= 0.114 Angle : 0.538 7.335 12354 Z= 0.262 Chirality : 0.047 0.382 1400 Planarity : 0.003 0.035 1478 Dihedral : 14.610 143.511 1570 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.98 % Allowed : 21.49 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.26), residues: 1060 helix: 1.67 (0.21), residues: 610 sheet: -0.28 (0.54), residues: 76 loop : 0.10 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 120 TYR 0.014 0.001 TYR A 115 PHE 0.011 0.001 PHE A 155 TRP 0.015 0.002 TRP C 81 HIS 0.002 0.001 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9140) covalent geometry : angle 0.53848 (12354) hydrogen bonds : bond 0.04509 ( 479) hydrogen bonds : angle 4.50278 ( 1413) *********************** 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 179 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.363 Fit side-chains REVERT: A 13 LYS cc_start: 0.8278 (pttp) cc_final: 0.7753 (pptt) REVERT: A 41 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7907 (tp) REVERT: A 90 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: A 186 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7602 (mmt90) REVERT: A 210 MET cc_start: 0.6779 (mmp) cc_final: 0.6387 (mmt) REVERT: A 265 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7293 (mp-120) REVERT: B 126 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7376 (mmpt) REVERT: C 13 LYS cc_start: 0.8129 (pttp) cc_final: 0.7753 (pptt) REVERT: C 41 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7909 (tp) REVERT: C 186 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7610 (mmt90) REVERT: C 210 MET cc_start: 0.6720 (mmp) cc_final: 0.6379 (mmt) REVERT: C 265 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7332 (mp-120) REVERT: D 255 LYS cc_start: 0.7585 (ttpp) cc_final: 0.7318 (tmmt) outliers start: 28 outliers final: 9 residues processed: 166 average time/residue: 0.7766 time to fit residues: 135.3667 Evaluate side-chains 164 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 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 = 0.3556 r_free = 0.3556 target = 0.132353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106314 restraints weight = 8349.904| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.63 r_work: 0.3120 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9140 Z= 0.153 Angle : 0.598 9.519 12354 Z= 0.292 Chirality : 0.049 0.430 1400 Planarity : 0.004 0.036 1478 Dihedral : 13.950 146.173 1570 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.77 % Allowed : 22.02 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.26), residues: 1060 helix: 1.61 (0.21), residues: 610 sheet: -0.36 (0.54), residues: 76 loop : 0.05 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 253 TYR 0.016 0.002 TYR A 115 PHE 0.015 0.002 PHE A 155 TRP 0.014 0.002 TRP C 81 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9140) covalent geometry : angle 0.59824 (12354) hydrogen bonds : bond 0.05631 ( 479) hydrogen bonds : angle 4.66850 ( 1413) *********************** 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 171 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.290 Fit side-chains REVERT: A 13 LYS cc_start: 0.8062 (pttp) cc_final: 0.7696 (pptt) REVERT: A 41 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7987 (tp) REVERT: A 186 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7758 (mmt90) REVERT: A 210 MET cc_start: 0.6777 (mmp) cc_final: 0.6503 (mmt) REVERT: A 265 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7371 (mp-120) REVERT: C 13 LYS cc_start: 0.8228 (pttp) cc_final: 0.7809 (pptt) REVERT: C 41 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7989 (tp) REVERT: C 186 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7771 (mmt90) REVERT: C 196 TRP cc_start: 0.8954 (OUTLIER) cc_final: 0.8417 (p90) REVERT: C 210 MET cc_start: 0.6747 (mmp) cc_final: 0.6476 (mmt) REVERT: C 265 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7384 (mp-120) outliers start: 26 outliers final: 11 residues processed: 156 average time/residue: 0.7948 time to fit residues: 130.0315 Evaluate side-chains 162 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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 100 ASN Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 196 TRP Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 103 ILE 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 62 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 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 = 0.3563 r_free = 0.3563 target = 0.132906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.106945 restraints weight = 8397.437| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.65 r_work: 0.3137 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9140 Z= 0.137 Angle : 0.566 6.090 12354 Z= 0.279 Chirality : 0.047 0.364 1400 Planarity : 0.004 0.036 1478 Dihedral : 13.638 145.681 1570 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.66 % Allowed : 22.34 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.26), residues: 1060 helix: 1.61 (0.21), residues: 610 sheet: -0.30 (0.53), residues: 76 loop : 0.06 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 253 TYR 0.016 0.001 TYR A 115 PHE 0.014 0.001 PHE A 155 TRP 0.014 0.002 TRP A 81 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9140) covalent geometry : angle 0.56632 (12354) hydrogen bonds : bond 0.05239 ( 479) hydrogen bonds : angle 4.63176 ( 1413) *********************** 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 172 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.359 Fit side-chains REVERT: A 13 LYS cc_start: 0.7989 (pttp) cc_final: 0.7642 (pptt) REVERT: A 41 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7917 (tp) REVERT: A 186 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7749 (mmt90) REVERT: A 210 MET cc_start: 0.6759 (mmp) cc_final: 0.6490 (mmt) REVERT: A 265 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7342 (mp-120) REVERT: C 13 LYS cc_start: 0.8144 (pttp) cc_final: 0.7741 (pptt) REVERT: C 41 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7921 (tp) REVERT: C 186 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7783 (mmt90) REVERT: C 210 MET cc_start: 0.6708 (mmp) cc_final: 0.6442 (mmt) REVERT: C 265 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7352 (mp-120) REVERT: D 255 LYS cc_start: 0.7617 (ttpp) cc_final: 0.7332 (tmmt) outliers start: 25 outliers final: 11 residues processed: 159 average time/residue: 0.8131 time to fit residues: 135.4168 Evaluate side-chains 164 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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 100 ASN 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 103 ILE 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 25 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 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 = 0.3554 r_free = 0.3554 target = 0.132006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106078 restraints weight = 8387.112| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.65 r_work: 0.3131 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9140 Z= 0.140 Angle : 0.579 11.178 12354 Z= 0.284 Chirality : 0.047 0.316 1400 Planarity : 0.004 0.037 1478 Dihedral : 13.515 146.260 1570 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.23 % Allowed : 22.66 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.26), residues: 1060 helix: 1.63 (0.21), residues: 610 sheet: -0.14 (0.52), residues: 76 loop : 0.07 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 253 TYR 0.016 0.001 TYR C 115 PHE 0.014 0.001 PHE A 155 TRP 0.014 0.002 TRP A 81 HIS 0.003 0.001 HIS C 11 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9140) covalent geometry : angle 0.57904 (12354) hydrogen bonds : bond 0.05343 ( 479) hydrogen bonds : angle 4.65374 ( 1413) ********************** 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 169 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.364 Fit side-chains REVERT: A 13 LYS cc_start: 0.7981 (pttp) cc_final: 0.7658 (pptt) REVERT: A 41 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7942 (tp) REVERT: A 186 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7748 (mmt90) REVERT: A 210 MET cc_start: 0.6760 (mmp) cc_final: 0.6494 (mmt) REVERT: A 265 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7318 (mp-120) REVERT: B 49 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: C 13 LYS cc_start: 0.8173 (pttp) cc_final: 0.7747 (pptt) REVERT: C 41 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7939 (tp) REVERT: C 186 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7747 (mmt90) REVERT: C 210 MET cc_start: 0.6721 (mmp) cc_final: 0.6461 (mmt) REVERT: C 265 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7348 (mp-120) REVERT: D 49 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: D 255 LYS cc_start: 0.7635 (ttpp) cc_final: 0.7349 (tmmt) outliers start: 21 outliers final: 10 residues processed: 157 average time/residue: 0.8021 time to fit residues: 131.9763 Evaluate side-chains 164 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 100 ASN Chi-restraints excluded: chain C residue 186 ARG 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 103 ILE 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: 2.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 101 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 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 = 0.3548 r_free = 0.3548 target = 0.131397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105524 restraints weight = 8295.776| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.63 r_work: 0.3112 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9140 Z= 0.157 Angle : 0.590 6.655 12354 Z= 0.291 Chirality : 0.048 0.300 1400 Planarity : 0.004 0.037 1478 Dihedral : 13.562 147.248 1570 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.34 % Allowed : 22.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.26), residues: 1060 helix: 1.57 (0.21), residues: 610 sheet: -0.07 (0.53), residues: 76 loop : 0.07 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 253 TYR 0.017 0.002 TYR A 115 PHE 0.016 0.002 PHE A 155 TRP 0.014 0.002 TRP A 81 HIS 0.003 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9140) covalent geometry : angle 0.59014 (12354) hydrogen bonds : bond 0.05694 ( 479) hydrogen bonds : angle 4.71074 ( 1413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4024.27 seconds wall clock time: 69 minutes 15.00 seconds (4155.00 seconds total)