Starting phenix.real_space_refine on Thu Jun 4 02:34:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wp9_66136/06_2026/9wp9_66136.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wp9_66136/06_2026/9wp9_66136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wp9_66136/06_2026/9wp9_66136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wp9_66136/06_2026/9wp9_66136.map" model { file = "/net/cci-nas-00/data/ceres_data/9wp9_66136/06_2026/9wp9_66136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wp9_66136/06_2026/9wp9_66136.cif" } resolution = 3.25 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= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 66 5.16 5 C 6190 2.51 5 N 1678 2.21 5 O 1815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9750 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1794 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1787 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2143 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 8, 'TRANS': 261} Chain breaks: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.26 Number of scatterers: 9750 At special positions: 0 Unit cell: (85.36, 130.24, 128.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 1 15.00 O 1815 8.00 N 1678 7.00 C 6190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 178 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 269 " - pdb=" SG CYS R 274 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 376.6 milliseconds 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 31.6% alpha, 22.2% 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 6 through 31 removed outlier: 3.849A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 45 removed outlier: 4.011A pdb=" N GLY A 45 " --> pdb=" O ASP A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 45' Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.530A pdb=" N ALA A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.359A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 removed outlier: 3.644A pdb=" N ALA A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 183 through 203 removed outlier: 3.622A pdb=" N THR A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.702A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.516A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'R' and resid 18 through 26 Processing helix chain 'R' and resid 42 through 63 Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'R' and resid 75 through 103 removed outlier: 3.730A pdb=" N GLY R 100 " --> pdb=" O ILE R 96 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LYS R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR R 103 " --> pdb=" O SER R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 142 removed outlier: 4.008A pdb=" N MET R 118 " --> pdb=" O ARG R 114 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE R 119 " --> pdb=" O GLU R 115 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS R 142 " --> pdb=" O LEU R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 175 removed outlier: 3.982A pdb=" N VAL R 154 " --> pdb=" O LYS R 150 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE R 155 " --> pdb=" O ARG R 151 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP R 162 " --> pdb=" O ILE R 158 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE R 164 " --> pdb=" O MET R 160 " (cutoff:3.500A) Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 193 through 230 removed outlier: 3.524A pdb=" N ILE R 201 " --> pdb=" O ILE R 197 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL R 212 " --> pdb=" O LEU R 208 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR R 219 " --> pdb=" O TYR R 215 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG R 227 " --> pdb=" O LYS R 223 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS R 228 " --> pdb=" O SER R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 269 removed outlier: 3.599A pdb=" N VAL R 245 " --> pdb=" O LEU R 241 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL R 249 " --> pdb=" O VAL R 245 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER R 250 " --> pdb=" O VAL R 246 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS R 255 " --> pdb=" O VAL R 251 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP R 256 " --> pdb=" O PHE R 252 " (cutoff:3.500A) Proline residue: R 258 - end of helix removed outlier: 3.621A pdb=" N ASP R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL R 267 " --> pdb=" O PHE R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 294 removed outlier: 4.306A pdb=" N PHE R 283 " --> pdb=" O LYS R 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76 removed outlier: 4.971A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLY A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 9.468A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.728A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.517A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.277A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.705A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.597A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.572A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.570A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.848A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 removed outlier: 4.898A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 148 removed outlier: 3.637A pdb=" N GLU C 246 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP C 176 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.713A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.555A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 433 hydrogen bonds defined for protein. 1233 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: 1.59 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3157 1.35 - 1.47: 2439 1.47 - 1.59: 4253 1.59 - 1.71: 1 1.71 - 1.83: 95 Bond restraints: 9945 Sorted by residual: bond pdb=" O1 S1P R1001 " pdb=" P22 S1P R1001 " ideal model delta sigma weight residual 1.677 1.613 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C6 S1P R1001 " pdb=" C7 S1P R1001 " ideal model delta sigma weight residual 1.540 1.496 0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" CA TYR A 243 " pdb=" C TYR A 243 " ideal model delta sigma weight residual 1.523 1.493 0.030 1.80e-02 3.09e+03 2.81e+00 bond pdb=" C4 S1P R1001 " pdb=" C5 S1P R1001 " ideal model delta sigma weight residual 1.329 1.297 0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" CA VAL R 248 " pdb=" C VAL R 248 " ideal model delta sigma weight residual 1.522 1.544 -0.022 1.38e-02 5.25e+03 2.56e+00 ... (remaining 9940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 13257 2.32 - 4.64: 167 4.64 - 6.96: 26 6.96 - 9.28: 8 9.28 - 11.60: 2 Bond angle restraints: 13460 Sorted by residual: angle pdb=" CA PRO R 258 " pdb=" N PRO R 258 " pdb=" CD PRO R 258 " ideal model delta sigma weight residual 112.00 105.69 6.31 1.40e+00 5.10e-01 2.03e+01 angle pdb=" N VAL N 2 " pdb=" CA VAL N 2 " pdb=" C VAL N 2 " ideal model delta sigma weight residual 111.91 108.18 3.73 8.90e-01 1.26e+00 1.76e+01 angle pdb=" C GLU A 242 " pdb=" N TYR A 243 " pdb=" CA TYR A 243 " ideal model delta sigma weight residual 122.31 114.04 8.27 2.00e+00 2.50e-01 1.71e+01 angle pdb=" CB PRO R 258 " pdb=" CG PRO R 258 " pdb=" CD PRO R 258 " ideal model delta sigma weight residual 106.10 94.69 11.41 3.20e+00 9.77e-02 1.27e+01 angle pdb=" C VAL R 248 " pdb=" N VAL R 249 " pdb=" CA VAL R 249 " ideal model delta sigma weight residual 120.30 114.57 5.73 1.64e+00 3.72e-01 1.22e+01 ... (remaining 13455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.77: 5623 29.77 - 59.54: 286 59.54 - 89.31: 18 89.31 - 119.08: 2 119.08 - 148.85: 3 Dihedral angle restraints: 5932 sinusoidal: 2333 harmonic: 3599 Sorted by residual: dihedral pdb=" N2 S1P R1001 " pdb=" C1 S1P R1001 " pdb=" C2 S1P R1001 " pdb=" O1 S1P R1001 " ideal model delta sinusoidal sigma weight residual -73.93 74.92 -148.85 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" C3 S1P R1001 " pdb=" C1 S1P R1001 " pdb=" C2 S1P R1001 " pdb=" O1 S1P R1001 " ideal model delta sinusoidal sigma weight residual 52.36 -161.19 -146.45 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" SG CYS R 178 " pdb=" CB CYS R 185 " pdb=" SG CYS R 185 " pdb=" CA CYS R 185 " ideal model delta sinusoidal sigma weight residual -73.00 1.86 -74.86 1 2.00e+01 2.50e-03 1.77e+01 ... (remaining 5929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1196 0.052 - 0.104: 256 0.104 - 0.156: 64 0.156 - 0.208: 6 0.208 - 0.260: 1 Chirality restraints: 1523 Sorted by residual: chirality pdb=" C3 S1P R1001 " pdb=" C2 S1P R1001 " pdb=" C4 S1P R1001 " pdb=" O3 S1P R1001 " both_signs ideal model delta sigma weight residual False -2.52 -2.26 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE R 64 " pdb=" CA ILE R 64 " pdb=" CG1 ILE R 64 " pdb=" CG2 ILE R 64 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CG LEU R 182 " pdb=" CB LEU R 182 " pdb=" CD1 LEU R 182 " pdb=" CD2 LEU R 182 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 1520 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 S1P R1001 " -0.049 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C4 S1P R1001 " 0.046 2.00e-02 2.50e+03 pdb=" C5 S1P R1001 " 0.054 2.00e-02 2.50e+03 pdb=" C6 S1P R1001 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 65 " 0.017 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP R 65 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP R 65 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP R 65 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 65 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 65 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 65 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 65 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 65 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 235 " 0.036 2.00e-02 2.50e+03 2.21e-02 9.75e+00 pdb=" CG TYR C 235 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR C 235 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 235 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 235 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 235 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 235 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 235 " 0.010 2.00e-02 2.50e+03 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 275 2.69 - 3.24: 8981 3.24 - 3.80: 14658 3.80 - 4.35: 19447 4.35 - 4.90: 33936 Nonbonded interactions: 77297 Sorted by model distance: nonbonded pdb=" OD1 ASP R 85 " pdb=" OG SER R 291 " model vdw 2.140 3.040 nonbonded pdb=" OG SER R 226 " pdb=" ND2 ASN R 234 " model vdw 2.145 3.120 nonbonded pdb=" O ILE R 247 " pdb=" OG SER R 250 " model vdw 2.165 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.175 3.040 nonbonded pdb=" OG SER B 281 " pdb=" O HIS G 44 " model vdw 2.204 3.040 ... (remaining 77292 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.004 0.064 9950 Z= 0.163 Angle : 0.671 11.604 13470 Z= 0.350 Chirality : 0.046 0.260 1523 Planarity : 0.004 0.050 1703 Dihedral : 17.080 148.853 3597 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.38 % Allowed : 26.32 % Favored : 73.30 % 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 are not related in a simple way. whole: -0.17 (0.24), residues: 1222 helix: 0.86 (0.28), residues: 373 sheet: 0.13 (0.29), residues: 316 loop : -0.91 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 237 TYR 0.050 0.002 TYR C 235 PHE 0.024 0.002 PHE R 112 TRP 0.058 0.002 TRP R 65 HIS 0.007 0.001 HIS R 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 9945) covalent geometry : angle 0.67025 / 0.35 (13460) SS BOND : bond 0.00454 / 0.18 ( 5) SS BOND : angle 1.46186 / 0.84 ( 10) hydrogen bonds : bond 0.11585 / 7.64 ( 433) hydrogen bonds : angle 5.53012 / 3.95 ( 1233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.380 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 116 average time/residue: 0.0900 time to fit residues: 15.3727 Evaluate side-chains 106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain N residue 81 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.0070 chunk 97 optimal weight: 0.0040 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0170 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 31 ASN R 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.130341 restraints weight = 10744.108| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.42 r_work: 0.3331 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9950 Z= 0.103 Angle : 0.511 7.918 13470 Z= 0.268 Chirality : 0.041 0.199 1523 Planarity : 0.003 0.038 1703 Dihedral : 8.872 155.339 1381 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.11 % Allowed : 24.53 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1222 helix: 1.50 (0.28), residues: 377 sheet: 0.27 (0.29), residues: 323 loop : -0.75 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.031 0.001 TYR C 235 PHE 0.026 0.001 PHE R 112 TRP 0.027 0.001 TRP R 65 HIS 0.006 0.001 HIS R 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 9945) covalent geometry : angle 0.51024 / 0.27 (13460) SS BOND : bond 0.00172 / 0.08 ( 5) SS BOND : angle 1.01140 / 0.60 ( 10) hydrogen bonds : bond 0.03495 / 2.28 ( 433) hydrogen bonds : angle 4.32510 / 3.03 ( 1233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.447 Fit side-chains REVERT: A 230 ASP cc_start: 0.8347 (m-30) cc_final: 0.7997 (m-30) REVERT: B 59 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.6526 (m-80) REVERT: N 108 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7644 (t80) REVERT: R 239 MET cc_start: 0.6983 (ttp) cc_final: 0.6729 (mtp) outliers start: 33 outliers final: 17 residues processed: 140 average time/residue: 0.0896 time to fit residues: 18.4342 Evaluate side-chains 127 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 299 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 0.0570 chunk 100 optimal weight: 4.9990 chunk 120 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN B 237 ASN B 268 ASN B 340 ASN G 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.172757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.127211 restraints weight = 10889.645| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.66 r_work: 0.3279 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9950 Z= 0.112 Angle : 0.495 6.841 13470 Z= 0.260 Chirality : 0.041 0.169 1523 Planarity : 0.003 0.042 1703 Dihedral : 8.748 154.549 1381 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.62 % Allowed : 23.87 % Favored : 71.51 % 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 are not related in a simple way. whole: 0.51 (0.25), residues: 1222 helix: 1.98 (0.28), residues: 370 sheet: 0.34 (0.29), residues: 333 loop : -0.86 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 72 TYR 0.023 0.001 TYR C 235 PHE 0.021 0.001 PHE R 112 TRP 0.020 0.001 TRP R 65 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9945) covalent geometry : angle 0.49433 / 0.26 (13460) SS BOND : bond 0.00160 / 0.08 ( 5) SS BOND : angle 0.88757 / 0.52 ( 10) hydrogen bonds : bond 0.03462 / 2.28 ( 433) hydrogen bonds : angle 4.16054 / 2.93 ( 1233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 0.438 Fit side-chains REVERT: A 144 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8522 (m-40) REVERT: A 230 ASP cc_start: 0.8413 (m-30) cc_final: 0.8044 (m-30) REVERT: B 59 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: C 136 SER cc_start: 0.5815 (OUTLIER) cc_final: 0.5568 (p) REVERT: N 108 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7750 (t80) REVERT: R 160 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.5698 (ttp) outliers start: 49 outliers final: 28 residues processed: 146 average time/residue: 0.0858 time to fit residues: 18.6677 Evaluate side-chains 144 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 67 ASN Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 299 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 114 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 49 optimal weight: 0.0000 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.171982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129070 restraints weight = 10832.237| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.20 r_work: 0.3306 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9950 Z= 0.105 Angle : 0.476 8.479 13470 Z= 0.249 Chirality : 0.041 0.166 1523 Planarity : 0.003 0.042 1703 Dihedral : 8.412 147.850 1381 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.81 % Allowed : 23.96 % Favored : 71.23 % 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 are not related in a simple way. whole: 0.60 (0.25), residues: 1222 helix: 2.06 (0.28), residues: 376 sheet: 0.41 (0.29), residues: 335 loop : -0.88 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 72 TYR 0.021 0.001 TYR C 235 PHE 0.016 0.001 PHE R 112 TRP 0.014 0.001 TRP R 65 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 9945) covalent geometry : angle 0.47593 / 0.25 (13460) SS BOND : bond 0.00190 / 0.09 ( 5) SS BOND : angle 0.76716 / 0.45 ( 10) hydrogen bonds : bond 0.03213 / 2.13 ( 433) hydrogen bonds : angle 4.00938 / 2.82 ( 1233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 0.394 Fit side-chains REVERT: A 230 ASP cc_start: 0.8438 (m-30) cc_final: 0.8191 (m-30) REVERT: B 59 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: C 187 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8736 (tp) REVERT: N 108 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7777 (t80) REVERT: R 98 MET cc_start: 0.6491 (mmm) cc_final: 0.6206 (mmt) REVERT: R 106 LEU cc_start: 0.7434 (tp) cc_final: 0.7232 (tp) REVERT: R 160 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5570 (ttp) outliers start: 51 outliers final: 30 residues processed: 149 average time/residue: 0.0904 time to fit residues: 19.5400 Evaluate side-chains 140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 299 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN G 59 ASN N 31 ASN ** R 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.170868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128127 restraints weight = 10747.129| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.18 r_work: 0.3314 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9950 Z= 0.102 Angle : 0.469 6.114 13470 Z= 0.246 Chirality : 0.041 0.165 1523 Planarity : 0.003 0.044 1703 Dihedral : 8.133 141.878 1381 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.34 % Allowed : 24.62 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.25), residues: 1222 helix: 2.30 (0.28), residues: 368 sheet: 0.41 (0.29), residues: 333 loop : -0.88 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 18 TYR 0.020 0.001 TYR C 235 PHE 0.013 0.001 PHE R 112 TRP 0.013 0.001 TRP R 65 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 9945) covalent geometry : angle 0.46868 / 0.25 (13460) SS BOND : bond 0.00130 / 0.06 ( 5) SS BOND : angle 0.78586 / 0.43 ( 10) hydrogen bonds : bond 0.03159 / 2.08 ( 433) hydrogen bonds : angle 3.94984 / 2.78 ( 1233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 116 time to evaluate : 0.400 Fit side-chains REVERT: A 144 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8578 (m-40) REVERT: A 230 ASP cc_start: 0.8338 (m-30) cc_final: 0.8092 (m-30) REVERT: B 59 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.6693 (m-80) REVERT: C 136 SER cc_start: 0.5865 (OUTLIER) cc_final: 0.5612 (p) REVERT: C 187 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8729 (tp) REVERT: N 108 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7653 (t80) REVERT: R 98 MET cc_start: 0.6456 (mmm) cc_final: 0.6153 (mmt) REVERT: R 160 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.5503 (ttp) outliers start: 46 outliers final: 33 residues processed: 150 average time/residue: 0.0856 time to fit residues: 18.9020 Evaluate side-chains 150 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 67 ASN Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 299 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 90 optimal weight: 0.7980 chunk 30 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 109 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.173648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128964 restraints weight = 10915.335| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.40 r_work: 0.3291 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9950 Z= 0.101 Angle : 0.462 6.089 13470 Z= 0.243 Chirality : 0.041 0.160 1523 Planarity : 0.003 0.044 1703 Dihedral : 7.648 131.751 1381 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.43 % Allowed : 25.09 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1222 helix: 2.29 (0.28), residues: 375 sheet: 0.46 (0.29), residues: 329 loop : -0.87 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.018 0.001 TYR C 235 PHE 0.012 0.001 PHE B 199 TRP 0.012 0.001 TRP R 65 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 9945) covalent geometry : angle 0.46204 / 0.24 (13460) SS BOND : bond 0.00173 / 0.08 ( 5) SS BOND : angle 0.81100 / 0.43 ( 10) hydrogen bonds : bond 0.03120 / 2.08 ( 433) hydrogen bonds : angle 3.88933 / 2.74 ( 1233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.401 Fit side-chains REVERT: A 144 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8548 (m-40) REVERT: A 230 ASP cc_start: 0.8284 (m-30) cc_final: 0.8032 (m-30) REVERT: B 59 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: C 136 SER cc_start: 0.5934 (OUTLIER) cc_final: 0.5677 (p) REVERT: C 187 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8657 (tp) REVERT: N 108 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7673 (t80) REVERT: R 160 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5465 (ttp) outliers start: 47 outliers final: 35 residues processed: 150 average time/residue: 0.0932 time to fit residues: 20.0749 Evaluate side-chains 151 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 299 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 268 ASN B 340 ASN ** R 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.170089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.127551 restraints weight = 10784.180| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.20 r_work: 0.3306 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9950 Z= 0.117 Angle : 0.481 6.568 13470 Z= 0.253 Chirality : 0.041 0.173 1523 Planarity : 0.003 0.045 1703 Dihedral : 6.870 115.766 1379 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.09 % Allowed : 24.62 % Favored : 70.28 % 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 are not related in a simple way. whole: 0.75 (0.25), residues: 1222 helix: 2.43 (0.28), residues: 370 sheet: 0.41 (0.29), residues: 333 loop : -0.88 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.019 0.001 TYR C 235 PHE 0.013 0.001 PHE B 199 TRP 0.010 0.001 TRP R 65 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9945) covalent geometry : angle 0.48049 / 0.25 (13460) SS BOND : bond 0.00175 / 0.08 ( 5) SS BOND : angle 0.79046 / 0.42 ( 10) hydrogen bonds : bond 0.03256 / 2.17 ( 433) hydrogen bonds : angle 3.87763 / 2.75 ( 1233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 111 time to evaluate : 0.360 Fit side-chains REVERT: A 230 ASP cc_start: 0.8357 (m-30) cc_final: 0.8126 (m-30) REVERT: B 59 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.6685 (m-80) REVERT: C 38 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7765 (ttm170) REVERT: C 136 SER cc_start: 0.5792 (OUTLIER) cc_final: 0.5531 (p) REVERT: C 187 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8747 (tp) REVERT: N 108 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7704 (t80) REVERT: R 106 LEU cc_start: 0.7731 (tp) cc_final: 0.7515 (tp) REVERT: R 160 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.5404 (ttp) outliers start: 54 outliers final: 35 residues processed: 152 average time/residue: 0.0921 time to fit residues: 20.3753 Evaluate side-chains 151 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 299 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 109 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 89 GLN A 144 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.172939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.127089 restraints weight = 10859.279| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.44 r_work: 0.3284 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9950 Z= 0.106 Angle : 0.468 6.203 13470 Z= 0.247 Chirality : 0.041 0.165 1523 Planarity : 0.003 0.044 1703 Dihedral : 6.539 100.674 1379 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.34 % Allowed : 25.38 % Favored : 70.28 % 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 are not related in a simple way. whole: 0.81 (0.25), residues: 1222 helix: 2.59 (0.27), residues: 365 sheet: 0.43 (0.29), residues: 333 loop : -0.91 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.018 0.001 TYR C 235 PHE 0.013 0.001 PHE B 199 TRP 0.014 0.001 TRP R 65 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9945) covalent geometry : angle 0.46804 / 0.25 (13460) SS BOND : bond 0.00161 / 0.08 ( 5) SS BOND : angle 0.75236 / 0.40 ( 10) hydrogen bonds : bond 0.03128 / 2.08 ( 433) hydrogen bonds : angle 3.83642 / 2.72 ( 1233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.433 Fit side-chains REVERT: A 230 ASP cc_start: 0.8441 (m-30) cc_final: 0.8213 (m-30) REVERT: B 59 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: C 38 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7800 (ttm170) REVERT: C 136 SER cc_start: 0.5819 (OUTLIER) cc_final: 0.5563 (p) REVERT: C 187 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8736 (tp) REVERT: N 108 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7780 (t80) REVERT: R 160 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.5502 (ttp) outliers start: 46 outliers final: 37 residues processed: 148 average time/residue: 0.0943 time to fit residues: 20.3393 Evaluate side-chains 155 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 299 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 0.0670 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 268 ASN G 59 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.123066 restraints weight = 10790.714| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.42 r_work: 0.3251 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9950 Z= 0.158 Angle : 0.521 7.231 13470 Z= 0.275 Chirality : 0.042 0.201 1523 Planarity : 0.003 0.046 1703 Dihedral : 6.481 83.381 1379 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.15 % Allowed : 25.75 % Favored : 70.09 % 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 are not related in a simple way. whole: 0.68 (0.25), residues: 1222 helix: 2.34 (0.27), residues: 372 sheet: 0.39 (0.29), residues: 327 loop : -0.91 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.019 0.002 TYR C 235 PHE 0.015 0.002 PHE B 199 TRP 0.019 0.001 TRP R 65 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 9945) covalent geometry : angle 0.52103 / 0.27 (13460) SS BOND : bond 0.00191 / 0.09 ( 5) SS BOND : angle 0.86502 / 0.43 ( 10) hydrogen bonds : bond 0.03631 / 2.41 ( 433) hydrogen bonds : angle 4.03690 / 2.88 ( 1233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.466 Fit side-chains REVERT: A 210 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8646 (mt) REVERT: A 230 ASP cc_start: 0.8382 (m-30) cc_final: 0.8133 (m-30) REVERT: B 59 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: C 136 SER cc_start: 0.5773 (OUTLIER) cc_final: 0.5498 (p) REVERT: C 187 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8804 (tp) REVERT: R 95 ASN cc_start: 0.6624 (m-40) cc_final: 0.6390 (t0) REVERT: R 160 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.5563 (ttp) outliers start: 44 outliers final: 31 residues processed: 144 average time/residue: 0.0904 time to fit residues: 19.2352 Evaluate side-chains 144 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 299 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 74 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.0270 chunk 99 optimal weight: 20.0000 chunk 56 optimal weight: 0.3980 chunk 95 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 268 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.167304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124699 restraints weight = 10743.720| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.17 r_work: 0.3263 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9950 Z= 0.155 Angle : 0.519 7.965 13470 Z= 0.273 Chirality : 0.042 0.203 1523 Planarity : 0.003 0.045 1703 Dihedral : 6.228 62.310 1379 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.77 % Allowed : 26.32 % Favored : 69.91 % 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 are not related in a simple way. whole: 0.66 (0.25), residues: 1222 helix: 2.29 (0.27), residues: 371 sheet: 0.43 (0.29), residues: 333 loop : -0.95 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.021 0.002 TYR C 235 PHE 0.017 0.002 PHE B 199 TRP 0.019 0.001 TRP R 65 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 9945) covalent geometry : angle 0.51858 / 0.27 (13460) SS BOND : bond 0.00244 / 0.11 ( 5) SS BOND : angle 0.80724 / 0.41 ( 10) hydrogen bonds : bond 0.03587 / 2.38 ( 433) hydrogen bonds : angle 4.06064 / 2.89 ( 1233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.408 Fit side-chains REVERT: A 230 ASP cc_start: 0.8324 (m-30) cc_final: 0.8076 (m-30) REVERT: B 59 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.6800 (m-80) REVERT: C 136 SER cc_start: 0.5827 (OUTLIER) cc_final: 0.5581 (p) REVERT: C 187 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8789 (tp) REVERT: N 98 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.7570 (ttt90) REVERT: R 160 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.5480 (ttp) REVERT: R 234 ASN cc_start: 0.6375 (m-40) cc_final: 0.6164 (m-40) outliers start: 40 outliers final: 31 residues processed: 139 average time/residue: 0.0949 time to fit residues: 19.2808 Evaluate side-chains 143 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 299 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 268 ASN G 59 ASN R 21 HIS R 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.168810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126235 restraints weight = 10791.097| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.19 r_work: 0.3297 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9950 Z= 0.122 Angle : 0.499 9.704 13470 Z= 0.260 Chirality : 0.041 0.177 1523 Planarity : 0.003 0.044 1703 Dihedral : 5.962 56.497 1379 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.68 % Allowed : 26.60 % Favored : 69.72 % 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 are not related in a simple way. whole: 0.73 (0.25), residues: 1222 helix: 2.49 (0.27), residues: 365 sheet: 0.40 (0.29), residues: 331 loop : -0.93 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.018 0.001 TYR C 235 PHE 0.015 0.001 PHE B 199 TRP 0.016 0.001 TRP R 65 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 9945) covalent geometry : angle 0.49899 / 0.26 (13460) SS BOND : bond 0.00193 / 0.09 ( 5) SS BOND : angle 0.78925 / 0.40 ( 10) hydrogen bonds : bond 0.03333 / 2.21 ( 433) hydrogen bonds : angle 3.96567 / 2.82 ( 1233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2789.59 seconds wall clock time: 48 minutes 38.83 seconds (2918.83 seconds total)