Starting phenix.real_space_refine on Wed Mar 4 01:51:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cad_30327/03_2026/7cad_30327.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cad_30327/03_2026/7cad_30327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cad_30327/03_2026/7cad_30327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cad_30327/03_2026/7cad_30327.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cad_30327/03_2026/7cad_30327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cad_30327/03_2026/7cad_30327.map" } resolution = 3.41 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 6464 2.51 5 N 1684 2.21 5 O 1845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10026 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2913 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2917 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2131 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2065 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 256} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 2.37, per 1000 atoms: 0.24 Number of scatterers: 10026 At special positions: 0 Unit cell: (80.36, 93.48, 139.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1845 8.00 N 1684 7.00 C 6464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 483.3 milliseconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2442 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 12 sheets defined 50.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 96 through 108 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 126 removed outlier: 4.125A pdb=" N ALA C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.914A pdb=" N LEU C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 154 Processing helix chain 'C' and resid 172 through 189 removed outlier: 4.120A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.739A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 266 through 276 removed outlier: 3.641A pdb=" N GLN C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.716A pdb=" N ARG C 304 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 301 through 305' Processing helix chain 'C' and resid 335 through 343 removed outlier: 3.523A pdb=" N ALA C 339 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 96 through 108 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 140 through 154 Processing helix chain 'D' and resid 173 through 189 removed outlier: 3.883A pdb=" N ASP D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.806A pdb=" N ALA D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 266 through 275 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.691A pdb=" N ALA D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'A' and resid 18 through 51 Proline residue: A 30 - end of helix removed outlier: 3.895A pdb=" N ALA A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 78 through 110 removed outlier: 3.784A pdb=" N ALA A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.960A pdb=" N VAL A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 131 through 141 removed outlier: 3.693A pdb=" N TYR A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 190 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 193 through 204 removed outlier: 3.730A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.707A pdb=" N LEU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 235 removed outlier: 3.816A pdb=" N ILE A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 267 through 292 Processing helix chain 'B' and resid 7 through 37 removed outlier: 3.918A pdb=" N VAL B 16 " --> pdb=" O TRP B 12 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN B 17 " --> pdb=" O TRP B 13 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 19 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Proline residue: B 27 - end of helix removed outlier: 4.023A pdb=" N ILE B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 66 through 95 removed outlier: 3.567A pdb=" N SER B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.957A pdb=" N LEU B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 132 removed outlier: 4.033A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix removed outlier: 3.876A pdb=" N ASN B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.526A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 191 through 207 Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 240 through 272 removed outlier: 3.910A pdb=" N SER B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Proline residue: B 255 - end of helix removed outlier: 6.832A pdb=" N ARG B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 31 removed outlier: 5.492A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 82 through 85 removed outlier: 5.909A pdb=" N ALA C 83 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASP C 163 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 85 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N VAL C 195 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N MET C 162 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 209 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE C 220 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 211 " --> pdb=" O GLN C 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AA4, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AA5, first strand: chain 'C' and resid 291 through 293 removed outlier: 3.712A pdb=" N PHE C 308 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 315 through 317 removed outlier: 3.877A pdb=" N GLU C 316 " --> pdb=" O TYR C 323 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 31 removed outlier: 5.038A pdb=" N LYS D 25 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS D 11 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET D 29 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP D 7 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE D 31 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL D 5 " --> pdb=" O ILE D 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 162 through 163 removed outlier: 7.456A pdb=" N MET D 162 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL D 209 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE D 220 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 245 through 246 Processing sheet with id=AB1, first strand: chain 'D' and resid 250 through 251 removed outlier: 3.519A pdb=" N THR D 250 " --> pdb=" O ARG D 257 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL D 256 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 263 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 291 through 293 removed outlier: 3.693A pdb=" N ILE D 368 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 315 through 317 removed outlier: 3.759A pdb=" N GLU D 316 " --> pdb=" O TYR D 323 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1338 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: 1.43 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1646 1.31 - 1.44: 2555 1.44 - 1.56: 5952 1.56 - 1.68: 0 1.68 - 1.81: 64 Bond restraints: 10217 Sorted by residual: bond pdb=" C LEU C 386 " pdb=" O LEU C 386 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.21e-02 6.83e+03 1.25e+01 bond pdb=" N ASP C 344 " pdb=" CA ASP C 344 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.15e-02 7.56e+03 9.37e+00 bond pdb=" N ASP D 344 " pdb=" CA ASP D 344 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 8.91e+00 bond pdb=" N THR A 177 " pdb=" CA THR A 177 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.33e-02 5.65e+03 8.02e+00 bond pdb=" N SER B 235 " pdb=" CA SER B 235 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.25e-02 6.40e+03 7.73e+00 ... (remaining 10212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 13566 1.92 - 3.84: 280 3.84 - 5.75: 49 5.75 - 7.67: 8 7.67 - 9.59: 6 Bond angle restraints: 13909 Sorted by residual: angle pdb=" N GLU B 239 " pdb=" CA GLU B 239 " pdb=" C GLU B 239 " ideal model delta sigma weight residual 113.16 104.58 8.58 1.24e+00 6.50e-01 4.79e+01 angle pdb=" N VAL C 254 " pdb=" CA VAL C 254 " pdb=" C VAL C 254 " ideal model delta sigma weight residual 113.20 107.80 5.40 9.60e-01 1.09e+00 3.16e+01 angle pdb=" N VAL B 42 " pdb=" CA VAL B 42 " pdb=" C VAL B 42 " ideal model delta sigma weight residual 112.98 108.06 4.92 1.25e+00 6.40e-01 1.55e+01 angle pdb=" N VAL C 235 " pdb=" CA VAL C 235 " pdb=" C VAL C 235 " ideal model delta sigma weight residual 112.98 108.21 4.77 1.25e+00 6.40e-01 1.46e+01 angle pdb=" CA GLU B 239 " pdb=" C GLU B 239 " pdb=" N GLU B 240 " ideal model delta sigma weight residual 118.32 113.21 5.11 1.35e+00 5.49e-01 1.43e+01 ... (remaining 13904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 5553 17.30 - 34.60: 476 34.60 - 51.89: 71 51.89 - 69.19: 13 69.19 - 86.49: 5 Dihedral angle restraints: 6118 sinusoidal: 2332 harmonic: 3786 Sorted by residual: dihedral pdb=" CA GLY D 63 " pdb=" C GLY D 63 " pdb=" N GLU D 64 " pdb=" CA GLU D 64 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA TRP B 138 " pdb=" C TRP B 138 " pdb=" N PRO B 139 " pdb=" CA PRO B 139 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA SER D 62 " pdb=" C SER D 62 " pdb=" N GLY D 63 " pdb=" CA GLY D 63 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 6115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1182 0.046 - 0.091: 373 0.091 - 0.137: 111 0.137 - 0.182: 6 0.182 - 0.228: 3 Chirality restraints: 1675 Sorted by residual: chirality pdb=" CB ILE C 379 " pdb=" CA ILE C 379 " pdb=" CG1 ILE C 379 " pdb=" CG2 ILE C 379 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA GLU B 239 " pdb=" N GLU B 239 " pdb=" C GLU B 239 " pdb=" CB GLU B 239 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ASP D 344 " pdb=" N ASP D 344 " pdb=" C ASP D 344 " pdb=" CB ASP D 344 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1672 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 386 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C LEU D 386 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU D 386 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN D 387 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 211 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C LEU A 211 " 0.034 2.00e-02 2.50e+03 pdb=" O LEU A 211 " -0.013 2.00e-02 2.50e+03 pdb=" N THR A 212 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 222 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO D 223 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " 0.026 5.00e-02 4.00e+02 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 819 2.74 - 3.28: 10403 3.28 - 3.82: 15566 3.82 - 4.36: 18566 4.36 - 4.90: 33159 Nonbonded interactions: 78513 Sorted by model distance: nonbonded pdb=" O ALA D 90 " pdb=" NH2 ARG D 151 " model vdw 2.196 3.120 nonbonded pdb=" O ALA A 46 " pdb=" OG SER A 272 " model vdw 2.200 3.040 nonbonded pdb=" OG SER D 88 " pdb=" OD2 ASP A 195 " model vdw 2.203 3.040 nonbonded pdb=" OG SER D 140 " pdb=" OE1 GLN D 143 " model vdw 2.217 3.040 nonbonded pdb=" O ALA A 68 " pdb=" OG1 THR A 72 " model vdw 2.275 3.040 ... (remaining 78508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 2 through 111 or (resid 112 through 113 and (name N or nam \ e CA or name C or name O or name CB )) or resid 114 through 391)) } 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: 3.730 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.790 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 0.043 10217 Z= 0.201 Angle : 0.721 9.590 13909 Z= 0.405 Chirality : 0.047 0.228 1675 Planarity : 0.005 0.047 1764 Dihedral : 13.110 86.489 3676 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.58 % Favored : 92.27 % Rotamer: Outliers : 0.57 % Allowed : 6.17 % Favored : 93.26 % 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: -4.35 (0.19), residues: 1306 helix: -1.71 (0.18), residues: 620 sheet: -4.06 (0.44), residues: 86 loop : -4.09 (0.18), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 155 TYR 0.015 0.001 TYR D 194 PHE 0.013 0.001 PHE B 263 TRP 0.009 0.001 TRP A 175 HIS 0.003 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00395 (10217) covalent geometry : angle 0.72076 (13909) hydrogen bonds : bond 0.14188 ( 462) hydrogen bonds : angle 6.47582 ( 1338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 0.341 Fit side-chains REVERT: D 127 ASP cc_start: 0.6754 (p0) cc_final: 0.6099 (p0) REVERT: D 146 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.7834 (mtm-85) REVERT: D 177 MET cc_start: 0.8287 (mmm) cc_final: 0.7934 (mmm) REVERT: A 48 TRP cc_start: 0.8223 (t60) cc_final: 0.7621 (t60) REVERT: A 250 ASP cc_start: 0.7611 (t70) cc_final: 0.7147 (t0) REVERT: A 287 PHE cc_start: 0.7000 (t80) cc_final: 0.6646 (t80) REVERT: A 291 LYS cc_start: 0.7674 (tttp) cc_final: 0.7205 (tttt) REVERT: B 146 ILE cc_start: 0.8354 (pt) cc_final: 0.8050 (mt) outliers start: 6 outliers final: 1 residues processed: 182 average time/residue: 0.1055 time to fit residues: 26.1506 Evaluate side-chains 140 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 386 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 129 optimal weight: 0.0000 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN D 197 HIS B 56 ASN B 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.173080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145991 restraints weight = 12862.743| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.06 r_work: 0.3602 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10217 Z= 0.160 Angle : 0.681 12.141 13909 Z= 0.335 Chirality : 0.046 0.211 1675 Planarity : 0.005 0.045 1764 Dihedral : 4.795 43.755 1417 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.61 % Allowed : 11.87 % Favored : 86.51 % 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: -3.22 (0.21), residues: 1306 helix: -0.59 (0.20), residues: 642 sheet: -3.85 (0.37), residues: 118 loop : -3.70 (0.20), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 257 TYR 0.016 0.001 TYR D 194 PHE 0.009 0.001 PHE D 326 TRP 0.007 0.001 TRP A 141 HIS 0.005 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00391 (10217) covalent geometry : angle 0.68127 (13909) hydrogen bonds : bond 0.04375 ( 462) hydrogen bonds : angle 5.12765 ( 1338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.282 Fit side-chains REVERT: C 257 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8054 (ttm-80) REVERT: D 177 MET cc_start: 0.8752 (mmm) cc_final: 0.8401 (mmm) REVERT: D 381 ASP cc_start: 0.8120 (m-30) cc_final: 0.7909 (m-30) REVERT: A 48 TRP cc_start: 0.8379 (t60) cc_final: 0.7651 (t60) REVERT: A 78 TYR cc_start: 0.7113 (t80) cc_final: 0.6555 (t80) REVERT: A 250 ASP cc_start: 0.7779 (t70) cc_final: 0.7205 (t0) REVERT: A 287 PHE cc_start: 0.7739 (t80) cc_final: 0.7239 (t80) REVERT: A 291 LYS cc_start: 0.7844 (tttp) cc_final: 0.7385 (tttt) outliers start: 17 outliers final: 12 residues processed: 160 average time/residue: 0.1102 time to fit residues: 23.9620 Evaluate side-chains 144 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 HIS D 168 ASN D 197 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146621 restraints weight = 12909.143| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.06 r_work: 0.3606 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10217 Z= 0.154 Angle : 0.648 9.726 13909 Z= 0.318 Chirality : 0.045 0.191 1675 Planarity : 0.005 0.046 1764 Dihedral : 4.608 25.936 1417 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.75 % Allowed : 13.77 % Favored : 83.48 % 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: -2.68 (0.22), residues: 1306 helix: -0.14 (0.21), residues: 640 sheet: -3.74 (0.37), residues: 118 loop : -3.40 (0.21), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 146 TYR 0.015 0.001 TYR D 194 PHE 0.010 0.001 PHE B 263 TRP 0.006 0.001 TRP A 175 HIS 0.018 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00381 (10217) covalent geometry : angle 0.64798 (13909) hydrogen bonds : bond 0.04102 ( 462) hydrogen bonds : angle 4.88487 ( 1338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.389 Fit side-chains REVERT: C 257 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8043 (ttm-80) REVERT: A 78 TYR cc_start: 0.7098 (t80) cc_final: 0.6569 (t80) REVERT: A 250 ASP cc_start: 0.7793 (t70) cc_final: 0.7259 (t0) REVERT: A 287 PHE cc_start: 0.7722 (t80) cc_final: 0.7235 (t80) REVERT: A 291 LYS cc_start: 0.7831 (tttp) cc_final: 0.7356 (tttt) outliers start: 29 outliers final: 20 residues processed: 153 average time/residue: 0.1024 time to fit residues: 22.0234 Evaluate side-chains 146 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN D 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.176510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.149781 restraints weight = 12879.159| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.07 r_work: 0.3640 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10217 Z= 0.148 Angle : 0.632 9.503 13909 Z= 0.308 Chirality : 0.044 0.182 1675 Planarity : 0.005 0.051 1764 Dihedral : 4.428 24.652 1415 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.13 % Allowed : 15.67 % Favored : 81.20 % 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: -2.36 (0.23), residues: 1306 helix: 0.07 (0.21), residues: 644 sheet: -3.51 (0.41), residues: 102 loop : -3.24 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 257 TYR 0.015 0.001 TYR D 194 PHE 0.030 0.001 PHE B 263 TRP 0.010 0.001 TRP A 141 HIS 0.004 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00365 (10217) covalent geometry : angle 0.63194 (13909) hydrogen bonds : bond 0.03942 ( 462) hydrogen bonds : angle 4.77810 ( 1338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.381 Fit side-chains REVERT: C 257 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7999 (ttm-80) REVERT: A 250 ASP cc_start: 0.7819 (t70) cc_final: 0.7239 (t0) REVERT: A 287 PHE cc_start: 0.7529 (t80) cc_final: 0.7056 (t80) REVERT: A 291 LYS cc_start: 0.7817 (tttp) cc_final: 0.7328 (tttt) outliers start: 33 outliers final: 22 residues processed: 154 average time/residue: 0.1051 time to fit residues: 22.8183 Evaluate side-chains 151 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 224 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 84 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN ** D 232 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 = 0.4071 r_free = 0.4071 target = 0.174012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146902 restraints weight = 12891.373| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.08 r_work: 0.3608 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10217 Z= 0.196 Angle : 0.675 9.716 13909 Z= 0.329 Chirality : 0.046 0.190 1675 Planarity : 0.005 0.051 1764 Dihedral : 4.530 26.123 1415 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.51 % Allowed : 16.14 % Favored : 80.34 % 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: -2.34 (0.23), residues: 1306 helix: 0.11 (0.21), residues: 642 sheet: -3.61 (0.41), residues: 106 loop : -3.22 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 302 TYR 0.015 0.001 TYR B 155 PHE 0.013 0.001 PHE C 326 TRP 0.006 0.001 TRP A 80 HIS 0.002 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00495 (10217) covalent geometry : angle 0.67545 (13909) hydrogen bonds : bond 0.04145 ( 462) hydrogen bonds : angle 4.80359 ( 1338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.358 Fit side-chains REVERT: C 257 ARG cc_start: 0.8308 (ttp80) cc_final: 0.8041 (ttm-80) REVERT: A 287 PHE cc_start: 0.7515 (t80) cc_final: 0.7031 (t80) REVERT: A 291 LYS cc_start: 0.7840 (tttp) cc_final: 0.7343 (tttt) outliers start: 37 outliers final: 29 residues processed: 157 average time/residue: 0.0987 time to fit residues: 22.0461 Evaluate side-chains 158 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 21 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 8 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN ** D 232 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 = 0.4103 r_free = 0.4103 target = 0.177046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150428 restraints weight = 12927.646| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.07 r_work: 0.3648 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10217 Z= 0.132 Angle : 0.620 9.492 13909 Z= 0.302 Chirality : 0.044 0.171 1675 Planarity : 0.005 0.051 1764 Dihedral : 4.332 24.750 1415 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.13 % Allowed : 18.23 % Favored : 78.63 % 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: -2.06 (0.23), residues: 1306 helix: 0.35 (0.22), residues: 637 sheet: -3.54 (0.41), residues: 106 loop : -3.04 (0.23), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 302 TYR 0.015 0.001 TYR D 194 PHE 0.009 0.001 PHE D 326 TRP 0.007 0.001 TRP A 175 HIS 0.002 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00320 (10217) covalent geometry : angle 0.62028 (13909) hydrogen bonds : bond 0.03763 ( 462) hydrogen bonds : angle 4.66412 ( 1338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.442 Fit side-chains REVERT: C 127 ASP cc_start: 0.6470 (t70) cc_final: 0.6001 (t0) REVERT: C 257 ARG cc_start: 0.8277 (ttp80) cc_final: 0.8016 (ttm-80) REVERT: D 100 ASN cc_start: 0.8475 (m-40) cc_final: 0.8177 (t0) REVERT: A 287 PHE cc_start: 0.7533 (t80) cc_final: 0.7059 (t80) REVERT: A 291 LYS cc_start: 0.7857 (tttp) cc_final: 0.7351 (tttt) outliers start: 33 outliers final: 26 residues processed: 162 average time/residue: 0.0980 time to fit residues: 22.5262 Evaluate side-chains 158 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 29 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 6 optimal weight: 0.0970 chunk 119 optimal weight: 0.0870 chunk 99 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 0.0170 chunk 120 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN ** D 232 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 = 0.4123 r_free = 0.4123 target = 0.179050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.152792 restraints weight = 12844.336| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.05 r_work: 0.3673 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10217 Z= 0.117 Angle : 0.607 10.537 13909 Z= 0.295 Chirality : 0.043 0.169 1675 Planarity : 0.004 0.050 1764 Dihedral : 4.175 23.877 1415 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.23 % Allowed : 18.33 % Favored : 78.44 % 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: -1.86 (0.23), residues: 1306 helix: 0.49 (0.22), residues: 638 sheet: -3.47 (0.41), residues: 106 loop : -2.91 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 257 TYR 0.015 0.001 TYR D 194 PHE 0.033 0.001 PHE B 263 TRP 0.008 0.001 TRP A 175 HIS 0.002 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00275 (10217) covalent geometry : angle 0.60707 (13909) hydrogen bonds : bond 0.03600 ( 462) hydrogen bonds : angle 4.62256 ( 1338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.451 Fit side-chains REVERT: C 127 ASP cc_start: 0.6472 (t70) cc_final: 0.6005 (t0) REVERT: C 257 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7961 (ttm-80) REVERT: D 100 ASN cc_start: 0.8454 (m-40) cc_final: 0.8153 (t0) REVERT: A 218 MET cc_start: 0.8403 (ttt) cc_final: 0.7834 (ttt) REVERT: A 250 ASP cc_start: 0.7648 (t70) cc_final: 0.7059 (t0) REVERT: A 287 PHE cc_start: 0.7536 (t80) cc_final: 0.7058 (t80) REVERT: A 291 LYS cc_start: 0.7777 (tttp) cc_final: 0.7231 (pttt) outliers start: 34 outliers final: 25 residues processed: 167 average time/residue: 0.1057 time to fit residues: 24.6312 Evaluate side-chains 160 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.177799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.151343 restraints weight = 12743.258| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.05 r_work: 0.3657 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10217 Z= 0.144 Angle : 0.634 9.188 13909 Z= 0.305 Chirality : 0.045 0.207 1675 Planarity : 0.004 0.049 1764 Dihedral : 4.201 24.156 1415 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.80 % Allowed : 17.95 % Favored : 78.25 % 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: -1.81 (0.23), residues: 1306 helix: 0.54 (0.21), residues: 638 sheet: -3.47 (0.40), residues: 106 loop : -2.88 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 146 TYR 0.014 0.001 TYR D 194 PHE 0.010 0.001 PHE B 263 TRP 0.010 0.001 TRP A 141 HIS 0.003 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00355 (10217) covalent geometry : angle 0.63384 (13909) hydrogen bonds : bond 0.03692 ( 462) hydrogen bonds : angle 4.61121 ( 1338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.393 Fit side-chains REVERT: C 127 ASP cc_start: 0.6459 (t70) cc_final: 0.5998 (t0) REVERT: C 257 ARG cc_start: 0.8244 (ttp80) cc_final: 0.8010 (ttm-80) REVERT: D 100 ASN cc_start: 0.8469 (m-40) cc_final: 0.8194 (t0) REVERT: A 141 TRP cc_start: 0.7989 (m100) cc_final: 0.7733 (m100) REVERT: A 250 ASP cc_start: 0.7699 (t70) cc_final: 0.7136 (t0) REVERT: A 287 PHE cc_start: 0.7530 (t80) cc_final: 0.7054 (t80) REVERT: A 291 LYS cc_start: 0.7780 (tttp) cc_final: 0.7306 (pttt) outliers start: 40 outliers final: 35 residues processed: 161 average time/residue: 0.1095 time to fit residues: 24.7455 Evaluate side-chains 166 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 2 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN ** D 232 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 = 0.4135 r_free = 0.4135 target = 0.180177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.153963 restraints weight = 12752.267| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.06 r_work: 0.3690 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10217 Z= 0.117 Angle : 0.614 11.494 13909 Z= 0.294 Chirality : 0.044 0.194 1675 Planarity : 0.004 0.049 1764 Dihedral : 4.069 23.052 1415 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.04 % Allowed : 18.90 % Favored : 78.06 % 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: -1.63 (0.23), residues: 1306 helix: 0.70 (0.22), residues: 640 sheet: -3.43 (0.39), residues: 106 loop : -2.81 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 146 TYR 0.014 0.001 TYR D 194 PHE 0.010 0.001 PHE B 263 TRP 0.009 0.001 TRP A 175 HIS 0.003 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00277 (10217) covalent geometry : angle 0.61430 (13909) hydrogen bonds : bond 0.03477 ( 462) hydrogen bonds : angle 4.52758 ( 1338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.377 Fit side-chains REVERT: C 127 ASP cc_start: 0.6704 (t70) cc_final: 0.6229 (t0) REVERT: C 257 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7982 (ttm-80) REVERT: D 100 ASN cc_start: 0.8527 (m-40) cc_final: 0.8266 (t0) REVERT: A 79 TRP cc_start: 0.8172 (t-100) cc_final: 0.7963 (t-100) REVERT: A 250 ASP cc_start: 0.7645 (t70) cc_final: 0.7043 (t0) REVERT: A 287 PHE cc_start: 0.7710 (t80) cc_final: 0.7220 (t80) REVERT: A 291 LYS cc_start: 0.7755 (tttp) cc_final: 0.7308 (pttt) outliers start: 32 outliers final: 28 residues processed: 157 average time/residue: 0.1061 time to fit residues: 23.2121 Evaluate side-chains 156 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 116 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN ** D 232 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 = 0.4108 r_free = 0.4108 target = 0.177587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151012 restraints weight = 12648.230| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.05 r_work: 0.3653 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10217 Z= 0.158 Angle : 0.651 11.173 13909 Z= 0.312 Chirality : 0.045 0.189 1675 Planarity : 0.005 0.054 1764 Dihedral : 4.171 23.762 1415 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.04 % Allowed : 19.09 % Favored : 77.87 % 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: -1.63 (0.23), residues: 1306 helix: 0.65 (0.21), residues: 639 sheet: -3.39 (0.40), residues: 106 loop : -2.75 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 146 TYR 0.014 0.001 TYR D 194 PHE 0.011 0.001 PHE B 263 TRP 0.033 0.001 TRP A 141 HIS 0.003 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00393 (10217) covalent geometry : angle 0.65055 (13909) hydrogen bonds : bond 0.03755 ( 462) hydrogen bonds : angle 4.57395 ( 1338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.358 Fit side-chains REVERT: C 127 ASP cc_start: 0.6565 (t70) cc_final: 0.6115 (t0) REVERT: C 257 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7967 (ttm-80) REVERT: D 100 ASN cc_start: 0.8473 (m-40) cc_final: 0.8183 (t0) REVERT: A 250 ASP cc_start: 0.7656 (t70) cc_final: 0.7097 (t0) REVERT: A 287 PHE cc_start: 0.7534 (t80) cc_final: 0.7049 (t80) REVERT: A 291 LYS cc_start: 0.7779 (tttp) cc_final: 0.7350 (pttt) outliers start: 32 outliers final: 32 residues processed: 155 average time/residue: 0.1010 time to fit residues: 21.8920 Evaluate side-chains 161 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.0010 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 52 optimal weight: 0.0570 chunk 1 optimal weight: 0.0060 chunk 14 optimal weight: 0.6980 overall best weight: 0.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.182466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156662 restraints weight = 12767.344| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.04 r_work: 0.3724 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10217 Z= 0.107 Angle : 0.606 10.662 13909 Z= 0.291 Chirality : 0.043 0.185 1675 Planarity : 0.004 0.049 1764 Dihedral : 3.977 21.728 1415 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.56 % Allowed : 19.66 % Favored : 77.78 % 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: -1.37 (0.24), residues: 1306 helix: 0.87 (0.22), residues: 640 sheet: -3.28 (0.39), residues: 106 loop : -2.62 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 146 TYR 0.013 0.001 TYR D 194 PHE 0.008 0.001 PHE C 380 TRP 0.020 0.001 TRP A 141 HIS 0.003 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00237 (10217) covalent geometry : angle 0.60582 (13909) hydrogen bonds : bond 0.03378 ( 462) hydrogen bonds : angle 4.47432 ( 1338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.87 seconds wall clock time: 37 minutes 14.28 seconds (2234.28 seconds total)