Starting phenix.real_space_refine on Mon Jul 28 03:32:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cad_30327/07_2025/7cad_30327.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cad_30327/07_2025/7cad_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7cad_30327/07_2025/7cad_30327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cad_30327/07_2025/7cad_30327.map" model { file = "/net/cci-nas-00/data/ceres_data/7cad_30327/07_2025/7cad_30327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cad_30327/07_2025/7cad_30327.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.19, per 1000 atoms: 0.72 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: 2.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.16 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: 3.03 Time building geometry restraints manager: 3.31 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: 3.000 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.720 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP A 175 HIS 0.003 0.001 HIS C 268 PHE 0.013 0.001 PHE B 263 TYR 0.015 0.001 TYR D 194 ARG 0.003 0.000 ARG D 155 Details of bonding type rmsd hydrogen bonds : bond 0.14188 ( 462) hydrogen bonds : angle 6.47582 ( 1338) covalent geometry : bond 0.00395 (10217) covalent geometry : angle 0.72076 (13909) *********************** 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 : 1.090 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: 0.6647 (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: 0.2640 time to fit residues: 64.5137 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 : 1.177 ------------------------------------------------------------------------------- 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 109 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 B 56 ASN B 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.172912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145573 restraints weight = 12787.657| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.08 r_work: 0.3599 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10217 Z= 0.162 Angle : 0.685 12.440 13909 Z= 0.337 Chirality : 0.046 0.216 1675 Planarity : 0.005 0.045 1764 Dihedral : 4.798 42.954 1417 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.71 % Allowed : 11.97 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.21), residues: 1306 helix: -0.57 (0.20), residues: 642 sheet: -3.85 (0.37), residues: 118 loop : -3.69 (0.20), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 141 HIS 0.005 0.001 HIS D 197 PHE 0.010 0.001 PHE D 326 TYR 0.017 0.001 TYR D 194 ARG 0.004 0.000 ARG C 257 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 462) hydrogen bonds : angle 5.10126 ( 1338) covalent geometry : bond 0.00393 (10217) covalent geometry : angle 0.68547 (13909) *********************** 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: 18 poor density : 152 time to evaluate : 1.146 Fit side-chains REVERT: C 257 ARG cc_start: 0.8366 (ttp80) cc_final: 0.8048 (ttm-80) REVERT: D 177 MET cc_start: 0.8760 (mmm) cc_final: 0.8407 (mmm) REVERT: D 381 ASP cc_start: 0.8126 (m-30) cc_final: 0.7919 (m-30) REVERT: A 48 TRP cc_start: 0.8363 (t60) cc_final: 0.7629 (t60) REVERT: A 78 TYR cc_start: 0.7128 (t80) cc_final: 0.6561 (t80) REVERT: A 250 ASP cc_start: 0.7778 (t70) cc_final: 0.7203 (t0) REVERT: A 287 PHE cc_start: 0.7734 (t80) cc_final: 0.7224 (t80) REVERT: A 291 LYS cc_start: 0.7839 (tttp) cc_final: 0.7376 (tttt) outliers start: 18 outliers final: 12 residues processed: 161 average time/residue: 0.2456 time to fit residues: 54.4026 Evaluate side-chains 143 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 87 optimal weight: 0.0970 chunk 73 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.174179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147631 restraints weight = 12986.118| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.19 r_work: 0.3606 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1346 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= 0.142 Angle : 0.642 9.750 13909 Z= 0.316 Chirality : 0.045 0.189 1675 Planarity : 0.005 0.047 1764 Dihedral : 4.587 25.789 1417 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.47 % Allowed : 14.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.22), residues: 1306 helix: -0.10 (0.21), residues: 643 sheet: -3.75 (0.39), residues: 106 loop : -3.37 (0.21), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 175 HIS 0.019 0.002 HIS D 197 PHE 0.011 0.001 PHE B 263 TYR 0.013 0.001 TYR B 155 ARG 0.006 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 462) hydrogen bonds : angle 4.86118 ( 1338) covalent geometry : bond 0.00346 (10217) covalent geometry : angle 0.64247 (13909) *********************** 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: 26 poor density : 137 time to evaluate : 1.293 Fit side-chains REVERT: C 257 ARG cc_start: 0.8350 (ttp80) cc_final: 0.8026 (ttm-80) REVERT: A 78 TYR cc_start: 0.7056 (t80) cc_final: 0.6528 (t80) REVERT: A 250 ASP cc_start: 0.7779 (t70) cc_final: 0.7244 (t0) REVERT: A 287 PHE cc_start: 0.7708 (t80) cc_final: 0.7224 (t80) REVERT: A 291 LYS cc_start: 0.7813 (tttp) cc_final: 0.7336 (tttt) outliers start: 26 outliers final: 18 residues processed: 151 average time/residue: 0.3474 time to fit residues: 74.9781 Evaluate side-chains 147 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 2.713 ------------------------------------------------------------------------------- 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 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 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 38 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.177166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.150757 restraints weight = 12632.566| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.03 r_work: 0.3653 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10217 Z= 0.137 Angle : 0.622 9.367 13909 Z= 0.303 Chirality : 0.044 0.182 1675 Planarity : 0.005 0.049 1764 Dihedral : 4.372 24.243 1415 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.13 % Allowed : 15.57 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.23), residues: 1306 helix: 0.14 (0.21), residues: 640 sheet: -3.48 (0.41), residues: 102 loop : -3.20 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.008 0.001 HIS D 197 PHE 0.030 0.001 PHE B 263 TYR 0.016 0.001 TYR D 194 ARG 0.004 0.000 ARG D 257 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 462) hydrogen bonds : angle 4.73407 ( 1338) covalent geometry : bond 0.00336 (10217) covalent geometry : angle 0.62195 (13909) *********************** 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 167 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.076 Fit side-chains REVERT: C 257 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8038 (ttm-80) REVERT: A 250 ASP cc_start: 0.7836 (t70) cc_final: 0.7233 (t0) REVERT: A 287 PHE cc_start: 0.7701 (t80) cc_final: 0.7216 (t80) REVERT: A 291 LYS cc_start: 0.7848 (tttp) cc_final: 0.7381 (tttt) outliers start: 33 outliers final: 23 residues processed: 155 average time/residue: 0.2223 time to fit residues: 48.2555 Evaluate side-chains 151 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 121 optimal weight: 0.0370 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.1464 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.176783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.150243 restraints weight = 12749.503| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.05 r_work: 0.3647 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10217 Z= 0.148 Angle : 0.630 9.336 13909 Z= 0.306 Chirality : 0.044 0.196 1675 Planarity : 0.004 0.050 1764 Dihedral : 4.330 24.879 1415 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.32 % Allowed : 16.05 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.23), residues: 1306 helix: 0.29 (0.21), residues: 641 sheet: -3.58 (0.41), residues: 106 loop : -3.12 (0.23), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 175 HIS 0.003 0.001 HIS D 268 PHE 0.010 0.001 PHE C 326 TYR 0.015 0.001 TYR D 194 ARG 0.005 0.000 ARG D 257 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 462) hydrogen bonds : angle 4.68507 ( 1338) covalent geometry : bond 0.00367 (10217) covalent geometry : angle 0.63044 (13909) *********************** 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 167 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 1.201 Fit side-chains REVERT: C 257 ARG cc_start: 0.8270 (ttp80) cc_final: 0.8011 (ttm-80) REVERT: D 100 ASN cc_start: 0.8488 (m-40) cc_final: 0.8175 (t0) REVERT: A 250 ASP cc_start: 0.7841 (t70) cc_final: 0.7273 (t0) REVERT: A 287 PHE cc_start: 0.7529 (t80) cc_final: 0.7053 (t80) REVERT: A 291 LYS cc_start: 0.7849 (tttp) cc_final: 0.7341 (tttt) outliers start: 35 outliers final: 29 residues processed: 154 average time/residue: 0.2603 time to fit residues: 57.7558 Evaluate side-chains 156 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 2.436 ------------------------------------------------------------------------------- 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 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 32 LEU 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 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 53 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.174279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147286 restraints weight = 12775.738| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.06 r_work: 0.3610 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10217 Z= 0.200 Angle : 0.671 9.803 13909 Z= 0.327 Chirality : 0.046 0.175 1675 Planarity : 0.005 0.050 1764 Dihedral : 4.471 25.716 1415 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.89 % Allowed : 16.81 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.23), residues: 1306 helix: 0.23 (0.21), residues: 642 sheet: -3.57 (0.42), residues: 106 loop : -3.13 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 207 HIS 0.003 0.001 HIS D 94 PHE 0.014 0.001 PHE C 326 TYR 0.016 0.001 TYR D 194 ARG 0.006 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 462) hydrogen bonds : angle 4.76140 ( 1338) covalent geometry : bond 0.00505 (10217) covalent geometry : angle 0.67111 (13909) *********************** 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 175 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6516 (t70) cc_final: 0.6047 (t0) REVERT: C 257 ARG cc_start: 0.8336 (ttp80) cc_final: 0.8053 (ttm-80) REVERT: A 287 PHE cc_start: 0.7533 (t80) cc_final: 0.7044 (t80) REVERT: A 291 LYS cc_start: 0.7874 (tttp) cc_final: 0.7371 (tttt) outliers start: 41 outliers final: 33 residues processed: 163 average time/residue: 0.2322 time to fit residues: 52.8236 Evaluate side-chains 161 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 C residue 379 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 28 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.0570 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.179106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.152798 restraints weight = 12863.264| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.06 r_work: 0.3675 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10217 Z= 0.116 Angle : 0.602 9.995 13909 Z= 0.293 Chirality : 0.043 0.169 1675 Planarity : 0.004 0.048 1764 Dihedral : 4.217 23.891 1415 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.04 % Allowed : 18.14 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.23), residues: 1306 helix: 0.51 (0.22), residues: 638 sheet: -3.46 (0.42), residues: 106 loop : -2.92 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 175 HIS 0.002 0.001 HIS D 268 PHE 0.034 0.001 PHE B 263 TYR 0.014 0.001 TYR D 194 ARG 0.006 0.000 ARG D 257 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 462) hydrogen bonds : angle 4.58706 ( 1338) covalent geometry : bond 0.00268 (10217) covalent geometry : angle 0.60217 (13909) *********************** 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 176 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 1.202 Fit side-chains REVERT: C 127 ASP cc_start: 0.6670 (t70) cc_final: 0.6166 (t0) REVERT: C 257 ARG cc_start: 0.8346 (ttp80) cc_final: 0.8026 (ttm-80) REVERT: D 100 ASN cc_start: 0.8553 (m-40) cc_final: 0.8265 (t0) REVERT: A 287 PHE cc_start: 0.7726 (t80) cc_final: 0.7238 (t80) REVERT: A 291 LYS cc_start: 0.7817 (tttp) cc_final: 0.7326 (pttt) outliers start: 32 outliers final: 26 residues processed: 165 average time/residue: 0.2366 time to fit residues: 54.2949 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 : 1.141 ------------------------------------------------------------------------------- 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 184 LEU 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 200 THR 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 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 32 LEU 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 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 29 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 126 optimal weight: 0.0030 chunk 86 optimal weight: 0.0570 chunk 26 optimal weight: 9.9990 overall best weight: 1.2112 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.176810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150072 restraints weight = 12773.768| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.07 r_work: 0.3644 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10217 Z= 0.154 Angle : 0.636 9.055 13909 Z= 0.309 Chirality : 0.045 0.206 1675 Planarity : 0.005 0.047 1764 Dihedral : 4.247 24.049 1415 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.13 % Allowed : 18.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.23), residues: 1306 helix: 0.53 (0.22), residues: 639 sheet: -3.40 (0.42), residues: 106 loop : -2.90 (0.23), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 141 HIS 0.003 0.001 HIS D 268 PHE 0.011 0.001 PHE B 263 TYR 0.014 0.001 TYR D 194 ARG 0.010 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 462) hydrogen bonds : angle 4.60139 ( 1338) covalent geometry : bond 0.00380 (10217) covalent geometry : angle 0.63640 (13909) *********************** 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 167 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.067 Fit side-chains REVERT: C 127 ASP cc_start: 0.6463 (t70) cc_final: 0.5998 (t0) REVERT: C 257 ARG cc_start: 0.8272 (ttp80) cc_final: 0.8033 (ttm-80) REVERT: D 100 ASN cc_start: 0.8496 (m-40) cc_final: 0.8211 (t0) REVERT: A 141 TRP cc_start: 0.8012 (m100) cc_final: 0.7786 (m100) REVERT: A 218 MET cc_start: 0.8466 (ttt) cc_final: 0.7941 (ttt) REVERT: A 250 ASP cc_start: 0.7657 (t70) cc_final: 0.7107 (t0) REVERT: A 287 PHE cc_start: 0.7565 (t80) cc_final: 0.7074 (t80) REVERT: A 291 LYS cc_start: 0.7792 (tttp) cc_final: 0.7332 (pttt) outliers start: 33 outliers final: 28 residues processed: 157 average time/residue: 0.2242 time to fit residues: 48.8999 Evaluate side-chains 159 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 184 LEU 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 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 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 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 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 232 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 91 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 93 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.179177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.152926 restraints weight = 12677.761| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.04 r_work: 0.3680 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10217 Z= 0.119 Angle : 0.612 11.312 13909 Z= 0.295 Chirality : 0.044 0.192 1675 Planarity : 0.004 0.048 1764 Dihedral : 4.136 23.596 1415 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.75 % Allowed : 19.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.23), residues: 1306 helix: 0.67 (0.22), residues: 640 sheet: -3.39 (0.41), residues: 106 loop : -2.81 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 175 HIS 0.003 0.001 HIS D 268 PHE 0.010 0.001 PHE B 263 TYR 0.013 0.001 TYR D 194 ARG 0.008 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 462) hydrogen bonds : angle 4.51406 ( 1338) covalent geometry : bond 0.00283 (10217) covalent geometry : angle 0.61170 (13909) *********************** 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: 29 poor density : 137 time to evaluate : 1.062 Fit side-chains REVERT: C 127 ASP cc_start: 0.6506 (t70) cc_final: 0.6051 (t0) REVERT: C 257 ARG cc_start: 0.8226 (ttp80) cc_final: 0.7943 (ttm-80) REVERT: A 141 TRP cc_start: 0.7966 (m100) cc_final: 0.7751 (m100) REVERT: A 218 MET cc_start: 0.8433 (ttt) cc_final: 0.7907 (ttt) REVERT: A 250 ASP cc_start: 0.7651 (t70) cc_final: 0.7072 (t0) REVERT: A 287 PHE cc_start: 0.7545 (t80) cc_final: 0.7056 (t80) REVERT: A 291 LYS cc_start: 0.7779 (tttp) cc_final: 0.7288 (pttt) outliers start: 29 outliers final: 26 residues processed: 158 average time/residue: 0.2277 time to fit residues: 49.7600 Evaluate side-chains 159 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 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 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 23 TYR Chi-restraints excluded: chain B residue 32 LEU 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 168 LEU 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 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.179157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.152795 restraints weight = 12773.049| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.06 r_work: 0.3681 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10217 Z= 0.124 Angle : 0.615 11.021 13909 Z= 0.296 Chirality : 0.044 0.188 1675 Planarity : 0.004 0.048 1764 Dihedral : 4.084 23.137 1415 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.66 % Allowed : 19.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1306 helix: 0.74 (0.22), residues: 639 sheet: -3.29 (0.42), residues: 106 loop : -2.73 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 175 HIS 0.003 0.001 HIS D 268 PHE 0.009 0.001 PHE B 263 TYR 0.013 0.001 TYR D 194 ARG 0.008 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 462) hydrogen bonds : angle 4.46595 ( 1338) covalent geometry : bond 0.00299 (10217) covalent geometry : angle 0.61523 (13909) ********************** 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 163 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.078 Fit side-chains REVERT: C 127 ASP cc_start: 0.6764 (t70) cc_final: 0.6279 (t0) REVERT: C 257 ARG cc_start: 0.8331 (ttp80) cc_final: 0.8018 (ttm-80) REVERT: D 100 ASN cc_start: 0.8549 (m-40) cc_final: 0.8266 (t0) REVERT: A 213 LYS cc_start: 0.8568 (mmtp) cc_final: 0.8347 (mttp) REVERT: A 218 MET cc_start: 0.8485 (ttt) cc_final: 0.7952 (ttt) REVERT: A 250 ASP cc_start: 0.7646 (t70) cc_final: 0.7073 (t0) REVERT: A 287 PHE cc_start: 0.7749 (t80) cc_final: 0.7258 (t80) REVERT: A 291 LYS cc_start: 0.7774 (tttp) cc_final: 0.7338 (pttt) outliers start: 28 outliers final: 27 residues processed: 154 average time/residue: 0.2403 time to fit residues: 51.2225 Evaluate side-chains 159 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 168 LEU 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 122 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 104 optimal weight: 0.0000 chunk 3 optimal weight: 0.6980 chunk 97 optimal weight: 0.0770 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.3342 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.182069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.156283 restraints weight = 12618.065| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.03 r_work: 0.3732 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10217 Z= 0.107 Angle : 0.594 10.727 13909 Z= 0.286 Chirality : 0.043 0.185 1675 Planarity : 0.004 0.049 1764 Dihedral : 3.968 21.705 1415 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.66 % Allowed : 19.75 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.24), residues: 1306 helix: 0.90 (0.22), residues: 639 sheet: -3.17 (0.41), residues: 106 loop : -2.62 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 141 HIS 0.002 0.001 HIS D 268 PHE 0.008 0.001 PHE B 263 TYR 0.012 0.001 TYR D 194 ARG 0.008 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 462) hydrogen bonds : angle 4.39830 ( 1338) covalent geometry : bond 0.00242 (10217) covalent geometry : angle 0.59432 (13909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5186.82 seconds wall clock time: 92 minutes 40.26 seconds (5560.26 seconds total)