Starting phenix.real_space_refine on Tue Jul 29 00:09:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e4h_30985/07_2025/7e4h_30985.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e4h_30985/07_2025/7e4h_30985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e4h_30985/07_2025/7e4h_30985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e4h_30985/07_2025/7e4h_30985.map" model { file = "/net/cci-nas-00/data/ceres_data/7e4h_30985/07_2025/7e4h_30985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e4h_30985/07_2025/7e4h_30985.cif" } resolution = 3.01 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= 0.003 sd= 0.087 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 44 5.16 5 C 6851 2.51 5 N 1837 2.21 5 O 2020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10752 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3494 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 17, 'TRANS': 421} Chain breaks: 2 Chain: "B" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2536 Classifications: {'peptide': 317} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 307} Chain: "C" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2378 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Time building chain proxies: 6.29, per 1000 atoms: 0.59 Number of scatterers: 10752 At special positions: 0 Unit cell: (128.266, 110.874, 106.526, 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 44 16.00 O 2020 8.00 N 1837 7.00 C 6851 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 32.8% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 removed outlier: 4.048A pdb=" N ALA A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.522A pdb=" N SER A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.738A pdb=" N GLN A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.604A pdb=" N LYS A 356 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.705A pdb=" N ALA B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 58 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.668A pdb=" N LEU B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 182 removed outlier: 3.679A pdb=" N ASP B 173 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.634A pdb=" N GLU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LYS B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N SER B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 248 through 273 removed outlier: 3.834A pdb=" N ASN B 253 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 297 removed outlier: 3.629A pdb=" N TYR B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 315 through 325 removed outlier: 3.875A pdb=" N GLN B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.590A pdb=" N ILE C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.562A pdb=" N SER C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.519A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 83 removed outlier: 3.601A pdb=" N LYS C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 132 removed outlier: 3.754A pdb=" N GLU C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.710A pdb=" N LEU C 144 " --> pdb=" O TYR C 140 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.731A pdb=" N LEU C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 241 removed outlier: 4.234A pdb=" N LEU C 223 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 234 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 263 removed outlier: 3.530A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 4.424A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 314 through 326 removed outlier: 3.824A pdb=" N TYR C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 removed outlier: 3.663A pdb=" N SER D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 364 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 37 removed outlier: 5.011A pdb=" N VAL A 31 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL A 112 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY A 33 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLN A 114 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 35 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASP A 116 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR A 37 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 85 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 131 removed outlier: 3.631A pdb=" N SER A 171 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE A 168 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN A 196 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 466 Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 43 removed outlier: 6.304A pdb=" N TYR B 60 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 116 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU B 62 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.578A pdb=" N THR B 45 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 47 removed outlier: 6.111A pdb=" N VAL C 6 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AA9, first strand: chain 'D' and resid 83 through 93 removed outlier: 6.483A pdb=" N PHE D 98 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1602 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: 3.84 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3491 1.34 - 1.46: 2117 1.46 - 1.58: 5291 1.58 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 10964 Sorted by residual: bond pdb=" C ARG C 305 " pdb=" N ASP C 306 " ideal model delta sigma weight residual 1.325 1.288 0.038 1.77e-02 3.19e+03 4.53e+00 bond pdb=" CG LEU C 115 " pdb=" CD2 LEU C 115 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 bond pdb=" C ILE B 154 " pdb=" O ILE B 154 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.27e+00 bond pdb=" CB PRO B 129 " pdb=" CG PRO B 129 " ideal model delta sigma weight residual 1.506 1.462 0.044 3.90e-02 6.57e+02 1.26e+00 bond pdb=" CB ASP C 119 " pdb=" CG ASP C 119 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.19e+00 ... (remaining 10959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 14489 1.87 - 3.74: 287 3.74 - 5.60: 34 5.60 - 7.47: 4 7.47 - 9.34: 3 Bond angle restraints: 14817 Sorted by residual: angle pdb=" N LEU C 60 " pdb=" CA LEU C 60 " pdb=" C LEU C 60 " ideal model delta sigma weight residual 109.81 118.43 -8.62 2.21e+00 2.05e-01 1.52e+01 angle pdb=" C LEU A 278 " pdb=" N GLY A 279 " pdb=" CA GLY A 279 " ideal model delta sigma weight residual 121.27 117.07 4.20 1.32e+00 5.74e-01 1.01e+01 angle pdb=" C ASP A 53 " pdb=" N THR A 54 " pdb=" CA THR A 54 " ideal model delta sigma weight residual 122.56 117.79 4.77 1.50e+00 4.44e-01 1.01e+01 angle pdb=" N ILE B 37 " pdb=" CA ILE B 37 " pdb=" C ILE B 37 " ideal model delta sigma weight residual 112.80 109.23 3.57 1.15e+00 7.56e-01 9.65e+00 angle pdb=" C LEU A 242 " pdb=" N GLU A 243 " pdb=" CA GLU A 243 " ideal model delta sigma weight residual 122.59 118.06 4.53 1.57e+00 4.06e-01 8.34e+00 ... (remaining 14812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 6215 17.23 - 34.46: 265 34.46 - 51.69: 64 51.69 - 68.91: 19 68.91 - 86.14: 12 Dihedral angle restraints: 6575 sinusoidal: 2645 harmonic: 3930 Sorted by residual: dihedral pdb=" CA THR A 54 " pdb=" C THR A 54 " pdb=" N ILE A 55 " pdb=" CA ILE A 55 " ideal model delta harmonic sigma weight residual -180.00 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA TRP A 197 " pdb=" C TRP A 197 " pdb=" N ASN A 198 " pdb=" CA ASN A 198 " ideal model delta harmonic sigma weight residual -180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASN D 95 " pdb=" C ASN D 95 " pdb=" N PRO D 96 " pdb=" CA PRO D 96 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 6572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1310 0.050 - 0.099: 308 0.099 - 0.149: 55 0.149 - 0.198: 0 0.198 - 0.248: 2 Chirality restraints: 1675 Sorted by residual: chirality pdb=" CA LEU C 60 " pdb=" N LEU C 60 " pdb=" C LEU C 60 " pdb=" CB LEU C 60 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE C 173 " pdb=" CA ILE C 173 " pdb=" CG1 ILE C 173 " pdb=" CG2 ILE C 173 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA ILE C 64 " pdb=" N ILE C 64 " pdb=" C ILE C 64 " pdb=" CB ILE C 64 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1672 not shown) Planarity restraints: 1889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 206 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO D 207 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 60 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO C 61 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 265 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO C 266 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 266 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 266 " -0.018 5.00e-02 4.00e+02 ... (remaining 1886 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 657 2.74 - 3.28: 10088 3.28 - 3.82: 16311 3.82 - 4.36: 19684 4.36 - 4.90: 35810 Nonbonded interactions: 82550 Sorted by model distance: nonbonded pdb=" OD1 ASN D 179 " pdb=" OG SER D 200 " model vdw 2.195 3.040 nonbonded pdb=" OG SER D 93 " pdb=" O PRO D 96 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 344 " pdb=" O SER A 348 " model vdw 2.205 3.040 nonbonded pdb=" NE2 GLN A 114 " pdb=" OD1 ASP A 116 " model vdw 2.221 3.120 nonbonded pdb=" OG SER C 49 " pdb=" OD1 ASN C 51 " model vdw 2.238 3.040 ... (remaining 82545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 30.540 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: 0.060 Set scattering table: 0.090 Process input model: 28.850 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 0.048 10964 Z= 0.175 Angle : 0.651 9.340 14817 Z= 0.372 Chirality : 0.042 0.248 1675 Planarity : 0.004 0.039 1889 Dihedral : 11.775 86.143 4035 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.23), residues: 1336 helix: -0.35 (0.27), residues: 392 sheet: 0.31 (0.23), residues: 445 loop : -0.78 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 301 HIS 0.005 0.001 HIS A 310 PHE 0.020 0.001 PHE A 237 TYR 0.012 0.001 TYR B 164 ARG 0.007 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.15053 ( 564) hydrogen bonds : angle 5.75204 ( 1602) covalent geometry : bond 0.00385 (10964) covalent geometry : angle 0.65069 (14817) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.449 Fit side-chains REVERT: A 55 ILE cc_start: 0.7943 (tp) cc_final: 0.7650 (tp) REVERT: A 69 ASP cc_start: 0.8613 (t0) cc_final: 0.8411 (t0) REVERT: A 161 GLU cc_start: 0.8389 (tt0) cc_final: 0.7830 (tt0) REVERT: B 241 MET cc_start: 0.8669 (mtm) cc_final: 0.8415 (mtp) REVERT: C 111 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7467 (tp30) REVERT: D 176 PHE cc_start: 0.8232 (p90) cc_final: 0.7853 (p90) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2662 time to fit residues: 40.8099 Evaluate side-chains 76 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 30.0000 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 120 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.166103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094817 restraints weight = 15014.877| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.74 r_work: 0.3087 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10964 Z= 0.129 Angle : 0.554 9.843 14817 Z= 0.288 Chirality : 0.041 0.223 1675 Planarity : 0.003 0.041 1889 Dihedral : 4.235 20.981 1440 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.58 % Allowed : 4.07 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.23), residues: 1336 helix: 0.40 (0.27), residues: 387 sheet: 0.43 (0.23), residues: 438 loop : -0.94 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 301 HIS 0.005 0.001 HIS A 310 PHE 0.020 0.001 PHE C 151 TYR 0.016 0.001 TYR B 164 ARG 0.003 0.000 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 564) hydrogen bonds : angle 4.55094 ( 1602) covalent geometry : bond 0.00306 (10964) covalent geometry : angle 0.55364 (14817) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 1.242 Fit side-chains REVERT: A 69 ASP cc_start: 0.8710 (t0) cc_final: 0.8460 (t0) REVERT: A 161 GLU cc_start: 0.8512 (tt0) cc_final: 0.7915 (tt0) REVERT: B 241 MET cc_start: 0.8690 (mtm) cc_final: 0.8093 (mtp) REVERT: C 59 LYS cc_start: 0.7396 (mtpt) cc_final: 0.7150 (mptt) REVERT: C 111 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7577 (tp30) REVERT: D 164 MET cc_start: 0.6854 (tmm) cc_final: 0.6502 (tmm) REVERT: D 176 PHE cc_start: 0.8378 (p90) cc_final: 0.8073 (p90) REVERT: D 178 VAL cc_start: 0.8408 (t) cc_final: 0.8170 (m) outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.2469 time to fit residues: 31.5887 Evaluate side-chains 79 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 0.0050 chunk 131 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.164490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092764 restraints weight = 15052.126| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.74 r_work: 0.3057 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10964 Z= 0.156 Angle : 0.562 14.398 14817 Z= 0.288 Chirality : 0.042 0.203 1675 Planarity : 0.003 0.042 1889 Dihedral : 4.250 20.990 1440 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.91 % Allowed : 5.23 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1336 helix: 0.63 (0.28), residues: 388 sheet: 0.47 (0.23), residues: 440 loop : -0.93 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 301 HIS 0.005 0.001 HIS A 310 PHE 0.014 0.001 PHE A 237 TYR 0.015 0.001 TYR B 164 ARG 0.004 0.000 ARG C 228 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 564) hydrogen bonds : angle 4.46317 ( 1602) covalent geometry : bond 0.00381 (10964) covalent geometry : angle 0.56182 (14817) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 1.144 Fit side-chains REVERT: A 69 ASP cc_start: 0.8718 (t0) cc_final: 0.8458 (t0) REVERT: A 161 GLU cc_start: 0.8565 (tt0) cc_final: 0.8232 (tt0) REVERT: A 164 ARG cc_start: 0.7668 (ptp90) cc_final: 0.7456 (ptp90) REVERT: A 298 MET cc_start: 0.8615 (tmt) cc_final: 0.8320 (tmt) REVERT: A 452 MET cc_start: 0.8970 (tpp) cc_final: 0.8745 (tpp) REVERT: B 241 MET cc_start: 0.8847 (mtm) cc_final: 0.8573 (mtp) REVERT: B 246 HIS cc_start: 0.6628 (m-70) cc_final: 0.6394 (m-70) REVERT: B 250 ASN cc_start: 0.8791 (m-40) cc_final: 0.8560 (m110) REVERT: C 59 LYS cc_start: 0.7430 (mtpt) cc_final: 0.7175 (mptt) REVERT: C 111 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7631 (tp30) REVERT: C 310 ARG cc_start: 0.7619 (mtt180) cc_final: 0.6899 (mmt180) REVERT: D 164 MET cc_start: 0.6975 (tmm) cc_final: 0.6585 (tmm) REVERT: D 176 PHE cc_start: 0.8342 (p90) cc_final: 0.8022 (p90) REVERT: D 178 VAL cc_start: 0.8392 (t) cc_final: 0.8156 (m) outliers start: 11 outliers final: 9 residues processed: 89 average time/residue: 0.2457 time to fit residues: 31.5398 Evaluate side-chains 85 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 7 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.164646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.091032 restraints weight = 15201.562| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.42 r_work: 0.2989 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10964 Z= 0.189 Angle : 0.570 8.825 14817 Z= 0.297 Chirality : 0.043 0.200 1675 Planarity : 0.003 0.042 1889 Dihedral : 4.367 21.724 1440 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.41 % Allowed : 6.23 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.23), residues: 1336 helix: 0.67 (0.27), residues: 388 sheet: 0.53 (0.23), residues: 444 loop : -0.93 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 301 HIS 0.005 0.001 HIS A 310 PHE 0.024 0.002 PHE C 151 TYR 0.017 0.001 TYR B 164 ARG 0.003 0.000 ARG C 228 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 564) hydrogen bonds : angle 4.48403 ( 1602) covalent geometry : bond 0.00465 (10964) covalent geometry : angle 0.57017 (14817) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.366 Fit side-chains REVERT: A 69 ASP cc_start: 0.8730 (t0) cc_final: 0.8459 (t0) REVERT: A 88 PHE cc_start: 0.4963 (OUTLIER) cc_final: 0.4504 (m-80) REVERT: A 161 GLU cc_start: 0.8615 (tt0) cc_final: 0.7996 (tt0) REVERT: A 164 ARG cc_start: 0.7744 (ptp90) cc_final: 0.7405 (ptp90) REVERT: B 28 ASP cc_start: 0.7723 (m-30) cc_final: 0.7311 (p0) REVERT: B 241 MET cc_start: 0.8827 (mtm) cc_final: 0.8493 (mtp) REVERT: B 246 HIS cc_start: 0.6740 (m-70) cc_final: 0.6496 (m-70) REVERT: B 250 ASN cc_start: 0.8755 (m-40) cc_final: 0.8498 (m110) REVERT: C 111 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7905 (tp30) REVERT: C 310 ARG cc_start: 0.7457 (mtt180) cc_final: 0.7110 (mmt180) REVERT: D 164 MET cc_start: 0.6988 (tmm) cc_final: 0.6648 (tmm) REVERT: D 176 PHE cc_start: 0.8369 (p90) cc_final: 0.8053 (p90) REVERT: D 178 VAL cc_start: 0.8415 (t) cc_final: 0.8176 (m) outliers start: 17 outliers final: 12 residues processed: 93 average time/residue: 0.2641 time to fit residues: 36.3684 Evaluate side-chains 89 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 36 optimal weight: 0.5980 chunk 76 optimal weight: 0.3980 chunk 119 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.164764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.092704 restraints weight = 15122.434| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.82 r_work: 0.3052 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10964 Z= 0.122 Angle : 0.506 8.286 14817 Z= 0.265 Chirality : 0.041 0.182 1675 Planarity : 0.003 0.042 1889 Dihedral : 4.110 20.957 1440 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.41 % Allowed : 6.89 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1336 helix: 0.95 (0.28), residues: 387 sheet: 0.60 (0.24), residues: 435 loop : -0.87 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 301 HIS 0.005 0.001 HIS A 310 PHE 0.013 0.001 PHE B 68 TYR 0.013 0.001 TYR B 164 ARG 0.002 0.000 ARG C 228 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 564) hydrogen bonds : angle 4.30293 ( 1602) covalent geometry : bond 0.00292 (10964) covalent geometry : angle 0.50614 (14817) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.489 Fit side-chains REVERT: A 69 ASP cc_start: 0.8712 (t0) cc_final: 0.8422 (t0) REVERT: A 88 PHE cc_start: 0.5116 (OUTLIER) cc_final: 0.4768 (m-80) REVERT: A 161 GLU cc_start: 0.8552 (tt0) cc_final: 0.7915 (tt0) REVERT: A 298 MET cc_start: 0.8616 (tmt) cc_final: 0.8338 (tmt) REVERT: A 452 MET cc_start: 0.8831 (tpp) cc_final: 0.8623 (tpp) REVERT: B 28 ASP cc_start: 0.7645 (m-30) cc_final: 0.7276 (p0) REVERT: B 241 MET cc_start: 0.8781 (mtm) cc_final: 0.8374 (mtp) REVERT: B 246 HIS cc_start: 0.6713 (m-70) cc_final: 0.6460 (m-70) REVERT: B 250 ASN cc_start: 0.8767 (m-40) cc_final: 0.8546 (m110) REVERT: C 111 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7590 (tp30) REVERT: C 300 ASN cc_start: 0.7251 (m-40) cc_final: 0.7010 (p0) REVERT: C 305 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7713 (ttp80) REVERT: C 310 ARG cc_start: 0.7359 (mtt180) cc_final: 0.7032 (mmt180) REVERT: D 164 MET cc_start: 0.7010 (tmm) cc_final: 0.6800 (tmm) REVERT: D 176 PHE cc_start: 0.8341 (p90) cc_final: 0.8010 (p90) REVERT: D 178 VAL cc_start: 0.8391 (t) cc_final: 0.8162 (m) outliers start: 17 outliers final: 12 residues processed: 95 average time/residue: 0.2895 time to fit residues: 39.7754 Evaluate side-chains 92 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 119 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 56 optimal weight: 0.1980 chunk 107 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN B 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.167970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098913 restraints weight = 15182.867| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.59 r_work: 0.3144 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10964 Z= 0.090 Angle : 0.474 7.878 14817 Z= 0.249 Chirality : 0.040 0.210 1675 Planarity : 0.003 0.042 1889 Dihedral : 3.854 21.048 1440 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.41 % Allowed : 7.39 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1336 helix: 1.18 (0.28), residues: 389 sheet: 0.66 (0.24), residues: 435 loop : -0.82 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 301 HIS 0.005 0.001 HIS A 310 PHE 0.028 0.001 PHE C 151 TYR 0.020 0.001 TYR C 320 ARG 0.001 0.000 ARG C 228 Details of bonding type rmsd hydrogen bonds : bond 0.02835 ( 564) hydrogen bonds : angle 4.16249 ( 1602) covalent geometry : bond 0.00207 (10964) covalent geometry : angle 0.47413 (14817) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.276 Fit side-chains REVERT: A 69 ASP cc_start: 0.8721 (t0) cc_final: 0.8447 (t0) REVERT: A 88 PHE cc_start: 0.5173 (OUTLIER) cc_final: 0.4806 (m-80) REVERT: A 161 GLU cc_start: 0.8732 (tt0) cc_final: 0.8487 (tt0) REVERT: A 298 MET cc_start: 0.8999 (tmt) cc_final: 0.8651 (tmt) REVERT: A 452 MET cc_start: 0.8884 (tpp) cc_final: 0.8653 (tpp) REVERT: B 241 MET cc_start: 0.8935 (mtm) cc_final: 0.8422 (mtp) REVERT: B 246 HIS cc_start: 0.6752 (m-70) cc_final: 0.6535 (m-70) REVERT: C 300 ASN cc_start: 0.7274 (m-40) cc_final: 0.7014 (p0) REVERT: C 305 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8103 (ttp80) REVERT: D 164 MET cc_start: 0.7080 (tmm) cc_final: 0.6843 (tmm) REVERT: D 176 PHE cc_start: 0.8300 (p90) cc_final: 0.7948 (p90) REVERT: D 178 VAL cc_start: 0.8348 (t) cc_final: 0.8144 (m) outliers start: 17 outliers final: 12 residues processed: 97 average time/residue: 0.2821 time to fit residues: 39.8071 Evaluate side-chains 89 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 30.0000 chunk 7 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 120 optimal weight: 40.0000 chunk 35 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS B 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.166147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094874 restraints weight = 15378.936| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.61 r_work: 0.3098 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10964 Z= 0.137 Angle : 0.515 7.617 14817 Z= 0.269 Chirality : 0.041 0.217 1675 Planarity : 0.003 0.042 1889 Dihedral : 4.002 20.586 1440 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.58 % Allowed : 7.64 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1336 helix: 1.08 (0.27), residues: 395 sheet: 0.65 (0.24), residues: 435 loop : -0.84 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 9 HIS 0.005 0.001 HIS A 310 PHE 0.014 0.001 PHE A 237 TYR 0.018 0.001 TYR C 320 ARG 0.002 0.000 ARG C 228 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 564) hydrogen bonds : angle 4.20952 ( 1602) covalent geometry : bond 0.00331 (10964) covalent geometry : angle 0.51491 (14817) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 1.146 Fit side-chains REVERT: A 69 ASP cc_start: 0.8755 (t0) cc_final: 0.8479 (t0) REVERT: A 88 PHE cc_start: 0.5176 (OUTLIER) cc_final: 0.4812 (m-80) REVERT: A 161 GLU cc_start: 0.8762 (tt0) cc_final: 0.8526 (tt0) REVERT: A 298 MET cc_start: 0.9021 (tmt) cc_final: 0.8734 (tmt) REVERT: A 452 MET cc_start: 0.8945 (tpp) cc_final: 0.8694 (tpp) REVERT: B 241 MET cc_start: 0.8970 (mtm) cc_final: 0.8582 (mtp) REVERT: C 111 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8501 (tp30) REVERT: C 300 ASN cc_start: 0.7339 (m-40) cc_final: 0.7023 (p0) REVERT: D 164 MET cc_start: 0.7049 (tmm) cc_final: 0.6817 (tmm) REVERT: D 176 PHE cc_start: 0.8317 (p90) cc_final: 0.7953 (p90) REVERT: D 178 VAL cc_start: 0.8383 (t) cc_final: 0.8159 (m) outliers start: 19 outliers final: 15 residues processed: 91 average time/residue: 0.2431 time to fit residues: 32.3025 Evaluate side-chains 91 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 130 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 117 optimal weight: 40.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 415 ASN A 424 ASN B 249 HIS B 250 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.160470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.087781 restraints weight = 15250.059| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.81 r_work: 0.2966 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 10964 Z= 0.312 Angle : 0.662 8.021 14817 Z= 0.344 Chirality : 0.046 0.229 1675 Planarity : 0.004 0.042 1889 Dihedral : 4.607 22.096 1440 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.74 % Allowed : 7.56 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1336 helix: 0.64 (0.27), residues: 390 sheet: 0.58 (0.24), residues: 435 loop : -1.04 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 301 HIS 0.007 0.002 HIS A 352 PHE 0.024 0.002 PHE A 237 TYR 0.026 0.002 TYR B 164 ARG 0.007 0.001 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 564) hydrogen bonds : angle 4.58987 ( 1602) covalent geometry : bond 0.00765 (10964) covalent geometry : angle 0.66208 (14817) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 4.154 Fit side-chains REVERT: A 69 ASP cc_start: 0.8729 (t0) cc_final: 0.8467 (t0) REVERT: A 88 PHE cc_start: 0.5075 (OUTLIER) cc_final: 0.4560 (m-80) REVERT: A 161 GLU cc_start: 0.8621 (tt0) cc_final: 0.8096 (tt0) REVERT: B 60 TYR cc_start: 0.8632 (p90) cc_final: 0.8382 (p90) REVERT: B 241 MET cc_start: 0.8760 (mtm) cc_final: 0.8291 (mtp) REVERT: B 246 HIS cc_start: 0.6731 (m-70) cc_final: 0.6498 (m-70) REVERT: C 111 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8062 (tp30) REVERT: C 154 TRP cc_start: 0.8036 (OUTLIER) cc_final: 0.7648 (m-10) REVERT: C 301 ASN cc_start: 0.8028 (m-40) cc_final: 0.7786 (m110) REVERT: D 164 MET cc_start: 0.6965 (tmm) cc_final: 0.6764 (tmm) REVERT: D 176 PHE cc_start: 0.8299 (p90) cc_final: 0.7920 (p90) REVERT: D 178 VAL cc_start: 0.8448 (t) cc_final: 0.8204 (m) outliers start: 21 outliers final: 13 residues processed: 98 average time/residue: 0.5108 time to fit residues: 77.5686 Evaluate side-chains 93 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 104 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS B 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.164052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092337 restraints weight = 15301.752| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.83 r_work: 0.3046 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10964 Z= 0.114 Angle : 0.518 8.367 14817 Z= 0.270 Chirality : 0.041 0.235 1675 Planarity : 0.003 0.042 1889 Dihedral : 4.128 21.037 1440 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.50 % Allowed : 8.22 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1336 helix: 1.01 (0.27), residues: 390 sheet: 0.62 (0.24), residues: 440 loop : -0.94 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 301 HIS 0.007 0.001 HIS B 249 PHE 0.012 0.001 PHE B 68 TYR 0.016 0.001 TYR C 320 ARG 0.002 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 564) hydrogen bonds : angle 4.27261 ( 1602) covalent geometry : bond 0.00267 (10964) covalent geometry : angle 0.51828 (14817) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.570 Fit side-chains REVERT: A 69 ASP cc_start: 0.8731 (t0) cc_final: 0.8458 (t0) REVERT: A 88 PHE cc_start: 0.4956 (OUTLIER) cc_final: 0.4514 (m-80) REVERT: A 161 GLU cc_start: 0.8567 (tt0) cc_final: 0.7923 (tt0) REVERT: B 60 TYR cc_start: 0.8688 (p90) cc_final: 0.8433 (p90) REVERT: B 241 MET cc_start: 0.8760 (mtm) cc_final: 0.8295 (mtp) REVERT: B 246 HIS cc_start: 0.6622 (m-70) cc_final: 0.6382 (m-70) REVERT: C 111 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7944 (tp30) REVERT: C 151 PHE cc_start: 0.8270 (t80) cc_final: 0.7980 (t80) REVERT: C 154 TRP cc_start: 0.8029 (OUTLIER) cc_final: 0.7633 (m-10) REVERT: D 164 MET cc_start: 0.6936 (tmm) cc_final: 0.6679 (tmm) REVERT: D 176 PHE cc_start: 0.8338 (p90) cc_final: 0.7984 (p90) REVERT: D 178 VAL cc_start: 0.8404 (t) cc_final: 0.8180 (m) outliers start: 18 outliers final: 14 residues processed: 93 average time/residue: 0.3451 time to fit residues: 48.3072 Evaluate side-chains 93 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 0.0670 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN B 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.163818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.091884 restraints weight = 15234.767| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.82 r_work: 0.3033 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10964 Z= 0.133 Angle : 0.523 7.341 14817 Z= 0.275 Chirality : 0.041 0.249 1675 Planarity : 0.003 0.041 1889 Dihedral : 4.094 21.074 1440 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.25 % Allowed : 8.64 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1336 helix: 1.11 (0.27), residues: 389 sheet: 0.61 (0.24), residues: 442 loop : -0.91 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 301 HIS 0.007 0.001 HIS B 249 PHE 0.013 0.001 PHE A 237 TYR 0.017 0.001 TYR C 320 ARG 0.005 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 564) hydrogen bonds : angle 4.23718 ( 1602) covalent geometry : bond 0.00321 (10964) covalent geometry : angle 0.52254 (14817) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.140 Fit side-chains REVERT: A 69 ASP cc_start: 0.8708 (t0) cc_final: 0.8463 (t0) REVERT: A 88 PHE cc_start: 0.4925 (OUTLIER) cc_final: 0.4484 (m-80) REVERT: A 161 GLU cc_start: 0.8551 (tt0) cc_final: 0.8255 (tt0) REVERT: B 241 MET cc_start: 0.8652 (mtm) cc_final: 0.8178 (mtp) REVERT: C 111 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7955 (tp30) REVERT: C 151 PHE cc_start: 0.8203 (t80) cc_final: 0.7936 (t80) REVERT: C 154 TRP cc_start: 0.7997 (OUTLIER) cc_final: 0.7625 (m-10) REVERT: D 164 MET cc_start: 0.6960 (tmm) cc_final: 0.6711 (tmm) REVERT: D 176 PHE cc_start: 0.8272 (p90) cc_final: 0.7889 (p90) REVERT: D 178 VAL cc_start: 0.8376 (t) cc_final: 0.8158 (m) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 0.2176 time to fit residues: 28.2438 Evaluate side-chains 88 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 72 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS D 102 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.163794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.092068 restraints weight = 15150.483| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.81 r_work: 0.3039 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10964 Z= 0.135 Angle : 0.518 7.263 14817 Z= 0.272 Chirality : 0.041 0.242 1675 Planarity : 0.003 0.041 1889 Dihedral : 4.072 20.825 1440 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.25 % Allowed : 8.64 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1336 helix: 1.07 (0.27), residues: 394 sheet: 0.60 (0.24), residues: 442 loop : -0.92 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 301 HIS 0.005 0.001 HIS A 310 PHE 0.013 0.001 PHE A 237 TYR 0.016 0.001 TYR C 320 ARG 0.002 0.000 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 564) hydrogen bonds : angle 4.21313 ( 1602) covalent geometry : bond 0.00327 (10964) covalent geometry : angle 0.51821 (14817) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7964.22 seconds wall clock time: 147 minutes 4.30 seconds (8824.30 seconds total)