Starting phenix.real_space_refine on Thu Jul 2 05:31:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dhr_30682/07_2026/7dhr_30682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dhr_30682/07_2026/7dhr_30682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dhr_30682/07_2026/7dhr_30682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dhr_30682/07_2026/7dhr_30682.map" model { file = "/net/cci-nas-00/data/ceres_data/7dhr_30682/07_2026/7dhr_30682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dhr_30682/07_2026/7dhr_30682.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dhr_30682/07_2026/7dhr_30682.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dhr_30682/07_2026/7dhr_30682.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 42 5.16 5 C 4538 2.51 5 N 1206 2.21 5 O 1271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7057 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1495 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 5 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 8, 'GLU:plan': 8, 'ASN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2301 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 5, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 14, 'GLN:plan1': 6, 'GLU:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 169 Chain: "G" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 317 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 851 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "R" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2078 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 2 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 7, 'TRP:plan': 2, 'PHE:plan': 4, 'TYR:plan': 2, 'GLN:plan1': 5, 'ASN:plan1': 4, 'ARG:plan': 5, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 149 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.63, per 1000 atoms: 0.23 Number of scatterers: 7057 At special positions: 0 Unit cell: (82.134, 98.358, 120.666, 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 42 16.00 O 1271 8.00 N 1206 7.00 C 4538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 432.6 milliseconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 29.0% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 removed outlier: 3.592A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.755A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.952A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 331 through 345 removed outlier: 3.516A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.819A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 345 through 350' Processing helix chain 'A' and resid 372 through 390 removed outlier: 3.914A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 removed outlier: 3.721A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.697A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.918A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 31 through 49 removed outlier: 3.520A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 70 Processing helix chain 'R' and resid 71 through 76 Processing helix chain 'R' and resid 77 through 86 removed outlier: 4.055A pdb=" N MET R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 93 removed outlier: 3.615A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS R 93 " --> pdb=" O PHE R 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 88 through 93' Processing helix chain 'R' and resid 105 through 116 removed outlier: 3.634A pdb=" N THR R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 136 removed outlier: 3.523A pdb=" N ALA R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 159 Processing helix chain 'R' and resid 159 through 164 Processing helix chain 'R' and resid 198 through 203 Processing helix chain 'R' and resid 213 through 218 Processing helix chain 'R' and resid 219 through 221 No H-bonds generated for 'chain 'R' and resid 219 through 221' Processing helix chain 'R' and resid 222 through 227 Processing helix chain 'R' and resid 228 through 237 removed outlier: 4.395A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 286 removed outlier: 3.785A pdb=" N ALA R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 281 through 286' Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 294 through 299 removed outlier: 3.504A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 316 Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.762A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix removed outlier: 3.623A pdb=" N TYR R 326 " --> pdb=" O ASN R 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 317 through 326' Processing helix chain 'R' and resid 329 through 336 removed outlier: 3.663A pdb=" N ARG R 333 " --> pdb=" O SER R 329 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE R 334 " --> pdb=" O PRO R 330 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA R 335 " --> pdb=" O ASP R 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.711A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.509A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.550A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.759A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 153 removed outlier: 6.870A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.519A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190 removed outlier: 4.826A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.720A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.619A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 17 through 21 Processing sheet with id=AB2, first strand: chain 'N' and resid 36 through 39 164 hydrogen bonds defined for protein. 426 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: 0.87 Time building geometry restraints manager: 0.67 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: 2272 1.34 - 1.46: 1719 1.46 - 1.58: 3153 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 7202 Sorted by residual: bond pdb=" C VAL R 210 " pdb=" N PRO R 211 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.89e+00 bond pdb=" C LEU R 167 " pdb=" N PRO R 168 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.53e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.97e+00 bond pdb=" N THR R 189 " pdb=" CA THR R 189 " ideal model delta sigma weight residual 1.462 1.485 -0.023 1.54e-02 4.22e+03 2.23e+00 bond pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 1.458 1.476 -0.017 1.35e-02 5.49e+03 1.66e+00 ... (remaining 7197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 9490 1.94 - 3.88: 277 3.88 - 5.81: 55 5.81 - 7.75: 11 7.75 - 9.69: 8 Bond angle restraints: 9841 Sorted by residual: angle pdb=" N VAL R 152 " pdb=" CA VAL R 152 " pdb=" C VAL R 152 " ideal model delta sigma weight residual 111.81 107.54 4.27 8.60e-01 1.35e+00 2.47e+01 angle pdb=" C SER N 112 " pdb=" N THR N 113 " pdb=" CA THR N 113 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 angle pdb=" N VAL R 31 " pdb=" CA VAL R 31 " pdb=" C VAL R 31 " ideal model delta sigma weight residual 113.42 108.46 4.96 1.17e+00 7.31e-01 1.80e+01 angle pdb=" C ARG R 304 " pdb=" N LYS R 305 " pdb=" CA LYS R 305 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 123.47 129.23 -5.76 1.53e+00 4.27e-01 1.42e+01 ... (remaining 9836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 3746 17.38 - 34.76: 336 34.76 - 52.14: 68 52.14 - 69.51: 8 69.51 - 86.89: 4 Dihedral angle restraints: 4162 sinusoidal: 1324 harmonic: 2838 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual -86.00 -11.85 -74.15 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CA ASN R 51 " pdb=" C ASN R 51 " pdb=" N VAL R 52 " pdb=" CA VAL R 52 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA SER R 137 " pdb=" C SER R 137 " pdb=" N PRO R 138 " pdb=" CA PRO R 138 " ideal model delta harmonic sigma weight residual -180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 977 0.064 - 0.128: 175 0.128 - 0.191: 26 0.191 - 0.255: 1 0.255 - 0.319: 1 Chirality restraints: 1180 Sorted by residual: chirality pdb=" CB ILE R 303 " pdb=" CA ILE R 303 " pdb=" CG1 ILE R 303 " pdb=" CG2 ILE R 303 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE R 153 " pdb=" CA ILE R 153 " pdb=" CG1 ILE R 153 " pdb=" CG2 ILE R 153 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL A 248 " pdb=" CA VAL A 248 " pdb=" CG1 VAL A 248 " pdb=" CG2 VAL A 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.28e-01 ... (remaining 1177 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO R 323 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO B 236 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO R 211 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " -0.037 5.00e-02 4.00e+02 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2471 2.84 - 3.36: 5803 3.36 - 3.87: 10703 3.87 - 4.39: 11913 4.39 - 4.90: 21258 Nonbonded interactions: 52148 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.329 3.040 nonbonded pdb=" O SER B 84 " pdb=" OG SER B 84 " model vdw 2.336 3.040 nonbonded pdb=" OD2 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.343 3.040 nonbonded pdb=" OG SER R 207 " pdb=" OAC 5FW R 601 " model vdw 2.349 3.040 nonbonded pdb=" O PHE R 133 " pdb=" OG SER R 137 " model vdw 2.352 3.040 ... (remaining 52143 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 group one per residue 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: 0.420 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 0.058 7204 Z= 0.187 Angle : 0.858 9.691 9845 Z= 0.470 Chirality : 0.052 0.319 1180 Planarity : 0.006 0.072 1240 Dihedral : 14.180 86.892 2312 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.06 % Favored : 90.83 % Rotamer: Outliers : 0.31 % Allowed : 9.71 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.33 (0.18), residues: 949 helix: -5.10 (0.08), residues: 306 sheet: -3.66 (0.31), residues: 191 loop : -3.70 (0.22), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 98 TYR 0.017 0.001 TYR B 59 PHE 0.013 0.002 PHE N 27 TRP 0.015 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 ( 7202) covalent geometry : angle 0.85808 / 0.47 ( 9841) SS BOND : bond 0.00650 / 0.32 ( 2) SS BOND : angle 1.34842 / 0.60 ( 4) hydrogen bonds : bond 0.32211 / 21.52 ( 164) hydrogen bonds : angle 12.49000 / 8.44 ( 426) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7889 (tttt) cc_final: 0.7687 (tttt) REVERT: A 343 ASP cc_start: 0.8084 (t70) cc_final: 0.7840 (t70) REVERT: B 99 TRP cc_start: 0.7046 (m-90) cc_final: 0.6773 (m-90) REVERT: R 279 MET cc_start: 0.8099 (tpt) cc_final: 0.7884 (tpt) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.0989 time to fit residues: 18.1339 Evaluate side-chains 112 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 183 HIS B 225 HIS B 239 ASN B 266 HIS B 295 ASN G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.159641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130160 restraints weight = 7968.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129466 restraints weight = 9491.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130867 restraints weight = 8966.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131138 restraints weight = 7083.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131257 restraints weight = 6461.059| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7204 Z= 0.169 Angle : 0.607 5.727 9845 Z= 0.328 Chirality : 0.044 0.130 1180 Planarity : 0.005 0.061 1240 Dihedral : 5.867 32.848 1028 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.77 % Allowed : 15.25 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.68 (0.20), residues: 949 helix: -4.27 (0.16), residues: 316 sheet: -3.64 (0.30), residues: 183 loop : -3.35 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 137 TYR 0.019 0.001 TYR B 59 PHE 0.013 0.002 PHE N 108 TRP 0.026 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 7202) covalent geometry : angle 0.60721 / 0.33 ( 9841) SS BOND : bond 0.00434 / 0.23 ( 2) SS BOND : angle 0.85019 / 0.44 ( 4) hydrogen bonds : bond 0.03721 / 2.60 ( 164) hydrogen bonds : angle 7.46123 / 5.08 ( 426) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.240 Fit side-chains REVERT: A 343 ASP cc_start: 0.8277 (t70) cc_final: 0.8042 (t70) REVERT: B 117 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8107 (tt) REVERT: B 211 TRP cc_start: 0.8589 (m100) cc_final: 0.8317 (m100) REVERT: N 33 LYS cc_start: 0.8217 (tttm) cc_final: 0.7949 (tttm) REVERT: R 43 ILE cc_start: 0.8524 (mm) cc_final: 0.8316 (mp) REVERT: R 279 MET cc_start: 0.8066 (tpt) cc_final: 0.7495 (ttp) outliers start: 18 outliers final: 9 residues processed: 132 average time/residue: 0.0807 time to fit residues: 14.4866 Evaluate side-chains 122 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 216 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 90 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 0.0670 chunk 88 optimal weight: 0.0970 chunk 85 optimal weight: 0.0020 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 267 GLN A 271 ASN A 390 GLN B 183 HIS G 24 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.166455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136464 restraints weight = 7757.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136450 restraints weight = 8541.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138082 restraints weight = 7198.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.138475 restraints weight = 5373.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.138665 restraints weight = 5079.320| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7204 Z= 0.085 Angle : 0.510 5.547 9845 Z= 0.274 Chirality : 0.042 0.143 1180 Planarity : 0.004 0.057 1240 Dihedral : 4.951 31.285 1028 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.31 % Allowed : 16.95 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.12 (0.22), residues: 949 helix: -3.62 (0.21), residues: 327 sheet: -3.39 (0.30), residues: 189 loop : -3.08 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.014 0.001 TYR A 360 PHE 0.008 0.001 PHE N 29 TRP 0.029 0.001 TRP B 82 HIS 0.003 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.08 ( 7202) covalent geometry : angle 0.50971 / 0.27 ( 9841) SS BOND : bond 0.00268 / 0.14 ( 2) SS BOND : angle 0.49133 / 0.25 ( 4) hydrogen bonds : bond 0.02784 / 1.94 ( 164) hydrogen bonds : angle 6.44460 / 4.39 ( 426) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7533 (mttt) cc_final: 0.7325 (mppt) REVERT: B 183 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7873 (t70) REVERT: B 283 ARG cc_start: 0.8321 (tpt-90) cc_final: 0.8091 (tpt-90) REVERT: N 33 LYS cc_start: 0.8016 (tttm) cc_final: 0.7739 (tttm) REVERT: R 38 ILE cc_start: 0.8492 (mt) cc_final: 0.8270 (mt) REVERT: R 43 ILE cc_start: 0.8438 (mm) cc_final: 0.8186 (mp) REVERT: R 156 MET cc_start: 0.6745 (ttm) cc_final: 0.6200 (tmm) outliers start: 15 outliers final: 7 residues processed: 127 average time/residue: 0.0784 time to fit residues: 13.3898 Evaluate side-chains 111 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.0670 chunk 91 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN B 183 HIS G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128044 restraints weight = 8039.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126726 restraints weight = 10461.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128096 restraints weight = 10041.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.128347 restraints weight = 7933.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128727 restraints weight = 7099.816| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7204 Z= 0.195 Angle : 0.603 7.197 9845 Z= 0.325 Chirality : 0.044 0.135 1180 Planarity : 0.004 0.053 1240 Dihedral : 5.573 35.580 1028 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 4.16 % Allowed : 17.87 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.23), residues: 949 helix: -3.37 (0.23), residues: 313 sheet: -3.33 (0.32), residues: 180 loop : -2.97 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 239 TYR 0.012 0.001 TYR N 32 PHE 0.017 0.002 PHE N 108 TRP 0.018 0.002 TRP B 82 HIS 0.015 0.002 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 7202) covalent geometry : angle 0.60336 / 0.32 ( 9841) SS BOND : bond 0.00365 / 0.19 ( 2) SS BOND : angle 0.63065 / 0.33 ( 4) hydrogen bonds : bond 0.03331 / 2.34 ( 164) hydrogen bonds : angle 6.29670 / 4.29 ( 426) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7742 (mttt) cc_final: 0.7476 (mppt) REVERT: A 270 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8100 (tt) REVERT: A 343 ASP cc_start: 0.8336 (t70) cc_final: 0.8072 (t70) REVERT: B 45 MET cc_start: 0.8292 (mtm) cc_final: 0.8029 (mtm) outliers start: 27 outliers final: 17 residues processed: 139 average time/residue: 0.0689 time to fit residues: 13.0988 Evaluate side-chains 132 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 91 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.162463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134707 restraints weight = 7851.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133259 restraints weight = 9852.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134735 restraints weight = 9437.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135058 restraints weight = 7016.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.135237 restraints weight = 6302.432| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7204 Z= 0.099 Angle : 0.526 5.877 9845 Z= 0.283 Chirality : 0.042 0.137 1180 Planarity : 0.004 0.053 1240 Dihedral : 4.963 35.151 1028 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.16 % Allowed : 19.11 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.58 (0.24), residues: 949 helix: -3.10 (0.24), residues: 321 sheet: -3.19 (0.33), residues: 176 loop : -2.84 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 239 TYR 0.014 0.001 TYR A 360 PHE 0.008 0.001 PHE A 340 TRP 0.037 0.001 TRP B 82 HIS 0.008 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7202) covalent geometry : angle 0.52557 / 0.28 ( 9841) SS BOND : bond 0.00271 / 0.14 ( 2) SS BOND : angle 0.39834 / 0.22 ( 4) hydrogen bonds : bond 0.02633 / 1.85 ( 164) hydrogen bonds : angle 5.90604 / 4.05 ( 426) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.256 Fit side-chains REVERT: A 270 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8165 (tt) REVERT: A 291 LEU cc_start: 0.7293 (mt) cc_final: 0.7066 (mt) REVERT: B 45 MET cc_start: 0.8230 (mtm) cc_final: 0.7989 (mtm) REVERT: B 188 MET cc_start: 0.8350 (mmm) cc_final: 0.8140 (mmm) REVERT: R 38 ILE cc_start: 0.8474 (mt) cc_final: 0.8199 (mt) outliers start: 27 outliers final: 17 residues processed: 131 average time/residue: 0.0714 time to fit residues: 12.7639 Evaluate side-chains 122 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.162677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.134450 restraints weight = 7883.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133063 restraints weight = 10344.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.134479 restraints weight = 9523.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134841 restraints weight = 7580.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.135191 restraints weight = 6715.408| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7204 Z= 0.102 Angle : 0.529 9.745 9845 Z= 0.279 Chirality : 0.042 0.133 1180 Planarity : 0.003 0.050 1240 Dihedral : 4.740 32.956 1028 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.85 % Allowed : 20.18 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.31 (0.24), residues: 949 helix: -2.84 (0.25), residues: 319 sheet: -3.13 (0.33), residues: 180 loop : -2.66 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 239 TYR 0.011 0.001 TYR A 360 PHE 0.008 0.001 PHE A 340 TRP 0.050 0.001 TRP B 82 HIS 0.007 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 7202) covalent geometry : angle 0.52952 / 0.28 ( 9841) SS BOND : bond 0.00241 / 0.12 ( 2) SS BOND : angle 0.33832 / 0.18 ( 4) hydrogen bonds : bond 0.02552 / 1.80 ( 164) hydrogen bonds : angle 5.66947 / 3.89 ( 426) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8193 (tt) REVERT: B 45 MET cc_start: 0.8247 (mtm) cc_final: 0.8005 (mtm) REVERT: R 38 ILE cc_start: 0.8474 (mt) cc_final: 0.8196 (mt) outliers start: 25 outliers final: 18 residues processed: 125 average time/residue: 0.0615 time to fit residues: 10.5611 Evaluate side-chains 124 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 8 optimal weight: 0.0270 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.161736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131988 restraints weight = 7807.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132588 restraints weight = 8828.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133658 restraints weight = 7536.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.134085 restraints weight = 5567.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134196 restraints weight = 5233.063| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7204 Z= 0.108 Angle : 0.537 8.998 9845 Z= 0.282 Chirality : 0.042 0.135 1180 Planarity : 0.003 0.048 1240 Dihedral : 4.703 32.731 1028 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.70 % Allowed : 19.88 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.25), residues: 949 helix: -2.65 (0.26), residues: 319 sheet: -3.31 (0.30), residues: 196 loop : -2.53 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 239 TYR 0.010 0.001 TYR A 360 PHE 0.008 0.001 PHE A 340 TRP 0.058 0.002 TRP B 82 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7202) covalent geometry : angle 0.53689 / 0.28 ( 9841) SS BOND : bond 0.00236 / 0.12 ( 2) SS BOND : angle 0.33881 / 0.18 ( 4) hydrogen bonds : bond 0.02591 / 1.82 ( 164) hydrogen bonds : angle 5.55035 / 3.80 ( 426) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8111 (tt) REVERT: B 45 MET cc_start: 0.8258 (mtm) cc_final: 0.8027 (mtm) REVERT: R 38 ILE cc_start: 0.8539 (mt) cc_final: 0.8262 (mt) outliers start: 24 outliers final: 19 residues processed: 125 average time/residue: 0.0719 time to fit residues: 12.3950 Evaluate side-chains 122 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN N 53 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.158076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129500 restraints weight = 8046.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128201 restraints weight = 10673.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.130068 restraints weight = 9734.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129667 restraints weight = 7102.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.130144 restraints weight = 6751.676| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7204 Z= 0.164 Angle : 0.580 7.872 9845 Z= 0.307 Chirality : 0.044 0.132 1180 Planarity : 0.004 0.049 1240 Dihedral : 5.125 31.964 1028 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.54 % Allowed : 20.65 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.25), residues: 949 helix: -2.67 (0.26), residues: 321 sheet: -3.30 (0.30), residues: 195 loop : -2.57 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 239 TYR 0.010 0.001 TYR A 360 PHE 0.013 0.001 PHE N 108 TRP 0.066 0.002 TRP B 82 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 7202) covalent geometry : angle 0.58038 / 0.31 ( 9841) SS BOND : bond 0.00308 / 0.16 ( 2) SS BOND : angle 0.54388 / 0.28 ( 4) hydrogen bonds : bond 0.02980 / 2.08 ( 164) hydrogen bonds : angle 5.69265 / 3.90 ( 426) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8164 (tt) REVERT: A 343 ASP cc_start: 0.8270 (t70) cc_final: 0.8029 (t70) REVERT: B 45 MET cc_start: 0.8286 (mtm) cc_final: 0.8022 (mtm) REVERT: R 38 ILE cc_start: 0.8541 (mt) cc_final: 0.8320 (mt) REVERT: R 279 MET cc_start: 0.7099 (tpt) cc_final: 0.6822 (ttt) outliers start: 23 outliers final: 19 residues processed: 127 average time/residue: 0.0618 time to fit residues: 10.7814 Evaluate side-chains 126 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 79 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.162411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132365 restraints weight = 7869.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132766 restraints weight = 8700.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.134159 restraints weight = 6956.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.134369 restraints weight = 5269.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.134596 restraints weight = 5144.019| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7204 Z= 0.103 Angle : 0.532 7.964 9845 Z= 0.281 Chirality : 0.042 0.130 1180 Planarity : 0.003 0.050 1240 Dihedral : 4.705 32.118 1028 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.08 % Allowed : 21.88 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.25), residues: 949 helix: -2.45 (0.27), residues: 322 sheet: -3.04 (0.32), residues: 181 loop : -2.50 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 239 TYR 0.012 0.001 TYR A 360 PHE 0.010 0.001 PHE N 29 TRP 0.042 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 7202) covalent geometry : angle 0.53179 / 0.28 ( 9841) SS BOND : bond 0.00247 / 0.13 ( 2) SS BOND : angle 0.39602 / 0.21 ( 4) hydrogen bonds : bond 0.02546 / 1.79 ( 164) hydrogen bonds : angle 5.44634 / 3.71 ( 426) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.244 Fit side-chains REVERT: A 270 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8193 (tt) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.0799 time to fit residues: 13.1304 Evaluate side-chains 118 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 23 optimal weight: 0.0970 chunk 5 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.163257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132925 restraints weight = 7753.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132911 restraints weight = 8307.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134421 restraints weight = 7259.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135055 restraints weight = 5589.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.135338 restraints weight = 5093.684| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7204 Z= 0.095 Angle : 0.527 7.773 9845 Z= 0.277 Chirality : 0.042 0.134 1180 Planarity : 0.003 0.049 1240 Dihedral : 4.478 31.271 1028 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.47 % Allowed : 23.42 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.84 (0.25), residues: 949 helix: -2.34 (0.27), residues: 327 sheet: -2.89 (0.32), residues: 190 loop : -2.41 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 239 TYR 0.013 0.001 TYR A 360 PHE 0.009 0.001 PHE N 29 TRP 0.036 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 7202) covalent geometry : angle 0.52708 / 0.28 ( 9841) SS BOND : bond 0.00202 / 0.10 ( 2) SS BOND : angle 0.29072 / 0.16 ( 4) hydrogen bonds : bond 0.02417 / 1.70 ( 164) hydrogen bonds : angle 5.26998 / 3.59 ( 426) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.262 Fit side-chains REVERT: A 270 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8139 (tt) REVERT: R 36 MET cc_start: 0.6575 (tpp) cc_final: 0.6369 (tpp) REVERT: R 38 ILE cc_start: 0.8565 (mt) cc_final: 0.8308 (mt) REVERT: R 156 MET cc_start: 0.6718 (ttm) cc_final: 0.6200 (tmm) outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 0.0722 time to fit residues: 11.8764 Evaluate side-chains 114 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 48 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.159844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129764 restraints weight = 7730.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.130724 restraints weight = 8340.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131782 restraints weight = 6702.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.132065 restraints weight = 5162.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132155 restraints weight = 5080.593| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7204 Z= 0.136 Angle : 0.559 7.601 9845 Z= 0.295 Chirality : 0.043 0.133 1180 Planarity : 0.003 0.048 1240 Dihedral : 4.780 31.461 1028 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.31 % Allowed : 24.50 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.84 (0.25), residues: 949 helix: -2.36 (0.27), residues: 327 sheet: -2.91 (0.31), residues: 187 loop : -2.39 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 239 TYR 0.012 0.001 TYR A 360 PHE 0.020 0.001 PHE N 103 TRP 0.042 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 7202) covalent geometry : angle 0.55945 / 0.29 ( 9841) SS BOND : bond 0.00265 / 0.13 ( 2) SS BOND : angle 0.41757 / 0.22 ( 4) hydrogen bonds : bond 0.02749 / 1.94 ( 164) hydrogen bonds : angle 5.39580 / 3.69 ( 426) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1114.41 seconds wall clock time: 19 minutes 56.72 seconds (1196.72 seconds total)