Starting phenix.real_space_refine on Thu Jul 2 16:26:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yae_33710/07_2026/7yae_33710.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yae_33710/07_2026/7yae_33710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yae_33710/07_2026/7yae_33710.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yae_33710/07_2026/7yae_33710.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yae_33710/07_2026/7yae_33710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yae_33710/07_2026/7yae_33710.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yae_33710/07_2026/7yae_33710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yae_33710/07_2026/7yae_33710.map" } resolution = 3.37 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= -0.004 sd= 0.083 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 70 5.16 5 C 5779 2.51 5 N 1513 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 9031 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1817 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2219 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DPN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {'THO': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'TRANS': 3, None: 1} Not linked: pdbres="CYS D 7 " pdbres="THO D 8 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.01, per 1000 atoms: 0.22 Number of scatterers: 9031 At special positions: 0 Unit cell: (88.32, 121.44, 129.72, 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 70 16.00 O 1669 8.00 N 1513 7.00 C 5779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 2 " - pdb=" SG CYS D 7 " distance=2.02 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=1, symmetry=0 Links applied TRANS " DTR D 4 " - " PHE D 3 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 324.6 milliseconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN D 1 " pdb=" CB DTR D 4 " Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 15 sheets defined 35.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.537A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.528A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.679A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.624A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.898A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.764A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.564A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 22 removed outlier: 4.017A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.614A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'S' and resid 28 through 32 removed outlier: 4.102A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.902A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 72 Processing helix chain 'E' and resid 76 through 93 removed outlier: 4.147A pdb=" N ILE E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 104 Processing helix chain 'E' and resid 111 through 146 removed outlier: 3.690A pdb=" N PHE E 127 " --> pdb=" O GLY E 123 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE E 131 " --> pdb=" O PHE E 127 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS E 132 " --> pdb=" O THR E 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 174 Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'E' and resid 217 through 240 removed outlier: 3.803A pdb=" N LEU E 221 " --> pdb=" O PHE E 217 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE E 240 " --> pdb=" O LYS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 Processing helix chain 'E' and resid 252 through 282 removed outlier: 3.509A pdb=" N TRP E 269 " --> pdb=" O PHE E 265 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 287 through 304 removed outlier: 3.670A pdb=" N LYS E 291 " --> pdb=" O THR E 287 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR E 301 " --> pdb=" O VAL E 297 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR E 302 " --> pdb=" O VAL E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 313 removed outlier: 4.094A pdb=" N ILE E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 322 removed outlier: 4.166A pdb=" N LYS E 321 " --> pdb=" O ASP E 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.574A pdb=" N THR A 187 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 198 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 265 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR A 324 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.286A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.174A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.720A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.657A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.859A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.855A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.679A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.812A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.502A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 34 through 38 removed outlier: 6.712A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 68 through 73 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.521A pdb=" N VAL S 147 " --> pdb=" O LYS S 244 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.874A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR S 213 " --> pdb=" O SER S 206 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER S 206 " --> pdb=" O THR S 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 7.507A pdb=" N ARG S 180 " --> pdb=" O PRO S 185 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1455 1.32 - 1.44: 2518 1.44 - 1.57: 5148 1.57 - 1.69: 0 1.69 - 1.82: 102 Bond restraints: 9223 Sorted by residual: bond pdb=" C THO D 8 " pdb=" O THO D 8 " ideal model delta sigma weight residual 1.231 1.432 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" CA PHE D 3 " pdb=" C PHE D 3 " ideal model delta sigma weight residual 1.525 1.415 0.110 2.10e-02 2.27e+03 2.73e+01 bond pdb=" CA ARG E 241 " pdb=" C ARG E 241 " ideal model delta sigma weight residual 1.525 1.476 0.049 1.25e-02 6.40e+03 1.56e+01 bond pdb=" C ASN E 84 " pdb=" O ASN E 84 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.26e-02 6.30e+03 1.30e+01 bond pdb=" N ASN E 304 " pdb=" CA ASN E 304 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.32e-02 5.74e+03 1.29e+01 ... (remaining 9218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 12304 2.61 - 5.22: 161 5.22 - 7.83: 18 7.83 - 10.44: 3 10.44 - 13.05: 3 Bond angle restraints: 12489 Sorted by residual: angle pdb=" N TYR S 101 " pdb=" CA TYR S 101 " pdb=" C TYR S 101 " ideal model delta sigma weight residual 108.58 121.63 -13.05 1.82e+00 3.02e-01 5.14e+01 angle pdb=" N ILE B 93 " pdb=" CA ILE B 93 " pdb=" C ILE B 93 " ideal model delta sigma weight residual 107.55 114.47 -6.92 9.90e-01 1.02e+00 4.88e+01 angle pdb=" CA THO D 8 " pdb=" C THO D 8 " pdb=" O THO D 8 " ideal model delta sigma weight residual 120.80 109.46 11.34 1.70e+00 3.46e-01 4.45e+01 angle pdb=" N GLU S 234 " pdb=" CA GLU S 234 " pdb=" C GLU S 234 " ideal model delta sigma weight residual 108.73 98.78 9.95 1.63e+00 3.76e-01 3.73e+01 angle pdb=" N PRO S 236 " pdb=" CA PRO S 236 " pdb=" C PRO S 236 " ideal model delta sigma weight residual 112.47 101.04 11.43 2.06e+00 2.36e-01 3.08e+01 ... (remaining 12484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 4906 17.59 - 35.17: 422 35.17 - 52.76: 95 52.76 - 70.35: 21 70.35 - 87.93: 10 Dihedral angle restraints: 5454 sinusoidal: 2138 harmonic: 3316 Sorted by residual: dihedral pdb=" C PHE D 3 " pdb=" N PHE D 3 " pdb=" CA PHE D 3 " pdb=" CB PHE D 3 " ideal model delta harmonic sigma weight residual -122.60 -109.38 -13.22 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" CA LEU E 105 " pdb=" C LEU E 105 " pdb=" N VAL E 106 " pdb=" CA VAL E 106 " ideal model delta harmonic sigma weight residual -180.00 -155.52 -24.48 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA TYR S 95 " pdb=" C TYR S 95 " pdb=" N CYS S 96 " pdb=" CA CYS S 96 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1240 0.065 - 0.129: 163 0.129 - 0.194: 10 0.194 - 0.259: 6 0.259 - 0.324: 3 Chirality restraints: 1422 Sorted by residual: chirality pdb=" C13 CLR E 401 " pdb=" C12 CLR E 401 " pdb=" C14 CLR E 401 " pdb=" C17 CLR E 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.61 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CB VAL E 242 " pdb=" CA VAL E 242 " pdb=" CG1 VAL E 242 " pdb=" CG2 VAL E 242 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C13 CLR E 402 " pdb=" C12 CLR E 402 " pdb=" C14 CLR E 402 " pdb=" C17 CLR E 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1419 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 308 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO E 309 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 309 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 309 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU S 233 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C LEU S 233 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU S 233 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU S 234 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 303 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C ALA E 303 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA E 303 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN E 304 " -0.014 2.00e-02 2.50e+03 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 898 2.75 - 3.28: 8854 3.28 - 3.82: 14491 3.82 - 4.36: 16383 4.36 - 4.90: 28891 Nonbonded interactions: 69517 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ASP B 298 " model vdw 2.243 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG1 THR S 57 " model vdw 2.249 3.040 nonbonded pdb=" O ALA E 44 " pdb=" OG1 THR E 47 " model vdw 2.250 3.040 nonbonded pdb=" NE1 TRP E 197 " pdb=" O ALA E 203 " model vdw 2.284 3.120 ... (remaining 69512 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 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 : 0.005 0.201 9228 Z= 0.262 Angle : 0.737 13.053 12498 Z= 0.427 Chirality : 0.047 0.324 1422 Planarity : 0.004 0.062 1555 Dihedral : 14.618 87.934 3306 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.92 % Allowed : 1.33 % Favored : 97.76 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.25), residues: 1127 helix: 1.42 (0.29), residues: 366 sheet: -0.07 (0.35), residues: 242 loop : -1.42 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.016 0.001 TYR B 264 PHE 0.013 0.001 PHE A 274 TRP 0.013 0.001 TRP A 258 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.25 ( 9223) covalent geometry : angle 0.73699 / 0.43 (12489) SS BOND : bond 0.00914 / 0.46 ( 3) SS BOND : angle 0.96431 / 0.53 ( 6) hydrogen bonds : bond 0.21922 / 14.20 ( 368) hydrogen bonds : angle 7.30945 / 5.17 ( 1047) Misc. bond : bond 0.06605 / 4.13 ( 1) link_TRANS : bond 0.00659 / 0.41 ( 1) link_TRANS : angle 1.52941 / 0.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: E 101 MET cc_start: 0.6058 (mmp) cc_final: 0.5631 (tpp) outliers start: 9 outliers final: 2 residues processed: 142 average time/residue: 0.1036 time to fit residues: 20.2323 Evaluate side-chains 100 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain E residue 119 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN E 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.222150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.182486 restraints weight = 11277.707| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 2.79 r_work: 0.4132 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9228 Z= 0.134 Angle : 0.613 9.951 12498 Z= 0.320 Chirality : 0.043 0.224 1422 Planarity : 0.004 0.049 1555 Dihedral : 5.930 56.228 1261 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.33 % Allowed : 8.15 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.25), residues: 1127 helix: 1.83 (0.28), residues: 372 sheet: 0.42 (0.36), residues: 229 loop : -1.36 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.013 0.001 TYR E 205 PHE 0.022 0.001 PHE E 48 TRP 0.016 0.001 TRP S 47 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9223) covalent geometry : angle 0.61298 / 0.32 (12489) SS BOND : bond 0.00546 / 0.34 ( 3) SS BOND : angle 0.53352 / 0.24 ( 6) hydrogen bonds : bond 0.04855 / 3.31 ( 368) hydrogen bonds : angle 5.12257 / 3.67 ( 1047) Misc. bond : bond 0.00052 / 0.03 ( 1) link_TRANS : bond 0.00225 / 0.14 ( 1) link_TRANS : angle 0.34148 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.339 Fit side-chains REVERT: A 198 MET cc_start: 0.7585 (ptp) cc_final: 0.7292 (ptp) REVERT: B 37 ILE cc_start: 0.6587 (tt) cc_final: 0.6060 (pt) REVERT: B 124 TYR cc_start: 0.7751 (m-80) cc_final: 0.7328 (m-80) REVERT: E 101 MET cc_start: 0.5660 (mmp) cc_final: 0.5399 (tpp) REVERT: E 269 TRP cc_start: 0.6927 (m100) cc_final: 0.6681 (m100) REVERT: E 274 ILE cc_start: 0.7161 (tp) cc_final: 0.6919 (pt) outliers start: 13 outliers final: 9 residues processed: 125 average time/residue: 0.0978 time to fit residues: 17.1369 Evaluate side-chains 105 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 264 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 8 optimal weight: 0.2980 chunk 75 optimal weight: 0.0980 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 0.0470 chunk 69 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.224762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.185548 restraints weight = 11221.223| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 2.59 r_work: 0.4139 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9228 Z= 0.105 Angle : 0.540 8.396 12498 Z= 0.284 Chirality : 0.041 0.228 1422 Planarity : 0.004 0.053 1555 Dihedral : 5.287 51.055 1258 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.33 % Allowed : 11.31 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.26), residues: 1127 helix: 2.05 (0.29), residues: 368 sheet: 0.33 (0.36), residues: 232 loop : -1.35 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 67 TYR 0.013 0.001 TYR S 95 PHE 0.027 0.001 PHE S 29 TRP 0.013 0.001 TRP S 47 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 9223) covalent geometry : angle 0.54034 / 0.28 (12489) SS BOND : bond 0.00546 / 0.34 ( 3) SS BOND : angle 0.73413 / 0.28 ( 6) hydrogen bonds : bond 0.03880 / 2.66 ( 368) hydrogen bonds : angle 4.77687 / 3.41 ( 1047) Misc. bond : bond 0.00016 / 0.01 ( 1) link_TRANS : bond 0.00195 / 0.12 ( 1) link_TRANS : angle 0.23490 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.7686 (ptp) cc_final: 0.7439 (ptp) REVERT: B 37 ILE cc_start: 0.6546 (tt) cc_final: 0.5919 (pt) REVERT: B 124 TYR cc_start: 0.7779 (m-80) cc_final: 0.7520 (m-80) REVERT: E 101 MET cc_start: 0.5498 (mmp) cc_final: 0.5165 (tpp) REVERT: E 269 TRP cc_start: 0.6978 (m100) cc_final: 0.6758 (m100) outliers start: 13 outliers final: 12 residues processed: 117 average time/residue: 0.0824 time to fit residues: 13.4053 Evaluate side-chains 109 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain E residue 195 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 61 optimal weight: 0.0270 chunk 99 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.223224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.186113 restraints weight = 11367.321| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 2.70 r_work: 0.4130 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9228 Z= 0.102 Angle : 0.531 10.809 12498 Z= 0.275 Chirality : 0.041 0.250 1422 Planarity : 0.004 0.056 1555 Dihedral : 5.052 48.965 1256 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.04 % Allowed : 12.33 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.26), residues: 1127 helix: 2.06 (0.28), residues: 367 sheet: 0.33 (0.35), residues: 239 loop : -1.32 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 67 TYR 0.018 0.001 TYR E 205 PHE 0.020 0.001 PHE S 29 TRP 0.015 0.001 TRP S 47 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9223) covalent geometry : angle 0.53078 / 0.28 (12489) SS BOND : bond 0.00441 / 0.27 ( 3) SS BOND : angle 0.70306 / 0.27 ( 6) hydrogen bonds : bond 0.03644 / 2.52 ( 368) hydrogen bonds : angle 4.56635 / 3.26 ( 1047) Misc. bond : bond 0.00009 / 0.01 ( 1) link_TRANS : bond 0.00198 / 0.12 ( 1) link_TRANS : angle 0.22055 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.7148 (ttm-80) REVERT: E 74 MET cc_start: 0.5580 (ttp) cc_final: 0.5365 (ttp) REVERT: E 101 MET cc_start: 0.5558 (mmp) cc_final: 0.5257 (tpp) REVERT: E 269 TRP cc_start: 0.7076 (m100) cc_final: 0.6823 (m100) outliers start: 20 outliers final: 17 residues processed: 117 average time/residue: 0.0872 time to fit residues: 14.1159 Evaluate side-chains 114 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 245 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 74 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.222032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.180281 restraints weight = 11406.849| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.55 r_work: 0.4123 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9228 Z= 0.106 Angle : 0.529 9.562 12498 Z= 0.275 Chirality : 0.042 0.288 1422 Planarity : 0.004 0.057 1555 Dihedral : 5.000 46.937 1256 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.94 % Allowed : 13.97 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1127 helix: 2.09 (0.28), residues: 366 sheet: 0.18 (0.34), residues: 244 loop : -1.25 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 67 TYR 0.010 0.001 TYR S 95 PHE 0.017 0.001 PHE S 29 TRP 0.015 0.001 TRP S 47 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9223) covalent geometry : angle 0.52924 / 0.28 (12489) SS BOND : bond 0.00383 / 0.24 ( 3) SS BOND : angle 0.63162 / 0.24 ( 6) hydrogen bonds : bond 0.03649 / 2.51 ( 368) hydrogen bonds : angle 4.45927 / 3.19 ( 1047) Misc. bond : bond 0.00006 / 0.00 ( 1) link_TRANS : bond 0.00227 / 0.14 ( 1) link_TRANS : angle 0.12967 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.7519 (ptp) cc_final: 0.7272 (ptp) REVERT: B 197 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.7120 (ttm-80) REVERT: E 101 MET cc_start: 0.5467 (mmp) cc_final: 0.5099 (tpp) outliers start: 19 outliers final: 18 residues processed: 120 average time/residue: 0.0868 time to fit residues: 14.4448 Evaluate side-chains 118 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 57 optimal weight: 0.0370 chunk 2 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 52 optimal weight: 0.1980 chunk 92 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.222341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.181563 restraints weight = 11331.274| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 3.20 r_work: 0.4097 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9228 Z= 0.101 Angle : 0.523 11.878 12498 Z= 0.270 Chirality : 0.041 0.148 1422 Planarity : 0.004 0.055 1555 Dihedral : 4.907 45.416 1256 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.34 % Allowed : 15.49 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1127 helix: 2.13 (0.28), residues: 367 sheet: 0.13 (0.34), residues: 246 loop : -1.23 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 67 TYR 0.021 0.001 TYR E 205 PHE 0.016 0.001 PHE S 177 TRP 0.016 0.001 TRP S 47 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 9223) covalent geometry : angle 0.52306 / 0.27 (12489) SS BOND : bond 0.00405 / 0.25 ( 3) SS BOND : angle 0.70828 / 0.28 ( 6) hydrogen bonds : bond 0.03445 / 2.39 ( 368) hydrogen bonds : angle 4.36839 / 3.13 ( 1047) Misc. bond : bond 0.00008 / 0.01 ( 1) link_TRANS : bond 0.00194 / 0.12 ( 1) link_TRANS : angle 0.14013 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6539 (mm) REVERT: B 197 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7214 (ttm-80) REVERT: E 274 ILE cc_start: 0.7152 (tp) cc_final: 0.6931 (pt) outliers start: 23 outliers final: 20 residues processed: 117 average time/residue: 0.0871 time to fit residues: 14.1453 Evaluate side-chains 117 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 245 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 68 optimal weight: 0.3980 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN S 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.211869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.171356 restraints weight = 11413.524| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.32 r_work: 0.4014 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9228 Z= 0.196 Angle : 0.664 11.683 12498 Z= 0.344 Chirality : 0.045 0.198 1422 Planarity : 0.005 0.055 1555 Dihedral : 5.509 50.012 1256 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.26 % Allowed : 15.39 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.25), residues: 1127 helix: 1.62 (0.28), residues: 372 sheet: 0.05 (0.34), residues: 238 loop : -1.43 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 15 TYR 0.031 0.002 TYR S 235 PHE 0.036 0.002 PHE S 29 TRP 0.013 0.002 TRP S 36 HIS 0.005 0.002 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 ( 9223) covalent geometry : angle 0.66358 / 0.34 (12489) SS BOND : bond 0.00271 / 0.17 ( 3) SS BOND : angle 0.79918 / 0.36 ( 6) hydrogen bonds : bond 0.05339 / 3.67 ( 368) hydrogen bonds : angle 4.74126 / 3.41 ( 1047) Misc. bond : bond 0.00003 / 0.00 ( 1) link_TRANS : bond 0.00415 / 0.26 ( 1) link_TRANS : angle 0.14987 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: B 119 ASN cc_start: 0.7310 (m-40) cc_final: 0.7095 (m-40) outliers start: 32 outliers final: 25 residues processed: 131 average time/residue: 0.0806 time to fit residues: 14.4730 Evaluate side-chains 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 264 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.216050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.174924 restraints weight = 11405.752| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.37 r_work: 0.4068 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3927 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9228 Z= 0.129 Angle : 0.589 11.052 12498 Z= 0.304 Chirality : 0.042 0.175 1422 Planarity : 0.004 0.057 1555 Dihedral : 5.299 48.759 1256 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.75 % Allowed : 16.00 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.25), residues: 1127 helix: 1.77 (0.28), residues: 373 sheet: -0.10 (0.34), residues: 245 loop : -1.39 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 67 TYR 0.017 0.001 TYR S 235 PHE 0.029 0.002 PHE S 29 TRP 0.019 0.001 TRP S 47 HIS 0.004 0.001 HIS S 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9223) covalent geometry : angle 0.58937 / 0.30 (12489) SS BOND : bond 0.00363 / 0.20 ( 3) SS BOND : angle 0.88934 / 0.43 ( 6) hydrogen bonds : bond 0.04211 / 2.91 ( 368) hydrogen bonds : angle 4.55422 / 3.28 ( 1047) Misc. bond : bond 0.00002 / 0.00 ( 1) link_TRANS : bond 0.00357 / 0.22 ( 1) link_TRANS : angle 0.13456 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.6129 (tt) cc_final: 0.5456 (pt) REVERT: E 161 MET cc_start: 0.5308 (tmm) cc_final: 0.4940 (tmm) outliers start: 27 outliers final: 22 residues processed: 124 average time/residue: 0.0840 time to fit residues: 14.3780 Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 245 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS S 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.217649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.177790 restraints weight = 11342.682| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.38 r_work: 0.4083 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9228 Z= 0.118 Angle : 0.582 13.887 12498 Z= 0.298 Chirality : 0.042 0.180 1422 Planarity : 0.004 0.053 1555 Dihedral : 5.168 50.710 1256 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.34 % Allowed : 16.00 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.25), residues: 1127 helix: 2.02 (0.28), residues: 366 sheet: -0.06 (0.33), residues: 248 loop : -1.42 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 67 TYR 0.015 0.001 TYR S 235 PHE 0.027 0.001 PHE S 29 TRP 0.022 0.001 TRP S 47 HIS 0.004 0.001 HIS S 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9223) covalent geometry : angle 0.58190 / 0.30 (12489) SS BOND : bond 0.00269 / 0.16 ( 3) SS BOND : angle 0.82410 / 0.36 ( 6) hydrogen bonds : bond 0.03853 / 2.66 ( 368) hydrogen bonds : angle 4.47521 / 3.21 ( 1047) Misc. bond : bond 0.00001 / 0.00 ( 1) link_TRANS : bond 0.00279 / 0.17 ( 1) link_TRANS : angle 0.05742 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 268 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6519 (mm) REVERT: B 37 ILE cc_start: 0.6347 (tt) cc_final: 0.5779 (pt) REVERT: E 71 TYR cc_start: 0.3769 (OUTLIER) cc_final: 0.3535 (p90) outliers start: 23 outliers final: 20 residues processed: 119 average time/residue: 0.0768 time to fit residues: 12.7584 Evaluate side-chains 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 245 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 88 optimal weight: 0.2980 chunk 92 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS S 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.218508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.178794 restraints weight = 11269.348| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.41 r_work: 0.4089 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9228 Z= 0.111 Angle : 0.573 13.424 12498 Z= 0.292 Chirality : 0.041 0.177 1422 Planarity : 0.004 0.056 1555 Dihedral : 5.047 50.766 1256 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.45 % Allowed : 16.00 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1127 helix: 1.94 (0.28), residues: 373 sheet: -0.12 (0.33), residues: 250 loop : -1.39 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 67 TYR 0.015 0.001 TYR S 235 PHE 0.026 0.001 PHE S 29 TRP 0.024 0.001 TRP S 47 HIS 0.005 0.001 HIS S 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 9223) covalent geometry : angle 0.57275 / 0.29 (12489) SS BOND : bond 0.00449 / 0.28 ( 3) SS BOND : angle 0.89984 / 0.36 ( 6) hydrogen bonds : bond 0.03632 / 2.52 ( 368) hydrogen bonds : angle 4.39206 / 3.15 ( 1047) Misc. bond : bond 0.00008 / 0.00 ( 1) link_TRANS : bond 0.00241 / 0.15 ( 1) link_TRANS : angle 0.09524 / 0.05 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 268 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6603 (mm) REVERT: B 37 ILE cc_start: 0.6319 (tt) cc_final: 0.5791 (pt) REVERT: C 21 MET cc_start: 0.5363 (ttp) cc_final: 0.5071 (ttt) outliers start: 24 outliers final: 21 residues processed: 125 average time/residue: 0.0870 time to fit residues: 15.3543 Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 245 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 67 optimal weight: 0.1980 chunk 62 optimal weight: 0.1980 chunk 96 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 110 optimal weight: 0.4980 chunk 31 optimal weight: 0.0470 chunk 98 optimal weight: 0.3980 chunk 108 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.2678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS S 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.222612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.184487 restraints weight = 11223.037| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.53 r_work: 0.4131 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9228 Z= 0.097 Angle : 0.550 13.339 12498 Z= 0.279 Chirality : 0.041 0.154 1422 Planarity : 0.004 0.054 1555 Dihedral : 4.836 50.211 1256 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.14 % Allowed : 16.21 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.25), residues: 1127 helix: 2.10 (0.28), residues: 372 sheet: -0.01 (0.33), residues: 248 loop : -1.33 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 67 TYR 0.010 0.001 TYR S 95 PHE 0.024 0.001 PHE S 29 TRP 0.024 0.001 TRP S 47 HIS 0.005 0.001 HIS S 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 9223) covalent geometry : angle 0.54980 / 0.28 (12489) SS BOND : bond 0.00424 / 0.26 ( 3) SS BOND : angle 0.87701 / 0.35 ( 6) hydrogen bonds : bond 0.03093 / 2.15 ( 368) hydrogen bonds : angle 4.26563 / 3.05 ( 1047) Misc. bond : bond 0.00012 / 0.01 ( 1) link_TRANS : bond 0.00143 / 0.09 ( 1) link_TRANS : angle 0.17817 / 0.11 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2276.40 seconds wall clock time: 39 minutes 39.82 seconds (2379.82 seconds total)