Starting phenix.real_space_refine on Wed Sep 17 15:03:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yae_33710/09_2025/7yae_33710.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yae_33710/09_2025/7yae_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yae_33710/09_2025/7yae_33710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yae_33710/09_2025/7yae_33710.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yae_33710/09_2025/7yae_33710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yae_33710/09_2025/7yae_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-2.0-5805/lib/python3.9/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} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 2} 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} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 4} 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=0, symmetry=0 Links applied TRANS " DTR D 4 " - " PHE D 3 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 333.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.19 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: 1.45 Time building geometry restraints manager: 1.02 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: 2519 1.44 - 1.57: 5148 1.57 - 1.69: 0 1.69 - 1.82: 102 Bond restraints: 9224 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=" CD2 DTR D 4 " pdb=" CE2 DTR D 4 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.70e-02 3.46e+03 1.31e+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 ... (remaining 9219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 12307 2.61 - 5.22: 161 5.22 - 7.83: 18 7.83 - 10.44: 3 10.44 - 13.05: 3 Bond angle restraints: 12492 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 12487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5009 17.59 - 35.17: 437 35.17 - 52.76: 98 52.76 - 70.35: 21 70.35 - 87.93: 10 Dihedral angle restraints: 5575 sinusoidal: 2258 harmonic: 3317 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 5572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1241 0.065 - 0.129: 162 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: 1557 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 1554 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.880 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 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= 0.256 Angle : 0.738 13.053 12501 Z= 0.430 Chirality : 0.047 0.324 1422 Planarity : 0.004 0.062 1556 Dihedral : 14.620 87.934 3427 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 aren 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 covalent geometry : bond 0.00451 ( 9224) covalent geometry : angle 0.73781 (12492) SS BOND : bond 0.00914 ( 3) SS BOND : angle 0.96431 ( 6) hydrogen bonds : bond 0.21922 ( 368) hydrogen bonds : angle 7.30945 ( 1047) link_TRANS : bond 0.00659 ( 1) link_TRANS : angle 1.52941 ( 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 : 0.355 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: 0.1004 time to fit residues: 19.2799 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 : 0.241 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4661 r_free = 0.4661 target = 0.221404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.180854 restraints weight = 11206.544| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 2.73 r_work: 0.4118 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.1467 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= 0.133 Angle : 0.611 10.220 12501 Z= 0.319 Chirality : 0.043 0.227 1422 Planarity : 0.004 0.048 1556 Dihedral : 6.395 54.448 1382 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.22 % Allowed : 8.15 % Favored : 90.62 % 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 aren not related in a simple way. whole: 0.18 (0.25), residues: 1127 helix: 1.84 (0.28), residues: 372 sheet: 0.44 (0.36), residues: 229 loop : -1.35 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.013 0.002 TYR A 296 PHE 0.023 0.001 PHE E 48 TRP 0.016 0.002 TRP S 47 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9224) covalent geometry : angle 0.61080 (12492) SS BOND : bond 0.00587 ( 3) SS BOND : angle 0.66644 ( 6) hydrogen bonds : bond 0.04756 ( 368) hydrogen bonds : angle 5.12934 ( 1047) link_TRANS : bond 0.00226 ( 1) link_TRANS : angle 0.45654 ( 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: 12 poor density : 119 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.7599 (ptp) cc_final: 0.7294 (ptp) REVERT: B 37 ILE cc_start: 0.6580 (tt) cc_final: 0.6003 (pt) REVERT: B 124 TYR cc_start: 0.7754 (m-80) cc_final: 0.7295 (m-80) REVERT: E 101 MET cc_start: 0.5577 (mmp) cc_final: 0.5313 (tpp) REVERT: E 269 TRP cc_start: 0.6938 (m100) cc_final: 0.6664 (m100) outliers start: 12 outliers final: 9 residues processed: 126 average time/residue: 0.0856 time to fit residues: 15.0339 Evaluate side-chains 104 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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: 2.9990 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 22 optimal weight: 5.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 167 HIS S 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.213906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.174957 restraints weight = 11272.763| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.34 r_work: 0.4026 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9228 Z= 0.180 Angle : 0.653 8.878 12501 Z= 0.343 Chirality : 0.045 0.255 1422 Planarity : 0.004 0.054 1556 Dihedral : 5.848 49.304 1379 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.24 % Allowed : 11.42 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.25), residues: 1127 helix: 1.67 (0.28), residues: 368 sheet: 0.11 (0.34), residues: 236 loop : -1.45 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 67 TYR 0.022 0.002 TYR S 235 PHE 0.033 0.002 PHE S 29 TRP 0.015 0.002 TRP S 47 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9224) covalent geometry : angle 0.65278 (12492) SS BOND : bond 0.00419 ( 3) SS BOND : angle 0.81479 ( 6) hydrogen bonds : bond 0.05319 ( 368) hydrogen bonds : angle 4.97856 ( 1047) link_TRANS : bond 0.00522 ( 1) link_TRANS : angle 0.36557 ( 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 130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.271 Fit side-chains REVERT: B 37 ILE cc_start: 0.6826 (tt) cc_final: 0.6051 (pt) outliers start: 22 outliers final: 18 residues processed: 122 average time/residue: 0.0941 time to fit residues: 15.7607 Evaluate side-chains 110 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 A residue 316 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 263 THR 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 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 195 ILE Chi-restraints excluded: chain E residue 264 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 167 HIS E 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.218067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.179106 restraints weight = 11358.915| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.62 r_work: 0.4057 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9228 Z= 0.114 Angle : 0.566 11.491 12501 Z= 0.295 Chirality : 0.042 0.203 1422 Planarity : 0.004 0.058 1556 Dihedral : 5.491 44.702 1377 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.24 % Allowed : 14.17 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.25), residues: 1127 helix: 1.89 (0.28), residues: 366 sheet: -0.04 (0.34), residues: 244 loop : -1.42 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 67 TYR 0.017 0.001 TYR E 205 PHE 0.018 0.001 PHE S 177 TRP 0.020 0.001 TRP S 47 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9224) covalent geometry : angle 0.56620 (12492) SS BOND : bond 0.00372 ( 3) SS BOND : angle 0.60503 ( 6) hydrogen bonds : bond 0.04097 ( 368) hydrogen bonds : angle 4.69710 ( 1047) link_TRANS : bond 0.00275 ( 1) link_TRANS : angle 0.09700 ( 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 120 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: B 124 TYR cc_start: 0.7987 (m-80) cc_final: 0.7659 (m-80) REVERT: E 101 MET cc_start: 0.5408 (mmp) cc_final: 0.5076 (tpp) outliers start: 22 outliers final: 16 residues processed: 114 average time/residue: 0.0955 time to fit residues: 15.1335 Evaluate side-chains 108 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 E residue 71 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 54 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN S 3 GLN S 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.214980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.175670 restraints weight = 11400.038| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.46 r_work: 0.4040 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9228 Z= 0.136 Angle : 0.586 9.805 12501 Z= 0.306 Chirality : 0.043 0.278 1422 Planarity : 0.004 0.057 1556 Dihedral : 5.444 39.824 1377 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.85 % Allowed : 15.29 % Favored : 81.86 % 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 aren not related in a simple way. whole: -0.09 (0.25), residues: 1127 helix: 1.84 (0.28), residues: 366 sheet: -0.20 (0.33), residues: 243 loop : -1.43 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 67 TYR 0.017 0.002 TYR S 235 PHE 0.017 0.002 PHE S 177 TRP 0.019 0.001 TRP S 47 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9224) covalent geometry : angle 0.58628 (12492) SS BOND : bond 0.00368 ( 3) SS BOND : angle 0.87261 ( 6) hydrogen bonds : bond 0.04403 ( 368) hydrogen bonds : angle 4.67257 ( 1047) link_TRANS : bond 0.00371 ( 1) link_TRANS : angle 0.18516 ( 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 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: B 124 TYR cc_start: 0.7959 (m-80) cc_final: 0.7635 (m-80) REVERT: S 82 GLN cc_start: 0.7659 (tp40) cc_final: 0.6905 (pm20) outliers start: 28 outliers final: 24 residues processed: 122 average time/residue: 0.0920 time to fit residues: 15.7886 Evaluate side-chains 119 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 43 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 B residue 269 ILE 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 E residue 71 TYR 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 195 ILE Chi-restraints excluded: chain E residue 264 VAL 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: 0.7980 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN S 3 GLN S 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.208375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.165451 restraints weight = 11420.800| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.58 r_work: 0.4017 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9228 Z= 0.150 Angle : 0.610 13.001 12501 Z= 0.315 Chirality : 0.043 0.186 1422 Planarity : 0.004 0.057 1556 Dihedral : 5.462 38.022 1377 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.36 % Allowed : 16.62 % Favored : 80.02 % 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 aren not related in a simple way. whole: -0.28 (0.25), residues: 1127 helix: 1.58 (0.28), residues: 373 sheet: -0.36 (0.33), residues: 244 loop : -1.46 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 15 TYR 0.022 0.002 TYR S 235 PHE 0.016 0.002 PHE S 27 TRP 0.020 0.002 TRP S 47 HIS 0.005 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9224) covalent geometry : angle 0.61027 (12492) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.89428 ( 6) hydrogen bonds : bond 0.04601 ( 368) hydrogen bonds : angle 4.67615 ( 1047) link_TRANS : bond 0.00356 ( 1) link_TRANS : angle 0.12075 ( 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 134 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 268 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6291 (mm) REVERT: B 119 ASN cc_start: 0.6973 (m-40) cc_final: 0.6767 (m-40) REVERT: B 124 TYR cc_start: 0.8072 (m-80) cc_final: 0.7731 (m-80) REVERT: S 82 GLN cc_start: 0.7632 (tp40) cc_final: 0.6899 (pm20) outliers start: 33 outliers final: 27 residues processed: 127 average time/residue: 0.0914 time to fit residues: 16.0223 Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 265 ILE 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 177 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 B residue 269 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU 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 195 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 0.9990 chunk 82 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4623 r_free = 0.4623 target = 0.217260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.176615 restraints weight = 11427.279| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.39 r_work: 0.4086 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9228 Z= 0.111 Angle : 0.559 11.766 12501 Z= 0.288 Chirality : 0.042 0.161 1422 Planarity : 0.004 0.055 1556 Dihedral : 5.189 36.540 1377 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.55 % Allowed : 17.84 % Favored : 79.61 % 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 aren not related in a simple way. whole: -0.12 (0.25), residues: 1127 helix: 1.79 (0.28), residues: 373 sheet: -0.31 (0.33), residues: 245 loop : -1.42 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 67 TYR 0.013 0.001 TYR S 235 PHE 0.017 0.001 PHE S 177 TRP 0.023 0.001 TRP S 47 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9224) covalent geometry : angle 0.55881 (12492) SS BOND : bond 0.00527 ( 3) SS BOND : angle 1.31002 ( 6) hydrogen bonds : bond 0.03729 ( 368) hydrogen bonds : angle 4.46939 ( 1047) link_TRANS : bond 0.00321 ( 1) link_TRANS : angle 0.15763 ( 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 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: B 124 TYR cc_start: 0.8001 (m-80) cc_final: 0.7734 (m-80) REVERT: C 21 MET cc_start: 0.6372 (tmm) cc_final: 0.5530 (tmm) outliers start: 25 outliers final: 20 residues processed: 120 average time/residue: 0.0915 time to fit residues: 15.1804 Evaluate side-chains 118 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 266 HIS S 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.214991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.173897 restraints weight = 11391.280| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 2.40 r_work: 0.4056 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.3053 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= 0.135 Angle : 0.593 11.507 12501 Z= 0.304 Chirality : 0.042 0.168 1422 Planarity : 0.004 0.056 1556 Dihedral : 5.234 37.380 1377 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.06 % Allowed : 18.25 % Favored : 78.70 % 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 aren not related in a simple way. whole: -0.21 (0.25), residues: 1127 helix: 1.76 (0.28), residues: 373 sheet: -0.39 (0.33), residues: 244 loop : -1.48 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 67 TYR 0.019 0.002 TYR S 235 PHE 0.036 0.002 PHE S 29 TRP 0.021 0.002 TRP S 47 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9224) covalent geometry : angle 0.59299 (12492) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.83872 ( 6) hydrogen bonds : bond 0.04171 ( 368) hydrogen bonds : angle 4.51380 ( 1047) link_TRANS : bond 0.00327 ( 1) link_TRANS : angle 0.10810 ( 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 137 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: B 124 TYR cc_start: 0.8108 (m-80) cc_final: 0.7772 (m-80) REVERT: C 21 MET cc_start: 0.6384 (tmm) cc_final: 0.5504 (tmm) outliers start: 30 outliers final: 27 residues processed: 128 average time/residue: 0.0872 time to fit residues: 15.5290 Evaluate side-chains 130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 221 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 177 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 B residue 269 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU 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 245 SER Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 266 HIS S 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.215452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.175746 restraints weight = 11410.148| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.25 r_work: 0.4068 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.3187 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= 0.128 Angle : 0.586 12.135 12501 Z= 0.301 Chirality : 0.042 0.171 1422 Planarity : 0.004 0.054 1556 Dihedral : 5.165 39.594 1377 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.85 % Allowed : 18.45 % Favored : 78.70 % 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 aren not related in a simple way. whole: -0.17 (0.25), residues: 1127 helix: 1.77 (0.28), residues: 373 sheet: -0.35 (0.33), residues: 250 loop : -1.46 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 67 TYR 0.018 0.002 TYR S 235 PHE 0.031 0.002 PHE S 29 TRP 0.022 0.001 TRP S 47 HIS 0.004 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9224) covalent geometry : angle 0.58572 (12492) SS BOND : bond 0.00409 ( 3) SS BOND : angle 0.95795 ( 6) hydrogen bonds : bond 0.04019 ( 368) hydrogen bonds : angle 4.46562 ( 1047) link_TRANS : bond 0.00300 ( 1) link_TRANS : angle 0.05942 ( 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 132 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: B 124 TYR cc_start: 0.8094 (m-80) cc_final: 0.7786 (m-80) outliers start: 28 outliers final: 25 residues processed: 125 average time/residue: 0.0885 time to fit residues: 15.2840 Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 221 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 177 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 B residue 269 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU 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 245 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 97 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 chunk 92 optimal weight: 5.9990 chunk 4 optimal weight: 0.0040 chunk 93 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4646 r_free = 0.4646 target = 0.220007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.181161 restraints weight = 11320.992| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 2.37 r_work: 0.4116 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.3222 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= 0.099 Angle : 0.557 11.736 12501 Z= 0.282 Chirality : 0.041 0.156 1422 Planarity : 0.004 0.056 1556 Dihedral : 4.912 39.719 1377 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.63 % Allowed : 19.37 % Favored : 79.00 % 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 aren not related in a simple way. whole: -0.05 (0.25), residues: 1127 helix: 1.83 (0.28), residues: 379 sheet: -0.23 (0.33), residues: 243 loop : -1.42 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 67 TYR 0.012 0.001 TYR S 95 PHE 0.029 0.001 PHE S 29 TRP 0.028 0.001 TRP S 47 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9224) covalent geometry : angle 0.55697 (12492) SS BOND : bond 0.00420 ( 3) SS BOND : angle 0.78053 ( 6) hydrogen bonds : bond 0.03240 ( 368) hydrogen bonds : angle 4.33076 ( 1047) link_TRANS : bond 0.00183 ( 1) link_TRANS : angle 0.15237 ( 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 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.6355 (tt) cc_final: 0.6033 (pt) outliers start: 16 outliers final: 15 residues processed: 117 average time/residue: 0.0931 time to fit residues: 15.1457 Evaluate side-chains 114 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 269 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU 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 177 ILE Chi-restraints excluded: chain E residue 195 ILE 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: 0.6980 chunk 96 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 98 optimal weight: 0.1980 chunk 108 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 266 HIS S 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.219146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.182274 restraints weight = 11296.070| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 2.64 r_work: 0.4112 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9228 Z= 0.105 Angle : 0.574 16.263 12501 Z= 0.288 Chirality : 0.041 0.158 1422 Planarity : 0.004 0.054 1556 Dihedral : 4.889 39.033 1377 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.83 % Allowed : 19.67 % Favored : 78.49 % 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 aren not related in a simple way. whole: -0.08 (0.25), residues: 1127 helix: 1.85 (0.28), residues: 379 sheet: -0.25 (0.33), residues: 248 loop : -1.48 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 67 TYR 0.012 0.001 TYR S 235 PHE 0.029 0.001 PHE S 29 TRP 0.025 0.001 TRP S 47 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9224) covalent geometry : angle 0.57386 (12492) SS BOND : bond 0.00357 ( 3) SS BOND : angle 0.75402 ( 6) hydrogen bonds : bond 0.03368 ( 368) hydrogen bonds : angle 4.30357 ( 1047) link_TRANS : bond 0.00194 ( 1) link_TRANS : angle 0.09186 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2488.18 seconds wall clock time: 43 minutes 20.23 seconds (2600.23 seconds total)