Starting phenix.real_space_refine on Thu Mar 13 22:17:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yae_33710/03_2025/7yae_33710.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yae_33710/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yae_33710/03_2025/7yae_33710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yae_33710/03_2025/7yae_33710.map" model { file = "/net/cci-nas-00/data/ceres_data/7yae_33710/03_2025/7yae_33710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yae_33710/03_2025/7yae_33710.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.17, per 1000 atoms: 0.57 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: 2.50 Conformation dependent library (CDL) restraints added in 896.6 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: 0.99 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: 2.21 Time building geometry restraints manager: 2.86 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: 0.950 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- 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 9224 Z= 0.337 Angle : 0.738 13.053 12492 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 : 12.85 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), 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 TRP 0.013 0.001 TRP A 258 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.001 PHE A 274 TYR 0.016 0.001 TYR B 264 ARG 0.009 0.000 ARG B 219 *********************** 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 : 0.965 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: 0.2224 time to fit residues: 43.2323 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 : 0.891 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.0670 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.4675 r_free = 0.4675 target = 0.222928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.181982 restraints weight = 11178.486| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.33 r_work: 0.4160 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.4022 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9224 Z= 0.182 Angle : 0.606 10.104 12492 Z= 0.316 Chirality : 0.043 0.225 1422 Planarity : 0.004 0.048 1556 Dihedral : 6.355 53.960 1382 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1127 helix: 1.86 (0.28), residues: 372 sheet: 0.44 (0.36), residues: 229 loop : -1.34 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.003 0.001 HIS B 225 PHE 0.024 0.001 PHE E 48 TYR 0.013 0.001 TYR A 296 ARG 0.004 0.000 ARG S 67 *********************** 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 132 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.7660 (ptp) cc_final: 0.7346 (ptp) REVERT: B 37 ILE cc_start: 0.6513 (tt) cc_final: 0.5909 (pt) REVERT: B 124 TYR cc_start: 0.7800 (m-80) cc_final: 0.7351 (m-80) REVERT: E 101 MET cc_start: 0.5574 (mmp) cc_final: 0.5330 (tpp) REVERT: E 269 TRP cc_start: 0.6947 (m100) cc_final: 0.6733 (m100) outliers start: 12 outliers final: 9 residues processed: 127 average time/residue: 0.2579 time to fit residues: 45.3322 Evaluate side-chains 106 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 110 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 10 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 E 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.217469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.178338 restraints weight = 11422.937| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 2.48 r_work: 0.4060 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9224 Z= 0.221 Angle : 0.602 8.451 12492 Z= 0.316 Chirality : 0.043 0.247 1422 Planarity : 0.004 0.054 1556 Dihedral : 5.675 49.101 1379 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.94 % Allowed : 11.42 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1127 helix: 1.85 (0.28), residues: 369 sheet: 0.22 (0.35), residues: 236 loop : -1.41 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS B 62 PHE 0.031 0.002 PHE S 29 TYR 0.014 0.002 TYR S 235 ARG 0.005 0.000 ARG S 67 *********************** 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 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.724 Fit side-chains REVERT: B 37 ILE cc_start: 0.6686 (tt) cc_final: 0.5921 (pt) REVERT: B 124 TYR cc_start: 0.8011 (m-80) cc_final: 0.7493 (m-80) REVERT: B 197 ARG cc_start: 0.7503 (ttm-80) cc_final: 0.7240 (ttm-80) REVERT: E 101 MET cc_start: 0.5579 (mmp) cc_final: 0.5236 (tpp) outliers start: 19 outliers final: 15 residues processed: 118 average time/residue: 0.2284 time to fit residues: 37.8464 Evaluate side-chains 108 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 80 ILE 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 70 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 52 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 80 optimal weight: 0.0370 chunk 84 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.220491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.179785 restraints weight = 11194.621| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 3.21 r_work: 0.4080 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9224 Z= 0.151 Angle : 0.547 11.074 12492 Z= 0.284 Chirality : 0.042 0.256 1422 Planarity : 0.004 0.057 1556 Dihedral : 5.338 44.224 1377 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.83 % Allowed : 13.76 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1127 helix: 2.00 (0.28), residues: 366 sheet: 0.17 (0.35), residues: 238 loop : -1.38 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.002 0.001 HIS B 225 PHE 0.018 0.001 PHE S 29 TYR 0.017 0.001 TYR E 205 ARG 0.006 0.000 ARG S 67 *********************** 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 119 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.062 Fit side-chains REVERT: A 198 MET cc_start: 0.7604 (ptp) cc_final: 0.7369 (ptp) REVERT: B 124 TYR cc_start: 0.7873 (m-80) cc_final: 0.7566 (m-80) REVERT: B 197 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7261 (ttm-80) REVERT: C 21 MET cc_start: 0.6384 (tmm) cc_final: 0.6168 (tmm) REVERT: E 101 MET cc_start: 0.5414 (mmp) cc_final: 0.5111 (tpp) REVERT: E 269 TRP cc_start: 0.7106 (m100) cc_final: 0.6858 (m100) outliers start: 18 outliers final: 13 residues processed: 111 average time/residue: 0.3073 time to fit residues: 46.9453 Evaluate side-chains 105 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 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 103 VAL 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 107 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 112 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.204847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.161253 restraints weight = 11397.594| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.52 r_work: 0.3965 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9224 Z= 0.357 Angle : 0.710 10.285 12492 Z= 0.370 Chirality : 0.047 0.289 1422 Planarity : 0.005 0.058 1556 Dihedral : 5.884 40.101 1377 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.47 % Allowed : 14.78 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1127 helix: 1.35 (0.28), residues: 372 sheet: -0.31 (0.34), residues: 239 loop : -1.56 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.006 0.002 HIS B 62 PHE 0.020 0.002 PHE S 29 TYR 0.034 0.003 TYR S 235 ARG 0.008 0.001 ARG A 15 *********************** 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 142 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7613 (ttm-80) cc_final: 0.7409 (ttm-80) REVERT: S 82 GLN cc_start: 0.7660 (tp40) cc_final: 0.6910 (pm20) REVERT: E 161 MET cc_start: 0.5417 (tmm) cc_final: 0.5056 (tmm) outliers start: 34 outliers final: 30 residues processed: 135 average time/residue: 0.2684 time to fit residues: 49.6664 Evaluate side-chains 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 190 THR 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 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 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 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 = 0.4602 r_free = 0.4602 target = 0.214968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.175412 restraints weight = 11343.559| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.31 r_work: 0.4057 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9224 Z= 0.190 Angle : 0.598 12.724 12492 Z= 0.308 Chirality : 0.043 0.239 1422 Planarity : 0.004 0.057 1556 Dihedral : 5.479 37.263 1377 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.75 % Allowed : 16.72 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1127 helix: 1.58 (0.28), residues: 373 sheet: -0.34 (0.33), residues: 245 loop : -1.49 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP S 47 HIS 0.003 0.001 HIS S 232 PHE 0.018 0.002 PHE S 177 TYR 0.016 0.001 TYR S 235 ARG 0.006 0.000 ARG S 67 *********************** 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 135 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.950 Fit side-chains REVERT: B 37 ILE cc_start: 0.6287 (tt) cc_final: 0.5682 (pt) REVERT: B 124 TYR cc_start: 0.8136 (m-80) cc_final: 0.7552 (m-80) REVERT: S 3 GLN cc_start: 0.6125 (tm130) cc_final: 0.5914 (tm-30) REVERT: E 161 MET cc_start: 0.5360 (tmm) cc_final: 0.4998 (tmm) outliers start: 27 outliers final: 22 residues processed: 127 average time/residue: 0.2343 time to fit residues: 40.5212 Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU 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 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 303 ASP 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 76 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 195 ILE 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 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.216044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.176275 restraints weight = 11427.827| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.37 r_work: 0.4068 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9224 Z= 0.180 Angle : 0.580 11.780 12492 Z= 0.299 Chirality : 0.043 0.327 1422 Planarity : 0.004 0.054 1556 Dihedral : 5.245 36.387 1377 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.16 % Allowed : 17.02 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1127 helix: 1.70 (0.28), residues: 373 sheet: -0.32 (0.33), residues: 244 loop : -1.48 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP S 47 HIS 0.003 0.001 HIS S 232 PHE 0.018 0.001 PHE S 177 TYR 0.020 0.001 TYR E 205 ARG 0.009 0.000 ARG S 67 *********************** 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 137 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.6360 (tt) cc_final: 0.5733 (pt) REVERT: B 124 TYR cc_start: 0.8125 (m-80) cc_final: 0.7660 (m-80) REVERT: S 3 GLN cc_start: 0.6139 (tm130) cc_final: 0.5886 (tm-30) outliers start: 31 outliers final: 27 residues processed: 128 average time/residue: 0.2150 time to fit residues: 38.3452 Evaluate side-chains 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 LEU 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 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 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 76 THR 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 245 SER Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4619 r_free = 0.4619 target = 0.216786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.177354 restraints weight = 11542.600| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.33 r_work: 0.4080 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9224 Z= 0.177 Angle : 0.577 11.269 12492 Z= 0.295 Chirality : 0.042 0.161 1422 Planarity : 0.004 0.055 1556 Dihedral : 5.199 37.502 1377 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1127 helix: 1.76 (0.28), residues: 373 sheet: -0.37 (0.33), residues: 249 loop : -1.51 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP S 47 HIS 0.002 0.001 HIS B 62 PHE 0.017 0.001 PHE S 177 TYR 0.019 0.001 TYR E 205 ARG 0.009 0.000 ARG S 67 *********************** 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 135 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.6529 (tt) cc_final: 0.6003 (pt) REVERT: B 124 TYR cc_start: 0.7944 (m-80) cc_final: 0.7616 (m-80) REVERT: B 217 MET cc_start: 0.8291 (ptm) cc_final: 0.7952 (ppp) REVERT: S 3 GLN cc_start: 0.6188 (tm130) cc_final: 0.5956 (tm-30) REVERT: E 71 TYR cc_start: 0.3815 (OUTLIER) cc_final: 0.3579 (p90) outliers start: 30 outliers final: 25 residues processed: 125 average time/residue: 0.2153 time to fit residues: 37.3427 Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU 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 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 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 76 THR 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 245 SER Chi-restraints excluded: chain E residue 264 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 14 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 4 optimal weight: 0.0370 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- 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 = 0.4608 r_free = 0.4608 target = 0.215445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.176174 restraints weight = 11307.594| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.29 r_work: 0.4063 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9224 Z= 0.200 Angle : 0.591 11.149 12492 Z= 0.303 Chirality : 0.042 0.160 1422 Planarity : 0.004 0.055 1556 Dihedral : 5.185 38.399 1377 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.96 % Allowed : 18.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1127 helix: 1.71 (0.28), residues: 373 sheet: -0.44 (0.33), residues: 249 loop : -1.52 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP S 47 HIS 0.005 0.001 HIS S 232 PHE 0.038 0.002 PHE S 29 TYR 0.020 0.002 TYR E 205 ARG 0.010 0.000 ARG S 67 *********************** 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 133 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.6493 (tt) cc_final: 0.5901 (pt) REVERT: B 124 TYR cc_start: 0.8108 (m-80) cc_final: 0.7689 (m-80) REVERT: S 3 GLN cc_start: 0.6184 (tm130) cc_final: 0.5942 (tm-30) outliers start: 29 outliers final: 27 residues processed: 125 average time/residue: 0.2263 time to fit residues: 39.0290 Evaluate side-chains 128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 LEU 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 265 ILE 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 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 76 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.0010 chunk 63 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7666 ------------------------------------------------------------------------------- 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 = 0.217203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.178415 restraints weight = 11494.645| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.30 r_work: 0.4090 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9224 Z= 0.173 Angle : 0.583 13.377 12492 Z= 0.295 Chirality : 0.042 0.151 1422 Planarity : 0.004 0.054 1556 Dihedral : 5.066 39.530 1377 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.75 % Allowed : 18.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1127 helix: 1.78 (0.28), residues: 373 sheet: -0.38 (0.33), residues: 248 loop : -1.49 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP S 47 HIS 0.003 0.001 HIS S 232 PHE 0.032 0.001 PHE S 29 TYR 0.020 0.001 TYR E 205 ARG 0.010 0.000 ARG S 67 ********************** 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 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: B 37 ILE cc_start: 0.6483 (tt) cc_final: 0.5966 (pt) REVERT: B 124 TYR cc_start: 0.8029 (m-80) cc_final: 0.7680 (m-80) REVERT: S 3 GLN cc_start: 0.6183 (tm130) cc_final: 0.5927 (tm-30) outliers start: 27 outliers final: 25 residues processed: 121 average time/residue: 0.2272 time to fit residues: 37.9550 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 : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU 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 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 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 76 THR 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 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.209328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.166758 restraints weight = 11321.966| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.52 r_work: 0.4029 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9224 Z= 0.223 Angle : 0.621 13.299 12492 Z= 0.315 Chirality : 0.043 0.166 1422 Planarity : 0.004 0.055 1556 Dihedral : 5.207 40.198 1377 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.16 % Allowed : 18.04 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1127 helix: 1.69 (0.28), residues: 371 sheet: -0.41 (0.33), residues: 250 loop : -1.52 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 47 HIS 0.004 0.001 HIS S 232 PHE 0.033 0.002 PHE S 29 TYR 0.020 0.002 TYR S 235 ARG 0.010 0.000 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5732.62 seconds wall clock time: 101 minutes 25.12 seconds (6085.12 seconds total)