Starting phenix.real_space_refine on Sat Dec 28 22:52:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yae_33710/12_2024/7yae_33710.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yae_33710/12_2024/7yae_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_33710/12_2024/7yae_33710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yae_33710/12_2024/7yae_33710.map" model { file = "/net/cci-nas-00/data/ceres_data/7yae_33710/12_2024/7yae_33710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yae_33710/12_2024/7yae_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-5532/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: 5.73, per 1000 atoms: 0.63 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: 2.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.16 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: 2.42 Time building geometry restraints manager: 2.98 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: 0.840 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.560 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.060 ------------------------------------------------------------------------------- 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 : 1.092 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: 0.2346 time to fit residues: 45.0942 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 : 0.953 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 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 53.959 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 : 1.013 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.7275 (ptp) cc_final: 0.7027 (ptp) REVERT: B 37 ILE cc_start: 0.6665 (tt) cc_final: 0.6160 (pt) REVERT: B 124 TYR cc_start: 0.7556 (m-80) cc_final: 0.7277 (m-80) REVERT: E 101 MET cc_start: 0.6027 (mmp) cc_final: 0.5727 (tpp) REVERT: E 269 TRP cc_start: 0.6901 (m100) cc_final: 0.6680 (m100) outliers start: 12 outliers final: 9 residues processed: 127 average time/residue: 0.2459 time to fit residues: 43.1470 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 : 1.070 ------------------------------------------------------------------------------- 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 57 optimal weight: 0.0020 chunk 31 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 0.0060 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9224 Z= 0.148 Angle : 0.541 8.010 12492 Z= 0.285 Chirality : 0.042 0.242 1422 Planarity : 0.004 0.053 1556 Dihedral : 5.521 48.857 1379 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.43 % Allowed : 11.01 % Favored : 87.56 % 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: 0.24 (0.26), residues: 1127 helix: 2.03 (0.29), residues: 368 sheet: 0.34 (0.36), residues: 232 loop : -1.34 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.001 HIS B 225 PHE 0.029 0.001 PHE S 29 TYR 0.013 0.001 TYR S 95 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 122 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 1.056 Fit side-chains REVERT: B 37 ILE cc_start: 0.6636 (tt) cc_final: 0.6038 (pt) REVERT: E 101 MET cc_start: 0.5922 (mmp) cc_final: 0.5546 (tpp) REVERT: E 269 TRP cc_start: 0.6993 (m100) cc_final: 0.6688 (m100) outliers start: 14 outliers final: 12 residues processed: 116 average time/residue: 0.2228 time to fit residues: 35.8567 Evaluate side-chains 109 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 195 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 0.0470 chunk 103 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.2088 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= 0.153 Angle : 0.541 11.273 12492 Z= 0.279 Chirality : 0.042 0.262 1422 Planarity : 0.004 0.058 1556 Dihedral : 5.275 43.853 1377 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.94 % Allowed : 12.64 % Favored : 85.42 % 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: 0.25 (0.25), residues: 1127 helix: 2.02 (0.28), residues: 369 sheet: 0.27 (0.35), residues: 238 loop : -1.31 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 47 HIS 0.002 0.001 HIS B 62 PHE 0.019 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 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.988 Fit side-chains REVERT: B 197 ARG cc_start: 0.6906 (ttm-80) cc_final: 0.6696 (ttm-80) REVERT: E 74 MET cc_start: 0.5632 (ttp) cc_final: 0.5403 (ttp) REVERT: E 101 MET cc_start: 0.5908 (mmp) cc_final: 0.5590 (tpp) REVERT: E 269 TRP cc_start: 0.7077 (m100) cc_final: 0.6780 (m100) outliers start: 19 outliers final: 16 residues processed: 116 average time/residue: 0.2268 time to fit residues: 36.0699 Evaluate side-chains 117 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 103 VAL Chi-restraints excluded: chain E residue 137 SER 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 62 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9224 Z= 0.234 Angle : 0.597 10.010 12492 Z= 0.311 Chirality : 0.043 0.188 1422 Planarity : 0.004 0.056 1556 Dihedral : 5.401 39.233 1377 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.75 % Allowed : 14.07 % Favored : 83.18 % 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: 0.04 (0.25), residues: 1127 helix: 1.89 (0.28), residues: 366 sheet: -0.01 (0.34), residues: 238 loop : -1.35 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 47 HIS 0.004 0.001 HIS B 62 PHE 0.018 0.002 PHE S 29 TYR 0.021 0.002 TYR S 235 ARG 0.007 0.000 ARG S 67 *********************** 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: 27 poor density : 102 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.6982 (ttm-80) cc_final: 0.6762 (ttm-80) outliers start: 27 outliers final: 22 residues processed: 120 average time/residue: 0.2341 time to fit residues: 38.3555 Evaluate side-chains 117 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain 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 240 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 98 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.0370 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN S 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.2591 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= 0.196 Angle : 0.576 12.667 12492 Z= 0.297 Chirality : 0.042 0.179 1422 Planarity : 0.004 0.056 1556 Dihedral : 5.265 37.522 1377 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.96 % Allowed : 15.39 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.01 (0.25), residues: 1127 helix: 1.93 (0.28), residues: 366 sheet: -0.13 (0.34), residues: 243 loop : -1.37 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 47 HIS 0.003 0.001 HIS B 62 PHE 0.017 0.001 PHE S 177 TYR 0.019 0.002 TYR E 205 ARG 0.007 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 134 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 1.144 Fit side-chains REVERT: B 197 ARG cc_start: 0.6962 (ttm-80) cc_final: 0.6735 (ttm-80) REVERT: E 101 MET cc_start: 0.5692 (mmp) cc_final: 0.5306 (tpp) outliers start: 29 outliers final: 25 residues processed: 126 average time/residue: 0.2488 time to fit residues: 42.5507 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 : 1.075 ------------------------------------------------------------------------------- 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 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 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 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 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 12 optimal weight: 0.0770 chunk 62 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.2750 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= 0.176 Angle : 0.559 11.776 12492 Z= 0.289 Chirality : 0.042 0.160 1422 Planarity : 0.004 0.056 1556 Dihedral : 5.164 37.213 1377 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.16 % Allowed : 15.19 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 1127 helix: 1.88 (0.28), residues: 373 sheet: -0.16 (0.33), residues: 248 loop : -1.39 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP S 47 HIS 0.003 0.001 HIS B 62 PHE 0.018 0.001 PHE S 177 TYR 0.015 0.001 TYR S 235 ARG 0.008 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 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: S 82 GLN cc_start: 0.7457 (tp40) cc_final: 0.6952 (pm20) REVERT: E 71 TYR cc_start: 0.4015 (OUTLIER) cc_final: 0.3747 (p90) outliers start: 31 outliers final: 23 residues processed: 122 average time/residue: 0.2471 time to fit residues: 40.8732 Evaluate side-chains 121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 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 77 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 245 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 104 optimal weight: 0.0970 chunk 95 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9224 Z= 0.147 Angle : 0.533 11.148 12492 Z= 0.275 Chirality : 0.041 0.146 1422 Planarity : 0.004 0.053 1556 Dihedral : 4.991 36.342 1377 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.24 % Allowed : 16.31 % Favored : 81.45 % 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: 0.18 (0.25), residues: 1127 helix: 2.11 (0.28), residues: 367 sheet: -0.03 (0.33), residues: 248 loop : -1.33 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP S 47 HIS 0.002 0.001 HIS S 232 PHE 0.018 0.001 PHE S 177 TYR 0.010 0.001 TYR S 235 ARG 0.008 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 128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: S 82 GLN cc_start: 0.7409 (tp40) cc_final: 0.6970 (pm20) REVERT: E 287 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7236 (m) outliers start: 22 outliers final: 20 residues processed: 121 average time/residue: 0.2312 time to fit residues: 38.7390 Evaluate side-chains 120 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 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 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 174 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.2934 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= 0.174 Angle : 0.556 11.059 12492 Z= 0.286 Chirality : 0.041 0.153 1422 Planarity : 0.004 0.054 1556 Dihedral : 4.987 36.999 1377 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.65 % Allowed : 16.11 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.25), residues: 1127 helix: 1.97 (0.28), residues: 374 sheet: -0.04 (0.33), residues: 248 loop : -1.34 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.003 0.001 HIS S 232 PHE 0.035 0.001 PHE S 29 TYR 0.015 0.001 TYR S 235 ARG 0.009 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 134 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.8041 (ptm) cc_final: 0.7754 (ptm) REVERT: S 82 GLN cc_start: 0.7448 (tp40) cc_final: 0.6947 (pm20) outliers start: 26 outliers final: 22 residues processed: 126 average time/residue: 0.2323 time to fit residues: 40.2241 Evaluate side-chains 124 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 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 105 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 0.1980 chunk 112 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.3056 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= 0.172 Angle : 0.569 13.195 12492 Z= 0.290 Chirality : 0.041 0.151 1422 Planarity : 0.004 0.053 1556 Dihedral : 4.976 37.507 1377 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.34 % Allowed : 16.31 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 379 sheet: -0.09 (0.33), residues: 248 loop : -1.32 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP S 47 HIS 0.003 0.001 HIS S 232 PHE 0.032 0.001 PHE S 29 TYR 0.016 0.001 TYR S 235 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 128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.8052 (ptm) cc_final: 0.7848 (ptm) REVERT: S 82 GLN cc_start: 0.7422 (tp40) cc_final: 0.6942 (pm20) outliers start: 23 outliers final: 22 residues processed: 121 average time/residue: 0.2438 time to fit residues: 40.3784 Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.0170 overall best weight: 1.1022 ------------------------------------------------------------------------------- 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 = 0.4612 r_free = 0.4612 target = 0.216150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.176428 restraints weight = 11206.508| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.31 r_work: 0.4065 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.3174 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= 0.206 Angle : 0.597 13.030 12492 Z= 0.304 Chirality : 0.042 0.159 1422 Planarity : 0.004 0.055 1556 Dihedral : 5.093 38.224 1377 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.34 % Allowed : 16.41 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 1127 helix: 1.78 (0.28), residues: 380 sheet: -0.19 (0.33), residues: 248 loop : -1.32 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP S 47 HIS 0.003 0.001 HIS B 62 PHE 0.032 0.001 PHE S 29 TYR 0.021 0.002 TYR S 235 ARG 0.009 0.000 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.17 seconds wall clock time: 40 minutes 5.53 seconds (2405.53 seconds total)