Starting phenix.real_space_refine on Sun Jun 8 04:54:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ts0_26104/06_2025/7ts0_26104.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ts0_26104/06_2025/7ts0_26104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ts0_26104/06_2025/7ts0_26104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ts0_26104/06_2025/7ts0_26104.map" model { file = "/net/cci-nas-00/data/ceres_data/7ts0_26104/06_2025/7ts0_26104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ts0_26104/06_2025/7ts0_26104.cif" } resolution = 2.8 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= -0.000 sd= 0.006 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 63 5.16 5 C 5979 2.51 5 N 1607 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9383 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2459 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 287} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "U" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 301 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "A" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1788 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "H" Number of atoms: 1783 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1780 Classifications: {'peptide': 232} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 232, 1780 Classifications: {'peptide': 232} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1820 Time building chain proxies: 6.69, per 1000 atoms: 0.71 Number of scatterers: 9383 At special positions: 0 Unit cell: (108.498, 132.834, 128.778, 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 63 16.00 O 1734 8.00 N 1607 7.00 C 5979 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS P 64 " - pdb=" SG CYS P 98 " distance=2.03 Simple disulfide: pdb=" SG CYS P 184 " - pdb=" SG CYS P 254 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2222 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 40.0% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'P' and resid 102 through 106 removed outlier: 4.115A pdb=" N LYS P 105 " --> pdb=" O LEU P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 138 removed outlier: 4.100A pdb=" N ALA P 133 " --> pdb=" O ALA P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 171 removed outlier: 4.094A pdb=" N LEU P 171 " --> pdb=" O PHE P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 179 Processing helix chain 'P' and resid 181 through 214 removed outlier: 3.709A pdb=" N ARG P 185 " --> pdb=" O GLU P 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 233 Processing helix chain 'P' and resid 234 through 250 removed outlier: 4.087A pdb=" N ILE P 238 " --> pdb=" O ILE P 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 256 Processing helix chain 'P' and resid 265 through 298 removed outlier: 3.919A pdb=" N GLN P 269 " --> pdb=" O ASP P 265 " (cutoff:3.500A) Proline residue: P 271 - end of helix removed outlier: 3.511A pdb=" N LEU P 274 " --> pdb=" O GLY P 270 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU P 277 " --> pdb=" O ILE P 273 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET P 291 " --> pdb=" O VAL P 287 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ALA P 296 " --> pdb=" O THR P 292 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER P 297 " --> pdb=" O LYS P 293 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR P 298 " --> pdb=" O LEU P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 320 removed outlier: 3.617A pdb=" N VAL P 314 " --> pdb=" O LYS P 310 " (cutoff:3.500A) Proline residue: P 317 - end of helix Processing helix chain 'P' and resid 321 through 326 removed outlier: 4.028A pdb=" N PHE P 326 " --> pdb=" O THR P 322 " (cutoff:3.500A) Processing helix chain 'P' and resid 334 through 362 removed outlier: 3.514A pdb=" N PHE P 350 " --> pdb=" O PHE P 346 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLY P 352 " --> pdb=" O GLN P 348 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE P 353 " --> pdb=" O SER P 349 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 383 removed outlier: 3.635A pdb=" N ARG P 367 " --> pdb=" O ASN P 363 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 37 Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.189A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.525A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 removed outlier: 4.362A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP A 218 " --> pdb=" O CYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.070A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.179A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.704A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 35' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.554A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.589A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 67 through 68 removed outlier: 3.711A pdb=" N PHE P 68 " --> pdb=" O VAL P 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.514A pdb=" N VAL A 34 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N ALA A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.846A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.977A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.035A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.667A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.546A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.904A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.821A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.649A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.906A pdb=" N ARG H 98 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 7.045A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1337 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: 2.71 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3013 1.34 - 1.46: 2216 1.46 - 1.58: 4271 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 9588 Sorted by residual: bond pdb=" C ASN U 2 " pdb=" N PRO U 3 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.70e+00 bond pdb=" C ASP H 74 " pdb=" N PRO H 75 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.28e-02 6.10e+03 3.26e+00 bond pdb=" C PHE P 236 " pdb=" N PRO P 237 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.08e+00 bond pdb=" C LEU P 316 " pdb=" N PRO P 317 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.19e-02 7.06e+03 3.02e+00 bond pdb=" CA ASN U 2 " pdb=" C ASN U 2 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.32e+00 ... (remaining 9583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 12490 1.76 - 3.51: 410 3.51 - 5.27: 63 5.27 - 7.03: 13 7.03 - 8.78: 11 Bond angle restraints: 12987 Sorted by residual: angle pdb=" CA ARG H 218 " pdb=" CB ARG H 218 " pdb=" CG ARG H 218 " ideal model delta sigma weight residual 114.10 122.59 -8.49 2.00e+00 2.50e-01 1.80e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 124.31 131.01 -6.70 1.67e+00 3.59e-01 1.61e+01 angle pdb=" CA ARG A 210 " pdb=" CB ARG A 210 " pdb=" CG ARG A 210 " ideal model delta sigma weight residual 114.10 120.98 -6.88 2.00e+00 2.50e-01 1.18e+01 angle pdb=" C ARG A 209 " pdb=" N ARG A 210 " pdb=" CA ARG A 210 " ideal model delta sigma weight residual 122.68 127.54 -4.86 1.47e+00 4.63e-01 1.09e+01 angle pdb=" C GLU A 237 " pdb=" N ASP A 238 " pdb=" CA ASP A 238 " ideal model delta sigma weight residual 123.47 128.46 -4.99 1.53e+00 4.27e-01 1.06e+01 ... (remaining 12982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 5462 15.03 - 30.06: 154 30.06 - 45.08: 47 45.08 - 60.11: 1 60.11 - 75.14: 3 Dihedral angle restraints: 5667 sinusoidal: 2223 harmonic: 3444 Sorted by residual: dihedral pdb=" CB CYS P 184 " pdb=" SG CYS P 184 " pdb=" SG CYS P 254 " pdb=" CB CYS P 254 " ideal model delta sinusoidal sigma weight residual 93.00 124.78 -31.78 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA SER A 310 " pdb=" C SER A 310 " pdb=" N LYS A 311 " pdb=" CA LYS A 311 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1045 0.047 - 0.095: 300 0.095 - 0.142: 85 0.142 - 0.189: 23 0.189 - 0.236: 4 Chirality restraints: 1457 Sorted by residual: chirality pdb=" CG LEU H 174 " pdb=" CB LEU H 174 " pdb=" CD1 LEU H 174 " pdb=" CD2 LEU H 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB THR B 223 " pdb=" CA THR B 223 " pdb=" OG1 THR B 223 " pdb=" CG2 THR B 223 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE A 185 " pdb=" CA ILE A 185 " pdb=" CG1 ILE A 185 " pdb=" CG2 ILE A 185 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1454 not shown) Planarity restraints: 1649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL P 314 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C VAL P 314 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL P 314 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU P 315 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 191 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C ARG H 191 " 0.046 2.00e-02 2.50e+03 pdb=" O ARG H 191 " -0.017 2.00e-02 2.50e+03 pdb=" N MET H 192 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO B 236 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.031 5.00e-02 4.00e+02 ... (remaining 1646 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2077 2.80 - 3.32: 8259 3.32 - 3.85: 14810 3.85 - 4.37: 16991 4.37 - 4.90: 30308 Nonbonded interactions: 72445 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASN A 270 " pdb=" OG1 THR A 324 " model vdw 2.309 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.329 3.040 nonbonded pdb=" OD1 ASN P 120 " pdb=" OG SER P 349 " model vdw 2.336 3.040 nonbonded pdb=" O THR P 298 " pdb=" NE2 GLN P 304 " model vdw 2.344 3.120 ... (remaining 72440 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=0.49 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: 0.890 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.980 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9592 Z= 0.201 Angle : 0.790 8.784 12995 Z= 0.457 Chirality : 0.051 0.236 1457 Planarity : 0.006 0.056 1649 Dihedral : 8.381 75.139 3433 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.10 % Allowed : 0.98 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.24 (0.22), residues: 1167 helix: -0.11 (0.22), residues: 419 sheet: -0.62 (0.29), residues: 287 loop : -1.51 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 111 HIS 0.016 0.001 HIS H 35 PHE 0.025 0.003 PHE A 190 TYR 0.020 0.002 TYR H 175 ARG 0.006 0.000 ARG P 223 Details of bonding type rmsd hydrogen bonds : bond 0.13452 ( 468) hydrogen bonds : angle 6.13878 ( 1337) SS BOND : bond 0.00461 ( 4) SS BOND : angle 2.67120 ( 8) covalent geometry : bond 0.00356 ( 9588) covalent geometry : angle 0.78700 (12987) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 265 ASP cc_start: 0.8104 (t70) cc_final: 0.7902 (t70) REVERT: P 305 TYR cc_start: 0.5611 (m-80) cc_final: 0.5388 (m-80) REVERT: P 372 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7507 (mmtt) REVERT: P 379 ASP cc_start: 0.8018 (t0) cc_final: 0.7813 (t0) REVERT: A 44 SER cc_start: 0.7860 (t) cc_final: 0.7650 (m) REVERT: A 232 ASP cc_start: 0.8365 (m-30) cc_final: 0.7949 (m-30) REVERT: A 298 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8053 (mp0) REVERT: B 205 ASP cc_start: 0.7717 (p0) cc_final: 0.7465 (p0) REVERT: H 80 PHE cc_start: 0.8193 (m-80) cc_final: 0.7931 (m-80) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 1.1192 time to fit residues: 358.5262 Evaluate side-chains 187 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.0050 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 69 ASN P 106 GLN P 198 ASN P 251 ASN U 24 GLN A 189 HIS B 44 GLN B 259 GLN H 194 ASN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109723 restraints weight = 16262.962| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.68 r_work: 0.3153 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9592 Z= 0.190 Angle : 0.621 8.467 12995 Z= 0.328 Chirality : 0.044 0.189 1457 Planarity : 0.005 0.047 1649 Dihedral : 4.202 23.227 1290 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.70 % Allowed : 12.13 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.66 (0.24), residues: 1167 helix: 2.00 (0.24), residues: 424 sheet: -0.11 (0.28), residues: 291 loop : -0.63 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 111 HIS 0.007 0.002 HIS B 142 PHE 0.020 0.002 PHE A 190 TYR 0.022 0.002 TYR A 231 ARG 0.006 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 468) hydrogen bonds : angle 4.55500 ( 1337) SS BOND : bond 0.01832 ( 4) SS BOND : angle 1.14313 ( 8) covalent geometry : bond 0.00451 ( 9588) covalent geometry : angle 0.62057 (12987) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 1.093 Fit side-chains REVERT: P 205 GLU cc_start: 0.7858 (tp30) cc_final: 0.7604 (tt0) REVERT: P 215 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6451 (tpt) REVERT: P 365 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7463 (mt-10) REVERT: P 372 LYS cc_start: 0.7788 (mtpt) cc_final: 0.6955 (mmtt) REVERT: U 24 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7484 (tp40) REVERT: A 44 SER cc_start: 0.8347 (t) cc_final: 0.7755 (m) REVERT: A 229 SER cc_start: 0.8151 (t) cc_final: 0.7923 (m) REVERT: A 298 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7514 (tp30) REVERT: A 314 SER cc_start: 0.8458 (m) cc_final: 0.8128 (t) REVERT: A 341 ASP cc_start: 0.8147 (m-30) cc_final: 0.7930 (m-30) REVERT: B 150 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8451 (mmt90) REVERT: G 20 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7874 (mtmm) REVERT: H 6 GLU cc_start: 0.8053 (mp0) cc_final: 0.7789 (mp0) REVERT: H 80 PHE cc_start: 0.8642 (m-80) cc_final: 0.8172 (m-80) REVERT: H 85 SER cc_start: 0.8445 (m) cc_final: 0.8098 (t) REVERT: H 160 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7579 (ttm-80) REVERT: H 208 SER cc_start: 0.7606 (t) cc_final: 0.7376 (m) outliers start: 48 outliers final: 16 residues processed: 225 average time/residue: 1.2129 time to fit residues: 291.8835 Evaluate side-chains 183 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 303 ILE Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.101275 restraints weight = 11815.893| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.31 r_work: 0.3037 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9592 Z= 0.213 Angle : 0.612 8.699 12995 Z= 0.322 Chirality : 0.044 0.190 1457 Planarity : 0.005 0.048 1649 Dihedral : 4.255 18.249 1290 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.79 % Allowed : 14.29 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.99 (0.24), residues: 1167 helix: 2.35 (0.25), residues: 421 sheet: -0.01 (0.28), residues: 284 loop : -0.45 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 111 HIS 0.006 0.002 HIS B 183 PHE 0.016 0.002 PHE H 110 TYR 0.031 0.002 TYR H 94 ARG 0.003 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 468) hydrogen bonds : angle 4.50308 ( 1337) SS BOND : bond 0.00960 ( 4) SS BOND : angle 1.02236 ( 8) covalent geometry : bond 0.00512 ( 9588) covalent geometry : angle 0.61119 (12987) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 163 time to evaluate : 1.247 Fit side-chains REVERT: P 175 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7719 (mm-30) REVERT: P 178 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7419 (mm-30) REVERT: P 215 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.6878 (tpt) REVERT: P 372 LYS cc_start: 0.7632 (mtpt) cc_final: 0.6803 (mmtt) REVERT: A 298 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7416 (tp30) REVERT: B 46 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8104 (mtp-110) REVERT: B 130 GLU cc_start: 0.8449 (mp0) cc_final: 0.8027 (mp0) REVERT: B 150 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8375 (mmt90) REVERT: G 46 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8342 (tppt) REVERT: H 85 SER cc_start: 0.8737 (m) cc_final: 0.8322 (t) REVERT: H 160 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7511 (ttm-80) REVERT: H 201 ASP cc_start: 0.8342 (p0) cc_final: 0.7993 (t0) outliers start: 49 outliers final: 23 residues processed: 189 average time/residue: 1.4370 time to fit residues: 289.9252 Evaluate side-chains 168 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 111 optimal weight: 0.0270 chunk 60 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 ASN A 295 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.147018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.101595 restraints weight = 20611.669| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.97 r_work: 0.3037 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9592 Z= 0.110 Angle : 0.493 7.937 12995 Z= 0.261 Chirality : 0.040 0.155 1457 Planarity : 0.004 0.044 1649 Dihedral : 3.857 16.567 1290 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.52 % Allowed : 16.93 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.44 (0.25), residues: 1167 helix: 2.96 (0.25), residues: 414 sheet: 0.26 (0.29), residues: 280 loop : -0.42 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS P 174 PHE 0.015 0.001 PHE P 256 TYR 0.021 0.001 TYR A 231 ARG 0.003 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 468) hydrogen bonds : angle 4.12955 ( 1337) SS BOND : bond 0.00466 ( 4) SS BOND : angle 0.65409 ( 8) covalent geometry : bond 0.00245 ( 9588) covalent geometry : angle 0.49263 (12987) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.063 Fit side-chains REVERT: P 175 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7727 (mm-30) REVERT: P 215 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.6699 (tpt) REVERT: P 372 LYS cc_start: 0.7549 (mtpt) cc_final: 0.6667 (mmmt) REVERT: A 44 SER cc_start: 0.8539 (t) cc_final: 0.8154 (p) REVERT: A 277 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7043 (mt-10) REVERT: A 278 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7938 (ptmt) REVERT: A 298 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7324 (tp30) REVERT: B 52 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8414 (ptp-170) REVERT: B 101 MET cc_start: 0.9308 (mtp) cc_final: 0.9055 (mtm) REVERT: B 130 GLU cc_start: 0.8253 (mp0) cc_final: 0.7752 (mp0) REVERT: B 150 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8418 (mmt90) REVERT: B 197 ARG cc_start: 0.8124 (mmt180) cc_final: 0.7822 (mmm160) REVERT: B 234 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8902 (t80) REVERT: G 46 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8294 (tppt) REVERT: H 80 PHE cc_start: 0.8543 (m-80) cc_final: 0.8049 (m-80) REVERT: H 85 SER cc_start: 0.8742 (m) cc_final: 0.8332 (t) REVERT: H 160 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7291 (ttm-80) REVERT: H 192 MET cc_start: 0.8630 (ptm) cc_final: 0.8328 (ppp) REVERT: H 201 ASP cc_start: 0.8278 (p0) cc_final: 0.7917 (t0) outliers start: 36 outliers final: 15 residues processed: 180 average time/residue: 1.2633 time to fit residues: 243.2623 Evaluate side-chains 167 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 208 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 111 optimal weight: 0.0170 chunk 13 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 120 ASN P 198 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN H 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.099200 restraints weight = 12561.012| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.35 r_work: 0.2990 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9592 Z= 0.212 Angle : 0.584 8.500 12995 Z= 0.308 Chirality : 0.043 0.162 1457 Planarity : 0.004 0.043 1649 Dihedral : 4.186 18.163 1290 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.40 % Allowed : 16.14 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.33 (0.25), residues: 1167 helix: 2.76 (0.25), residues: 415 sheet: 0.22 (0.29), residues: 288 loop : -0.40 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 111 HIS 0.005 0.002 HIS B 142 PHE 0.015 0.002 PHE H 110 TYR 0.020 0.002 TYR A 231 ARG 0.003 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04724 ( 468) hydrogen bonds : angle 4.35590 ( 1337) SS BOND : bond 0.00833 ( 4) SS BOND : angle 0.93034 ( 8) covalent geometry : bond 0.00514 ( 9588) covalent geometry : angle 0.58377 (12987) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 1.145 Fit side-chains REVERT: P 175 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7825 (mm-30) REVERT: P 178 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: P 215 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7082 (tpt) REVERT: P 250 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: P 372 LYS cc_start: 0.7738 (mtpt) cc_final: 0.6863 (mmtt) REVERT: A 44 SER cc_start: 0.8656 (t) cc_final: 0.8249 (p) REVERT: A 246 GLU cc_start: 0.8158 (tt0) cc_final: 0.7446 (tp30) REVERT: A 261 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8567 (pp) REVERT: A 273 ASP cc_start: 0.7756 (p0) cc_final: 0.7060 (p0) REVERT: A 277 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7014 (mm-30) REVERT: A 278 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7929 (ptmt) REVERT: A 298 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7397 (tp30) REVERT: A 332 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7937 (mt) REVERT: B 130 GLU cc_start: 0.8425 (mp0) cc_final: 0.7954 (mp0) REVERT: B 132 ASN cc_start: 0.7812 (t0) cc_final: 0.7064 (p0) REVERT: B 150 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8422 (mmt90) REVERT: G 46 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8344 (tppt) REVERT: H 85 SER cc_start: 0.8753 (m) cc_final: 0.8314 (t) REVERT: H 145 SER cc_start: 0.7360 (OUTLIER) cc_final: 0.7017 (t) REVERT: H 160 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7377 (ttm-80) REVERT: H 192 MET cc_start: 0.8770 (ptm) cc_final: 0.8436 (ppp) REVERT: H 201 ASP cc_start: 0.8341 (p0) cc_final: 0.7974 (t0) outliers start: 45 outliers final: 24 residues processed: 183 average time/residue: 1.3046 time to fit residues: 254.2549 Evaluate side-chains 168 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 263 LEU Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 101 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 92 optimal weight: 0.0770 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 70 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 152 HIS P 170 GLN P 177 HIS P 198 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 295 ASN B 6 GLN B 44 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.147147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102552 restraints weight = 20332.812| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.91 r_work: 0.3033 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9592 Z= 0.093 Angle : 0.482 8.521 12995 Z= 0.251 Chirality : 0.039 0.147 1457 Planarity : 0.003 0.038 1649 Dihedral : 3.750 16.799 1290 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.74 % Allowed : 18.10 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.59 (0.25), residues: 1167 helix: 3.15 (0.25), residues: 414 sheet: 0.36 (0.29), residues: 274 loop : -0.40 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS P 174 PHE 0.015 0.001 PHE P 256 TYR 0.011 0.001 TYR H 59 ARG 0.004 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 468) hydrogen bonds : angle 4.01732 ( 1337) SS BOND : bond 0.00357 ( 4) SS BOND : angle 0.44891 ( 8) covalent geometry : bond 0.00195 ( 9588) covalent geometry : angle 0.48188 (12987) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.974 Fit side-chains REVERT: P 175 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7737 (mm-30) REVERT: P 215 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.6848 (tpt) REVERT: P 372 LYS cc_start: 0.7556 (mtpt) cc_final: 0.6656 (mmmt) REVERT: A 44 SER cc_start: 0.8471 (t) cc_final: 0.8065 (p) REVERT: A 273 ASP cc_start: 0.7724 (p0) cc_final: 0.7437 (p0) REVERT: A 277 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7059 (mt-10) REVERT: A 278 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7848 (ptmt) REVERT: A 295 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7381 (t0) REVERT: A 298 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7309 (tp30) REVERT: A 332 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7707 (mt) REVERT: B 46 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7803 (mtp-110) REVERT: B 130 GLU cc_start: 0.8314 (mp0) cc_final: 0.7940 (mp0) REVERT: B 132 ASN cc_start: 0.7597 (t0) cc_final: 0.6932 (p0) REVERT: B 197 ARG cc_start: 0.8093 (mmt180) cc_final: 0.7669 (mmm160) REVERT: B 303 ASP cc_start: 0.8654 (p0) cc_final: 0.8366 (p0) REVERT: G 46 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8258 (tppt) REVERT: H 85 SER cc_start: 0.8742 (m) cc_final: 0.8332 (t) REVERT: H 145 SER cc_start: 0.7186 (OUTLIER) cc_final: 0.6871 (t) REVERT: H 160 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7159 (ttm-80) REVERT: H 186 GLN cc_start: 0.8313 (tt0) cc_final: 0.7984 (pt0) REVERT: H 192 MET cc_start: 0.8649 (ptm) cc_final: 0.8385 (ppp) REVERT: H 201 ASP cc_start: 0.8172 (p0) cc_final: 0.7863 (t0) REVERT: H 206 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7754 (t) outliers start: 28 outliers final: 10 residues processed: 166 average time/residue: 1.2581 time to fit residues: 223.0416 Evaluate side-chains 162 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 48 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 chunk 107 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 177 HIS B 44 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.147226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102648 restraints weight = 20613.307| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.92 r_work: 0.3061 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9592 Z= 0.097 Angle : 0.474 8.174 12995 Z= 0.248 Chirality : 0.039 0.146 1457 Planarity : 0.003 0.040 1649 Dihedral : 3.655 16.584 1290 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.84 % Allowed : 18.40 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.71 (0.25), residues: 1167 helix: 3.23 (0.25), residues: 415 sheet: 0.33 (0.29), residues: 282 loop : -0.28 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS P 174 PHE 0.016 0.001 PHE P 256 TYR 0.010 0.001 TYR H 59 ARG 0.003 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 468) hydrogen bonds : angle 3.93679 ( 1337) SS BOND : bond 0.00397 ( 4) SS BOND : angle 0.48601 ( 8) covalent geometry : bond 0.00214 ( 9588) covalent geometry : angle 0.47415 (12987) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.967 Fit side-chains REVERT: P 175 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7714 (mm-30) REVERT: P 215 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.6898 (tpt) REVERT: P 250 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7391 (pt0) REVERT: P 372 LYS cc_start: 0.7637 (mtpt) cc_final: 0.6735 (mmmt) REVERT: A 261 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8419 (pp) REVERT: A 273 ASP cc_start: 0.7724 (p0) cc_final: 0.7415 (p0) REVERT: A 277 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7000 (mt-10) REVERT: A 278 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7823 (ptmt) REVERT: A 295 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7230 (t0) REVERT: A 298 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7264 (tp30) REVERT: A 332 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7681 (mt) REVERT: B 46 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7932 (mtp180) REVERT: B 130 GLU cc_start: 0.8370 (mp0) cc_final: 0.8089 (mp0) REVERT: B 132 ASN cc_start: 0.7697 (t0) cc_final: 0.6875 (p0) REVERT: B 197 ARG cc_start: 0.8128 (mmt180) cc_final: 0.7709 (mmm160) REVERT: H 80 PHE cc_start: 0.8529 (m-80) cc_final: 0.8068 (m-80) REVERT: H 85 SER cc_start: 0.8744 (m) cc_final: 0.8318 (t) REVERT: H 145 SER cc_start: 0.7160 (OUTLIER) cc_final: 0.6849 (t) REVERT: H 160 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7180 (ttm-80) REVERT: H 186 GLN cc_start: 0.8473 (tt0) cc_final: 0.8150 (pt0) REVERT: H 192 MET cc_start: 0.8707 (ptm) cc_final: 0.8448 (ppp) REVERT: H 201 ASP cc_start: 0.8250 (p0) cc_final: 0.7854 (t0) outliers start: 29 outliers final: 14 residues processed: 170 average time/residue: 1.3203 time to fit residues: 238.9562 Evaluate side-chains 170 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 208 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 3.9990 chunk 86 optimal weight: 0.0870 chunk 83 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 113 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 177 HIS P 198 ASN A 52 GLN A 242 ASN A 295 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.104727 restraints weight = 13886.754| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.43 r_work: 0.3091 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9592 Z= 0.095 Angle : 0.471 8.175 12995 Z= 0.244 Chirality : 0.039 0.144 1457 Planarity : 0.003 0.040 1649 Dihedral : 3.575 16.631 1290 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.94 % Allowed : 17.81 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.76 (0.25), residues: 1167 helix: 3.31 (0.25), residues: 415 sheet: 0.35 (0.29), residues: 270 loop : -0.27 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS P 174 PHE 0.016 0.001 PHE P 256 TYR 0.010 0.001 TYR H 59 ARG 0.003 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 468) hydrogen bonds : angle 3.87922 ( 1337) SS BOND : bond 0.00356 ( 4) SS BOND : angle 0.50051 ( 8) covalent geometry : bond 0.00210 ( 9588) covalent geometry : angle 0.47090 (12987) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 1.059 Fit side-chains REVERT: P 178 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7399 (mm-30) REVERT: P 215 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.6937 (tpt) REVERT: P 250 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: P 372 LYS cc_start: 0.7702 (mtpt) cc_final: 0.6799 (mmmt) REVERT: U 27 ARG cc_start: 0.8171 (tmm-80) cc_final: 0.7934 (tmm-80) REVERT: A 261 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8530 (pp) REVERT: A 277 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7498 (mt-10) REVERT: A 278 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7870 (ptmt) REVERT: A 295 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7299 (t0) REVERT: A 298 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7381 (tp30) REVERT: A 332 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7705 (mt) REVERT: B 46 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7911 (mtp180) REVERT: B 132 ASN cc_start: 0.7723 (t0) cc_final: 0.6979 (p0) REVERT: B 197 ARG cc_start: 0.8139 (mmt180) cc_final: 0.7720 (mmm160) REVERT: H 80 PHE cc_start: 0.8561 (m-80) cc_final: 0.8111 (m-80) REVERT: H 85 SER cc_start: 0.8703 (m) cc_final: 0.8320 (t) REVERT: H 145 SER cc_start: 0.7231 (OUTLIER) cc_final: 0.6912 (t) REVERT: H 160 ARG cc_start: 0.7857 (ttp80) cc_final: 0.7249 (ttm-80) REVERT: H 186 GLN cc_start: 0.8489 (tt0) cc_final: 0.8204 (pt0) REVERT: H 192 MET cc_start: 0.8673 (ptm) cc_final: 0.8359 (ppp) REVERT: H 201 ASP cc_start: 0.8220 (p0) cc_final: 0.7835 (t0) REVERT: H 206 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7696 (t) outliers start: 30 outliers final: 17 residues processed: 176 average time/residue: 1.2732 time to fit residues: 239.2181 Evaluate side-chains 175 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 208 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 0.0050 chunk 91 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 242 ASN A 295 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.103146 restraints weight = 19001.268| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.82 r_work: 0.3073 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9592 Z= 0.099 Angle : 0.485 10.676 12995 Z= 0.249 Chirality : 0.039 0.146 1457 Planarity : 0.003 0.040 1649 Dihedral : 3.596 16.710 1290 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.94 % Allowed : 18.69 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.81 (0.25), residues: 1167 helix: 3.30 (0.24), residues: 419 sheet: 0.30 (0.29), residues: 277 loop : -0.17 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS P 174 PHE 0.016 0.001 PHE P 256 TYR 0.010 0.001 TYR H 59 ARG 0.002 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 468) hydrogen bonds : angle 3.88747 ( 1337) SS BOND : bond 0.00380 ( 4) SS BOND : angle 0.49352 ( 8) covalent geometry : bond 0.00224 ( 9588) covalent geometry : angle 0.48484 (12987) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.104 Fit side-chains REVERT: P 109 TYR cc_start: 0.6328 (OUTLIER) cc_final: 0.4649 (p90) REVERT: P 215 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.6895 (tpt) REVERT: P 250 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: P 372 LYS cc_start: 0.7670 (mtpt) cc_final: 0.6768 (mmmt) REVERT: A 29 LYS cc_start: 0.7117 (mtmt) cc_final: 0.6900 (ttmm) REVERT: A 261 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8470 (pp) REVERT: A 277 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7484 (mt-10) REVERT: A 278 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7900 (ptmt) REVERT: A 295 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7438 (t0) REVERT: A 298 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7253 (tp30) REVERT: A 332 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7691 (mt) REVERT: B 46 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7953 (mtp180) REVERT: B 130 GLU cc_start: 0.8397 (mp0) cc_final: 0.8180 (mp0) REVERT: B 132 ASN cc_start: 0.7678 (t0) cc_final: 0.6876 (p0) REVERT: B 150 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8394 (mmt90) REVERT: B 197 ARG cc_start: 0.8120 (mmt180) cc_final: 0.7680 (mmm160) REVERT: G 46 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8253 (tppt) REVERT: H 80 PHE cc_start: 0.8524 (m-80) cc_final: 0.8020 (m-80) REVERT: H 85 SER cc_start: 0.8720 (m) cc_final: 0.8320 (t) REVERT: H 145 SER cc_start: 0.7201 (OUTLIER) cc_final: 0.6882 (t) REVERT: H 160 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7209 (ttm-80) REVERT: H 186 GLN cc_start: 0.8483 (tt0) cc_final: 0.8199 (pt0) REVERT: H 192 MET cc_start: 0.8669 (ptm) cc_final: 0.8420 (ppp) REVERT: H 201 ASP cc_start: 0.8251 (p0) cc_final: 0.7839 (t0) outliers start: 30 outliers final: 17 residues processed: 168 average time/residue: 1.3695 time to fit residues: 245.8115 Evaluate side-chains 179 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 95 optimal weight: 0.0070 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 ASN A 189 HIS A 194 ASN A 242 ASN A 295 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104897 restraints weight = 14215.197| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.49 r_work: 0.3104 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9592 Z= 0.092 Angle : 0.480 10.208 12995 Z= 0.247 Chirality : 0.039 0.145 1457 Planarity : 0.003 0.039 1649 Dihedral : 3.565 16.642 1290 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.64 % Allowed : 18.98 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.85 (0.25), residues: 1167 helix: 3.33 (0.24), residues: 419 sheet: 0.35 (0.29), residues: 275 loop : -0.15 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.009 0.001 HIS P 174 PHE 0.016 0.001 PHE P 256 TYR 0.010 0.001 TYR H 59 ARG 0.002 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 468) hydrogen bonds : angle 3.84891 ( 1337) SS BOND : bond 0.00348 ( 4) SS BOND : angle 0.49855 ( 8) covalent geometry : bond 0.00202 ( 9588) covalent geometry : angle 0.48002 (12987) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.048 Fit side-chains REVERT: P 109 TYR cc_start: 0.6323 (OUTLIER) cc_final: 0.4642 (p90) REVERT: P 215 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.6865 (tpt) REVERT: P 250 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7264 (pt0) REVERT: P 372 LYS cc_start: 0.7613 (mtpt) cc_final: 0.6709 (mmmt) REVERT: U 27 ARG cc_start: 0.8123 (tmm-80) cc_final: 0.7913 (tmm-80) REVERT: A 29 LYS cc_start: 0.7051 (mtmt) cc_final: 0.6848 (ttmm) REVERT: A 196 HIS cc_start: 0.7161 (t-90) cc_final: 0.6847 (t-170) REVERT: A 198 ARG cc_start: 0.8637 (mtp180) cc_final: 0.8249 (mtm-85) REVERT: A 277 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 278 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7882 (ptmt) REVERT: A 295 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7334 (t0) REVERT: A 298 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7222 (tp30) REVERT: A 332 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7654 (mt) REVERT: B 46 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7882 (mtp180) REVERT: B 124 TYR cc_start: 0.9108 (m-80) cc_final: 0.8892 (m-80) REVERT: B 130 GLU cc_start: 0.8350 (mp0) cc_final: 0.8082 (mp0) REVERT: B 132 ASN cc_start: 0.7647 (t0) cc_final: 0.6855 (p0) REVERT: B 150 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8385 (mmt90) REVERT: B 197 ARG cc_start: 0.8087 (mmt180) cc_final: 0.7644 (mmm160) REVERT: G 46 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8227 (tppt) REVERT: H 80 PHE cc_start: 0.8487 (m-80) cc_final: 0.7992 (m-80) REVERT: H 85 SER cc_start: 0.8712 (m) cc_final: 0.8311 (t) REVERT: H 145 SER cc_start: 0.7185 (t) cc_final: 0.6798 (p) REVERT: H 160 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7175 (ttm-80) REVERT: H 186 GLN cc_start: 0.8447 (tt0) cc_final: 0.8176 (pt0) REVERT: H 192 MET cc_start: 0.8624 (ptm) cc_final: 0.8406 (ppp) REVERT: H 201 ASP cc_start: 0.8236 (p0) cc_final: 0.7832 (t0) outliers start: 27 outliers final: 17 residues processed: 169 average time/residue: 1.2533 time to fit residues: 225.9969 Evaluate side-chains 179 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 57 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 242 ASN A 295 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.104587 restraints weight = 13765.016| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.46 r_work: 0.3078 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9592 Z= 0.098 Angle : 0.481 9.863 12995 Z= 0.250 Chirality : 0.039 0.148 1457 Planarity : 0.003 0.039 1649 Dihedral : 3.610 16.775 1290 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.84 % Allowed : 18.88 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.86 (0.25), residues: 1167 helix: 3.33 (0.24), residues: 419 sheet: 0.30 (0.29), residues: 277 loop : -0.10 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.010 0.001 HIS P 174 PHE 0.016 0.001 PHE P 256 TYR 0.010 0.001 TYR H 59 ARG 0.002 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 468) hydrogen bonds : angle 3.85758 ( 1337) SS BOND : bond 0.00385 ( 4) SS BOND : angle 0.53076 ( 8) covalent geometry : bond 0.00216 ( 9588) covalent geometry : angle 0.48119 (12987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11078.01 seconds wall clock time: 192 minutes 14.23 seconds (11534.23 seconds total)