Starting phenix.real_space_refine on Thu Mar 13 15:58:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h2g_34437/03_2025/8h2g_34437.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h2g_34437/03_2025/8h2g_34437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h2g_34437/03_2025/8h2g_34437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h2g_34437/03_2025/8h2g_34437.map" model { file = "/net/cci-nas-00/data/ceres_data/8h2g_34437/03_2025/8h2g_34437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h2g_34437/03_2025/8h2g_34437.cif" } resolution = 3.01 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= 0.059 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 64 5.16 5 C 5756 2.51 5 N 1540 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9023 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2365 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.44, per 1000 atoms: 0.60 Number of scatterers: 9023 At special positions: 0 Unit cell: (88.395, 122.01, 131.97, 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 64 16.00 O 1663 8.00 N 1540 7.00 C 5756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 13 sheets defined 34.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 29 through 54 removed outlier: 4.098A pdb=" N ILE A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 89 removed outlier: 4.013A pdb=" N ARG A 63 " --> pdb=" O TRP A 59 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 131 Processing helix chain 'A' and resid 140 through 158 removed outlier: 3.566A pdb=" N LEU A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.604A pdb=" N LYS A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 187 through 218 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 225 through 261 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 265 through 268 removed outlier: 4.203A pdb=" N VAL A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 269 through 295 removed outlier: 4.060A pdb=" N PHE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.525A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.132A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.668A pdb=" N GLU B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.768A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 352 removed outlier: 4.229A pdb=" N ASN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 removed outlier: 3.520A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.511A pdb=" N THR C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 24 removed outlier: 3.530A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 190 removed outlier: 9.225A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 52 removed outlier: 4.335A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.918A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.744A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.703A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.629A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.460A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.515A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.525A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.548A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.629A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1215 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: 2.53 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2913 1.35 - 1.47: 2298 1.47 - 1.59: 3917 1.59 - 1.71: 0 1.71 - 1.83: 92 Bond restraints: 9220 Sorted by residual: bond pdb=" C2 NIO A 401 " pdb=" C3 NIO A 401 " ideal model delta sigma weight residual 1.390 1.351 0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" C3 NIO A 401 " pdb=" C4 NIO A 401 " ideal model delta sigma weight residual 1.386 1.353 0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C ILE A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.335 1.357 -0.021 1.36e-02 5.41e+03 2.49e+00 bond pdb=" CB GLU E 89 " pdb=" CG GLU E 89 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CG ARG B 32 " pdb=" CD ARG B 32 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.27e+00 ... (remaining 9215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12306 1.95 - 3.89: 136 3.89 - 5.84: 26 5.84 - 7.79: 6 7.79 - 9.73: 2 Bond angle restraints: 12476 Sorted by residual: angle pdb=" C ASP A 97 " pdb=" N ILE A 98 " pdb=" CA ILE A 98 " ideal model delta sigma weight residual 120.24 122.61 -2.37 6.30e-01 2.52e+00 1.41e+01 angle pdb=" C ILE A 98 " pdb=" CA ILE A 98 " pdb=" CB ILE A 98 " ideal model delta sigma weight residual 114.35 110.94 3.41 1.06e+00 8.90e-01 1.04e+01 angle pdb=" CA TRP A 256 " pdb=" CB TRP A 256 " pdb=" CG TRP A 256 " ideal model delta sigma weight residual 113.60 119.62 -6.02 1.90e+00 2.77e-01 1.01e+01 angle pdb=" CB GLU E 89 " pdb=" CG GLU E 89 " pdb=" CD GLU E 89 " ideal model delta sigma weight residual 112.60 117.35 -4.75 1.70e+00 3.46e-01 7.79e+00 angle pdb=" CA LEU A 195 " pdb=" CB LEU A 195 " pdb=" CG LEU A 195 " ideal model delta sigma weight residual 116.30 126.03 -9.73 3.50e+00 8.16e-02 7.73e+00 ... (remaining 12471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4656 17.92 - 35.83: 625 35.83 - 53.75: 154 53.75 - 71.67: 20 71.67 - 89.58: 8 Dihedral angle restraints: 5463 sinusoidal: 2146 harmonic: 3317 Sorted by residual: dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 177 " pdb=" CB CYS A 177 " ideal model delta sinusoidal sigma weight residual -86.00 -156.72 70.72 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CA LEU B 268 " pdb=" C LEU B 268 " pdb=" N ASN B 269 " pdb=" CA ASN B 269 " ideal model delta harmonic sigma weight residual 180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual -86.00 -118.16 32.16 1 1.00e+01 1.00e-02 1.47e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 887 0.031 - 0.062: 331 0.062 - 0.093: 107 0.093 - 0.124: 63 0.124 - 0.155: 12 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CB ILE A 78 " pdb=" CA ILE A 78 " pdb=" CG1 ILE A 78 " pdb=" CG2 ILE A 78 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CG LEU A 195 " pdb=" CB LEU A 195 " pdb=" CD1 LEU A 195 " pdb=" CD2 LEU A 195 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ASN A 171 " pdb=" N ASN A 171 " pdb=" C ASN A 171 " pdb=" CB ASN A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1397 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 171 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C ASN A 171 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN A 171 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 172 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 199 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO A 200 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 192 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C MET E 192 " -0.029 2.00e-02 2.50e+03 pdb=" O MET E 192 " 0.011 2.00e-02 2.50e+03 pdb=" N SER E 193 " 0.010 2.00e-02 2.50e+03 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 184 2.68 - 3.23: 8546 3.23 - 3.79: 13875 3.79 - 4.34: 18792 4.34 - 4.90: 32064 Nonbonded interactions: 73461 Sorted by model distance: nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.123 3.040 nonbonded pdb=" CB SER A 298 " pdb=" O GLY B 352 " model vdw 2.153 3.440 nonbonded pdb=" O ASN A 171 " pdb=" ND2 ASN A 171 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.226 3.040 nonbonded pdb=" O SER E 52 " pdb=" NH1 ARG E 72 " model vdw 2.246 3.120 ... (remaining 73456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.390 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 27.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.003 0.041 9220 Z= 0.202 Angle : 0.567 9.733 12476 Z= 0.299 Chirality : 0.042 0.155 1400 Planarity : 0.004 0.047 1580 Dihedral : 16.846 89.584 3304 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.61 % Allowed : 29.29 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1131 helix: 1.59 (0.28), residues: 377 sheet: -0.23 (0.34), residues: 264 loop : -0.99 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 93 HIS 0.004 0.001 HIS A 184 PHE 0.021 0.001 PHE A 95 TYR 0.021 0.001 TYR B 302 ARG 0.015 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.6779 (m) cc_final: 0.6543 (m) REVERT: A 154 ILE cc_start: 0.7938 (mt) cc_final: 0.7725 (mt) outliers start: 6 outliers final: 3 residues processed: 155 average time/residue: 0.2424 time to fit residues: 52.2013 Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 38 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 131 HIS A 171 ASN A 223 HIS B 322 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.197083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.158326 restraints weight = 10216.228| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.61 r_work: 0.3384 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 9220 Z= 0.588 Angle : 0.824 11.241 12476 Z= 0.426 Chirality : 0.053 0.211 1400 Planarity : 0.007 0.171 1580 Dihedral : 5.259 31.861 1241 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 7.65 % Allowed : 24.18 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.34 (0.25), residues: 1131 helix: 1.33 (0.28), residues: 370 sheet: -0.52 (0.32), residues: 277 loop : -1.25 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 93 HIS 0.009 0.002 HIS E 35 PHE 0.026 0.003 PHE A 105 TYR 0.021 0.003 TYR E 190 ARG 0.032 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 134 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.6748 (OUTLIER) cc_final: 0.6442 (m) REVERT: A 112 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: A 120 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8208 (t) REVERT: A 187 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6686 (pt0) REVERT: A 272 VAL cc_start: 0.7045 (OUTLIER) cc_final: 0.6800 (p) REVERT: B 255 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.6986 (p0) REVERT: B 285 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7313 (pt) REVERT: C 44 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6766 (mp10) REVERT: C 51 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8241 (mt) REVERT: C 251 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8030 (mtt-85) outliers start: 75 outliers final: 41 residues processed: 190 average time/residue: 0.1993 time to fit residues: 53.5782 Evaluate side-chains 178 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 0.9980 chunk 86 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS A 68 ASN A 110 ASN A 223 HIS B 244 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.203437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.165751 restraints weight = 10372.071| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.58 r_work: 0.3444 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9220 Z= 0.168 Angle : 0.557 6.731 12476 Z= 0.296 Chirality : 0.042 0.154 1400 Planarity : 0.004 0.073 1580 Dihedral : 4.470 21.075 1236 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.18 % Allowed : 27.04 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.02 (0.25), residues: 1131 helix: 1.69 (0.28), residues: 378 sheet: -0.37 (0.31), residues: 267 loop : -1.15 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS C 311 PHE 0.012 0.001 PHE B 334 TYR 0.016 0.001 TYR B 302 ARG 0.010 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 120 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8041 (t) REVERT: A 187 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6655 (pt0) REVERT: A 272 VAL cc_start: 0.6934 (m) cc_final: 0.6695 (p) REVERT: A 285 MET cc_start: 0.7347 (mtt) cc_final: 0.6958 (mtt) REVERT: B 249 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7191 (tt) REVERT: C 44 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: C 234 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: C 316 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8212 (p) REVERT: E 89 GLU cc_start: 0.7306 (pp20) cc_final: 0.6897 (pp20) REVERT: E 189 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7904 (mt) outliers start: 41 outliers final: 19 residues processed: 169 average time/residue: 0.2077 time to fit residues: 49.7703 Evaluate side-chains 152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.200570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.154590 restraints weight = 10305.103| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.28 r_work: 0.3454 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9220 Z= 0.248 Angle : 0.591 7.468 12476 Z= 0.309 Chirality : 0.044 0.154 1400 Planarity : 0.004 0.068 1580 Dihedral : 4.486 22.374 1236 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 6.43 % Allowed : 25.20 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.05 (0.25), residues: 1131 helix: 1.66 (0.28), residues: 378 sheet: -0.41 (0.30), residues: 268 loop : -1.15 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 93 HIS 0.005 0.001 HIS E 35 PHE 0.017 0.002 PHE A 38 TYR 0.016 0.002 TYR B 302 ARG 0.013 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 130 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7235 (tt0) REVERT: A 120 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8176 (t) REVERT: A 187 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6645 (pt0) REVERT: A 272 VAL cc_start: 0.7011 (OUTLIER) cc_final: 0.6731 (p) REVERT: A 285 MET cc_start: 0.7447 (mtt) cc_final: 0.7229 (mtp) REVERT: B 285 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7245 (pt) REVERT: C 44 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6765 (mp10) REVERT: C 234 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: C 316 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8279 (p) REVERT: E 234 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7420 (mm-30) outliers start: 63 outliers final: 44 residues processed: 177 average time/residue: 0.1983 time to fit residues: 49.7552 Evaluate side-chains 178 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 126 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 0.0060 chunk 14 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.203117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.156606 restraints weight = 10280.165| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.18 r_work: 0.3515 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9220 Z= 0.194 Angle : 0.556 9.340 12476 Z= 0.290 Chirality : 0.042 0.160 1400 Planarity : 0.004 0.041 1580 Dihedral : 4.331 22.574 1236 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 6.33 % Allowed : 25.31 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1131 helix: 1.72 (0.28), residues: 380 sheet: -0.35 (0.30), residues: 267 loop : -1.11 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 93 HIS 0.004 0.001 HIS E 35 PHE 0.010 0.001 PHE A 127 TYR 0.019 0.001 TYR B 302 ARG 0.010 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 132 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7287 (tt0) REVERT: A 120 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8178 (t) REVERT: A 272 VAL cc_start: 0.7106 (OUTLIER) cc_final: 0.6804 (p) REVERT: B 10 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7234 (mtmm) REVERT: B 195 HIS cc_start: 0.7811 (t-170) cc_final: 0.7444 (t-170) REVERT: B 249 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7160 (tt) REVERT: C 234 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8486 (m-80) REVERT: C 316 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8292 (p) REVERT: C 336 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7920 (mp) REVERT: E 189 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7991 (mt) REVERT: E 234 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7381 (mm-30) outliers start: 62 outliers final: 41 residues processed: 178 average time/residue: 0.1945 time to fit residues: 49.2341 Evaluate side-chains 179 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.200012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.161576 restraints weight = 10256.097| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.57 r_work: 0.3452 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9220 Z= 0.288 Angle : 0.612 9.258 12476 Z= 0.317 Chirality : 0.044 0.164 1400 Planarity : 0.004 0.042 1580 Dihedral : 4.523 23.659 1236 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 7.55 % Allowed : 25.00 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.08 (0.25), residues: 1131 helix: 1.67 (0.28), residues: 378 sheet: -0.48 (0.30), residues: 273 loop : -1.18 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 93 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.002 PHE A 38 TYR 0.021 0.002 TYR B 302 ARG 0.008 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 132 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: A 120 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8191 (t) REVERT: A 187 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6592 (pt0) REVERT: A 272 VAL cc_start: 0.7057 (OUTLIER) cc_final: 0.6730 (p) REVERT: A 285 MET cc_start: 0.7075 (mtp) cc_final: 0.6833 (mtp) REVERT: B 10 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7312 (ttmp) REVERT: B 53 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5873 (mpt) REVERT: B 195 HIS cc_start: 0.7825 (t-170) cc_final: 0.7456 (t-170) REVERT: B 255 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.6925 (p0) REVERT: B 285 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7240 (pt) REVERT: C 44 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6720 (mp10) REVERT: C 234 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: C 336 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7905 (mp) REVERT: E 234 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7349 (mm-30) outliers start: 74 outliers final: 50 residues processed: 186 average time/residue: 0.1939 time to fit residues: 51.0274 Evaluate side-chains 191 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 129 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 57 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.201355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.163682 restraints weight = 10393.342| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.64 r_work: 0.3474 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9220 Z= 0.180 Angle : 0.550 8.175 12476 Z= 0.287 Chirality : 0.042 0.168 1400 Planarity : 0.004 0.042 1580 Dihedral : 4.289 24.103 1236 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 6.33 % Allowed : 25.71 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.08 (0.25), residues: 1131 helix: 1.82 (0.28), residues: 377 sheet: -0.35 (0.30), residues: 262 loop : -1.11 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS C 91 PHE 0.018 0.001 PHE B 334 TYR 0.019 0.001 TYR B 302 ARG 0.006 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 141 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.6304 (mm) cc_final: 0.5822 (tp) REVERT: A 112 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7162 (tt0) REVERT: A 120 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8159 (t) REVERT: A 187 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6556 (pt0) REVERT: A 222 ARG cc_start: 0.7606 (mpp80) cc_final: 0.7258 (mpp80) REVERT: A 272 VAL cc_start: 0.7040 (OUTLIER) cc_final: 0.6695 (p) REVERT: B 10 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7179 (mtmm) REVERT: B 195 HIS cc_start: 0.7621 (t-170) cc_final: 0.7242 (t-170) REVERT: B 249 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7206 (tt) REVERT: B 285 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7221 (pt) REVERT: C 234 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: C 332 TRP cc_start: 0.8139 (m-10) cc_final: 0.7901 (m-10) REVERT: E 189 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7917 (mt) REVERT: E 234 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7219 (mm-30) outliers start: 62 outliers final: 45 residues processed: 187 average time/residue: 0.1990 time to fit residues: 52.8682 Evaluate side-chains 190 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 136 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 0.0870 chunk 106 optimal weight: 0.2980 chunk 59 optimal weight: 0.3980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.204516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.157788 restraints weight = 10373.409| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.24 r_work: 0.3580 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9220 Z= 0.156 Angle : 0.543 8.702 12476 Z= 0.281 Chirality : 0.042 0.154 1400 Planarity : 0.003 0.043 1580 Dihedral : 4.159 22.843 1236 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.61 % Allowed : 25.82 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.08 (0.25), residues: 1131 helix: 1.80 (0.27), residues: 380 sheet: -0.37 (0.30), residues: 264 loop : -1.11 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.024 0.001 PHE A 38 TYR 0.018 0.001 TYR B 302 ARG 0.004 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 102 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5834 (tp) REVERT: A 112 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: A 120 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8138 (t) REVERT: A 187 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6836 (pt0) REVERT: A 222 ARG cc_start: 0.7648 (mpp80) cc_final: 0.7220 (mpp80) REVERT: A 272 VAL cc_start: 0.7012 (OUTLIER) cc_final: 0.6664 (p) REVERT: B 10 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7280 (mtmm) REVERT: B 32 ARG cc_start: 0.8009 (ptp-110) cc_final: 0.7625 (mtm110) REVERT: B 195 HIS cc_start: 0.7540 (t-170) cc_final: 0.7076 (t-170) REVERT: B 209 LYS cc_start: 0.8274 (pttm) cc_final: 0.7859 (ptpt) REVERT: B 249 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6980 (tt) REVERT: B 285 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.7180 (pt) REVERT: B 334 PHE cc_start: 0.7670 (t80) cc_final: 0.7429 (t80) REVERT: C 234 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: C 332 TRP cc_start: 0.8149 (m-10) cc_final: 0.7891 (m-10) REVERT: D 47 GLU cc_start: 0.6894 (mp0) cc_final: 0.6652 (mt-10) REVERT: E 18 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7256 (tpp80) REVERT: E 189 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7983 (mt) outliers start: 55 outliers final: 38 residues processed: 176 average time/residue: 0.2147 time to fit residues: 54.6426 Evaluate side-chains 185 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 19 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 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 223 HIS B 255 ASN ** C 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 = 0.4201 r_free = 0.4201 target = 0.203227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.166021 restraints weight = 10277.606| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.63 r_work: 0.3508 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9220 Z= 0.178 Angle : 0.560 8.935 12476 Z= 0.288 Chirality : 0.042 0.161 1400 Planarity : 0.004 0.041 1580 Dihedral : 4.171 22.720 1236 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 6.22 % Allowed : 25.31 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.08 (0.25), residues: 1131 helix: 1.77 (0.27), residues: 380 sheet: -0.38 (0.30), residues: 269 loop : -1.06 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 188 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 38 TYR 0.019 0.001 TYR B 302 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 133 time to evaluate : 1.783 Fit side-chains revert: symmetry clash REVERT: A 102 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.5922 (tp) REVERT: A 112 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: A 120 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8193 (t) REVERT: A 187 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6985 (pt0) REVERT: A 222 ARG cc_start: 0.7649 (mpp80) cc_final: 0.7271 (mpp80) REVERT: A 272 VAL cc_start: 0.7002 (OUTLIER) cc_final: 0.6645 (p) REVERT: B 10 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7247 (mtmm) REVERT: B 32 ARG cc_start: 0.8028 (ptp-110) cc_final: 0.7688 (mtm110) REVERT: B 195 HIS cc_start: 0.7617 (t-170) cc_final: 0.7208 (t-170) REVERT: B 209 LYS cc_start: 0.8334 (pttm) cc_final: 0.7960 (ptpt) REVERT: B 249 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7133 (tt) REVERT: B 285 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7194 (pt) REVERT: C 234 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: C 316 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8305 (p) REVERT: C 332 TRP cc_start: 0.8148 (m-10) cc_final: 0.7806 (m-10) REVERT: D 32 LYS cc_start: 0.5193 (OUTLIER) cc_final: 0.4976 (tptt) REVERT: D 47 GLU cc_start: 0.6836 (mp0) cc_final: 0.6622 (mt-10) REVERT: E 18 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7083 (ttm170) REVERT: E 189 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7928 (mt) REVERT: E 234 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7282 (mm-30) outliers start: 61 outliers final: 42 residues processed: 177 average time/residue: 0.2590 time to fit residues: 67.4069 Evaluate side-chains 186 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 0.0470 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 255 ASN ** C 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 = 0.4215 r_free = 0.4215 target = 0.204572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167291 restraints weight = 10404.247| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.70 r_work: 0.3494 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9220 Z= 0.166 Angle : 0.553 9.149 12476 Z= 0.285 Chirality : 0.042 0.164 1400 Planarity : 0.004 0.043 1580 Dihedral : 4.154 22.228 1236 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 6.43 % Allowed : 24.90 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.09 (0.25), residues: 1131 helix: 1.77 (0.28), residues: 380 sheet: -0.39 (0.29), residues: 269 loop : -1.03 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 188 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 38 TYR 0.021 0.001 TYR B 302 ARG 0.007 0.000 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 134 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 102 LEU cc_start: 0.6390 (mm) cc_final: 0.5909 (tp) REVERT: A 112 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: A 120 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8178 (t) REVERT: A 187 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6960 (pt0) REVERT: A 222 ARG cc_start: 0.7639 (mpp80) cc_final: 0.7249 (mpp80) REVERT: A 272 VAL cc_start: 0.6991 (OUTLIER) cc_final: 0.6633 (p) REVERT: B 10 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7251 (mtmm) REVERT: B 32 ARG cc_start: 0.8046 (ptp-110) cc_final: 0.7688 (mtm110) REVERT: B 195 HIS cc_start: 0.7597 (t-170) cc_final: 0.7150 (t-170) REVERT: B 209 LYS cc_start: 0.8330 (pttm) cc_final: 0.7952 (ptpt) REVERT: B 249 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7146 (tt) REVERT: B 285 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7186 (pt) REVERT: C 234 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8504 (m-80) REVERT: C 316 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8287 (p) REVERT: C 332 TRP cc_start: 0.8142 (m-10) cc_final: 0.7810 (m-10) REVERT: D 32 LYS cc_start: 0.5180 (OUTLIER) cc_final: 0.4970 (tptt) REVERT: D 47 GLU cc_start: 0.6858 (mp0) cc_final: 0.6657 (mt-10) REVERT: E 18 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7126 (ttm170) REVERT: E 189 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7932 (mt) REVERT: E 234 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7401 (mm-30) outliers start: 63 outliers final: 47 residues processed: 182 average time/residue: 0.1810 time to fit residues: 47.3280 Evaluate side-chains 192 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 132 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 0.0050 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 255 ASN ** C 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 = 0.4199 r_free = 0.4199 target = 0.202973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.155355 restraints weight = 10369.356| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.32 r_work: 0.3532 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9220 Z= 0.190 Angle : 0.562 9.003 12476 Z= 0.290 Chirality : 0.043 0.165 1400 Planarity : 0.004 0.042 1580 Dihedral : 4.186 22.666 1236 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.89 % Favored : 96.02 % Rotamer: Outliers : 6.43 % Allowed : 24.90 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.08 (0.25), residues: 1131 helix: 1.75 (0.28), residues: 381 sheet: -0.42 (0.29), residues: 269 loop : -1.03 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 188 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE A 38 TYR 0.022 0.001 TYR B 302 ARG 0.007 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5370.36 seconds wall clock time: 95 minutes 30.32 seconds (5730.32 seconds total)