Starting phenix.real_space_refine on Mon May 12 13:24:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h2g_34437/05_2025/8h2g_34437.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h2g_34437/05_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_34437/05_2025/8h2g_34437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h2g_34437/05_2025/8h2g_34437.map" model { file = "/net/cci-nas-00/data/ceres_data/8h2g_34437/05_2025/8h2g_34437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h2g_34437/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.37, 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: 2.60 Conformation dependent library (CDL) restraints added in 1.1 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: 1.20 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: 2.59 Time building geometry restraints manager: 2.99 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: 0.450 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.820 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- 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 : 0.004 0.183 9226 Z= 0.234 Angle : 0.570 9.733 12486 Z= 0.300 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 Details of bonding type rmsd hydrogen bonds : bond 0.17411 ( 424) hydrogen bonds : angle 6.93122 ( 1215) SS BOND : bond 0.00653 ( 5) SS BOND : angle 2.05845 ( 10) covalent geometry : bond 0.00312 ( 9220) covalent geometry : angle 0.56683 (12476) Misc. bond : bond 0.18270 ( 1) *********************** 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 : 1.013 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: 0.2055 time to fit residues: 44.3712 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 : 1.015 ------------------------------------------------------------------------------- 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: 0.3383 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- 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 9226 Z= 0.372 Angle : 0.827 11.241 12486 Z= 0.428 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 Details of bonding type rmsd hydrogen bonds : bond 0.05948 ( 424) hydrogen bonds : angle 5.49485 ( 1215) SS BOND : bond 0.01574 ( 5) SS BOND : angle 2.77564 ( 10) covalent geometry : bond 0.00901 ( 9220) covalent geometry : angle 0.82384 (12476) Misc. bond : bond 0.00400 ( 1) *********************** 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 : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.6744 (OUTLIER) cc_final: 0.6437 (m) REVERT: A 112 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: A 120 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8205 (t) REVERT: A 187 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6689 (pt0) REVERT: A 272 VAL cc_start: 0.7044 (OUTLIER) cc_final: 0.6798 (p) REVERT: B 255 ASN cc_start: 0.7869 (OUTLIER) cc_final: 0.6984 (p0) REVERT: B 285 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7313 (pt) REVERT: C 44 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6770 (mp10) REVERT: C 51 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8239 (mt) REVERT: C 251 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8032 (mtt-85) outliers start: 75 outliers final: 41 residues processed: 190 average time/residue: 0.2077 time to fit residues: 56.1350 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 : 0.933 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 223 HIS B 244 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.202779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.164855 restraints weight = 10347.023| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.64 r_work: 0.3460 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9226 Z= 0.129 Angle : 0.562 6.862 12486 Z= 0.298 Chirality : 0.043 0.152 1400 Planarity : 0.004 0.071 1580 Dihedral : 4.485 21.250 1236 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.69 % Allowed : 26.53 % 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: -0.04 (0.25), residues: 1131 helix: 1.66 (0.28), residues: 378 sheet: -0.38 (0.31), residues: 267 loop : -1.17 (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 91 PHE 0.012 0.001 PHE B 334 TYR 0.017 0.001 TYR B 302 ARG 0.011 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 424) hydrogen bonds : angle 4.88815 ( 1215) SS BOND : bond 0.00709 ( 5) SS BOND : angle 1.43031 ( 10) covalent geometry : bond 0.00284 ( 9220) covalent geometry : angle 0.56056 (12476) Misc. bond : bond 0.00194 ( 1) *********************** 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 182 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 120 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8098 (t) REVERT: A 187 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6669 (pt0) REVERT: A 232 PHE cc_start: 0.6304 (m-80) cc_final: 0.6067 (m-80) REVERT: A 272 VAL cc_start: 0.6952 (m) cc_final: 0.6721 (p) REVERT: A 285 MET cc_start: 0.7333 (mtt) cc_final: 0.6896 (mtt) REVERT: B 249 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7203 (tt) REVERT: C 44 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6695 (mp10) REVERT: C 234 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: E 89 GLU cc_start: 0.7313 (pp20) cc_final: 0.6900 (pp20) REVERT: E 189 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7899 (mt) outliers start: 46 outliers final: 24 residues processed: 171 average time/residue: 0.1825 time to fit residues: 44.6062 Evaluate side-chains 156 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 287 SER 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 67 SER Chi-restraints excluded: chain C residue 72 SER 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 243 THR 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 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: 4.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 66 optimal weight: 0.0050 chunk 79 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 111 optimal weight: 0.2980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 223 HIS ** 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 = 0.203167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.157850 restraints weight = 10349.370| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.20 r_work: 0.3540 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9226 Z= 0.117 Angle : 0.541 7.476 12486 Z= 0.284 Chirality : 0.042 0.146 1400 Planarity : 0.004 0.108 1580 Dihedral : 4.276 20.901 1236 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.61 % Allowed : 25.61 % 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: 0.11 (0.25), residues: 1131 helix: 1.82 (0.28), residues: 376 sheet: -0.32 (0.30), residues: 268 loop : -1.08 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 93 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE A 127 TYR 0.015 0.001 TYR B 302 ARG 0.008 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 424) hydrogen bonds : angle 4.65780 ( 1215) SS BOND : bond 0.00954 ( 5) SS BOND : angle 1.25549 ( 10) covalent geometry : bond 0.00260 ( 9220) covalent geometry : angle 0.53969 (12476) Misc. bond : bond 0.00364 ( 1) *********************** 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 191 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 136 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7012 (tt0) REVERT: A 120 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8158 (t) REVERT: A 187 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6688 (pt0) REVERT: A 272 VAL cc_start: 0.6978 (m) cc_final: 0.6697 (p) REVERT: B 249 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7194 (tt) REVERT: C 234 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: D 47 GLU cc_start: 0.6862 (mp0) cc_final: 0.6578 (mt-10) REVERT: E 43 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7784 (tppt) REVERT: E 89 GLU cc_start: 0.7319 (pp20) cc_final: 0.6852 (pp20) REVERT: E 189 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7950 (mt) outliers start: 55 outliers final: 36 residues processed: 176 average time/residue: 0.1873 time to fit residues: 46.8944 Evaluate side-chains 172 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 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 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 284 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 43 LYS 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 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 0.0040 chunk 89 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 overall best weight: 1.0396 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.202993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.164327 restraints weight = 10280.644| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.63 r_work: 0.3501 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9226 Z= 0.144 Angle : 0.570 9.441 12486 Z= 0.297 Chirality : 0.043 0.161 1400 Planarity : 0.004 0.072 1580 Dihedral : 4.323 22.319 1236 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 6.22 % Allowed : 24.69 % Favored : 69.08 % 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: 1.74 (0.28), residues: 379 sheet: -0.36 (0.30), residues: 268 loop : -1.12 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 93 HIS 0.004 0.001 HIS C 91 PHE 0.018 0.001 PHE A 38 TYR 0.018 0.002 TYR B 302 ARG 0.013 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 424) hydrogen bonds : angle 4.61976 ( 1215) SS BOND : bond 0.00804 ( 5) SS BOND : angle 1.43910 ( 10) covalent geometry : bond 0.00334 ( 9220) covalent geometry : angle 0.56889 (12476) Misc. bond : bond 0.00228 ( 1) *********************** 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: 61 poor density : 133 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7196 (tt0) REVERT: A 120 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8190 (t) REVERT: A 222 ARG cc_start: 0.7618 (mpp80) cc_final: 0.7198 (mpp80) REVERT: A 272 VAL cc_start: 0.6959 (OUTLIER) cc_final: 0.6680 (p) REVERT: B 10 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7213 (mtmm) REVERT: B 195 HIS cc_start: 0.7877 (t-170) cc_final: 0.7528 (t-170) REVERT: B 285 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7241 (pt) REVERT: C 44 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6773 (mp10) REVERT: C 234 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: E 43 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7776 (tppt) REVERT: E 234 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7299 (mm-30) outliers start: 61 outliers final: 44 residues processed: 179 average time/residue: 0.1777 time to fit residues: 45.5168 Evaluate side-chains 180 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 43 LYS 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 193 SER Chi-restraints excluded: chain E residue 199 VAL 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: 5.9990 chunk 78 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.0970 chunk 71 optimal weight: 0.0020 chunk 97 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.203893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.157742 restraints weight = 10272.297| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.25 r_work: 0.3510 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9226 Z= 0.114 Angle : 0.537 8.244 12486 Z= 0.280 Chirality : 0.042 0.165 1400 Planarity : 0.004 0.044 1580 Dihedral : 4.167 21.415 1236 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 6.12 % Allowed : 25.61 % Favored : 68.27 % 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: 0.11 (0.25), residues: 1131 helix: 1.81 (0.28), residues: 379 sheet: -0.34 (0.30), residues: 268 loop : -1.07 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.009 0.001 PHE A 197 TYR 0.018 0.001 TYR B 302 ARG 0.010 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 424) hydrogen bonds : angle 4.50994 ( 1215) SS BOND : bond 0.00636 ( 5) SS BOND : angle 1.11653 ( 10) covalent geometry : bond 0.00251 ( 9220) covalent geometry : angle 0.53618 (12476) Misc. bond : bond 0.00153 ( 1) *********************** 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 195 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 135 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5388 (mt) REVERT: A 112 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: A 120 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8135 (t) REVERT: A 187 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6545 (pt0) REVERT: A 222 ARG cc_start: 0.7594 (mpp80) cc_final: 0.7128 (mpp80) REVERT: A 272 VAL cc_start: 0.7073 (OUTLIER) cc_final: 0.6755 (p) REVERT: B 195 HIS cc_start: 0.7594 (t-170) cc_final: 0.7123 (t-170) REVERT: B 249 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7092 (tt) REVERT: C 234 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8452 (m-80) REVERT: E 43 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7763 (tppt) REVERT: E 234 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7292 (mm-30) outliers start: 60 outliers final: 43 residues processed: 177 average time/residue: 0.1819 time to fit residues: 46.5862 Evaluate side-chains 180 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 104 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 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 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 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 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 43 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 57 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 61 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.203826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.157827 restraints weight = 10410.760| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.20 r_work: 0.3503 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9226 Z= 0.119 Angle : 0.546 8.189 12486 Z= 0.283 Chirality : 0.042 0.152 1400 Planarity : 0.004 0.042 1580 Dihedral : 4.142 21.808 1236 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 6.84 % Allowed : 24.80 % 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: 0.11 (0.25), residues: 1131 helix: 1.78 (0.27), residues: 380 sheet: -0.36 (0.30), residues: 270 loop : -1.04 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE A 38 TYR 0.018 0.001 TYR B 302 ARG 0.008 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 424) hydrogen bonds : angle 4.47328 ( 1215) SS BOND : bond 0.00671 ( 5) SS BOND : angle 1.25905 ( 10) covalent geometry : bond 0.00268 ( 9220) covalent geometry : angle 0.54512 (12476) Misc. bond : bond 0.00123 ( 1) *********************** 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: 67 poor density : 136 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: A 120 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8140 (t) REVERT: A 187 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6691 (pt0) REVERT: A 201 LEU cc_start: 0.5093 (OUTLIER) cc_final: 0.4350 (tp) REVERT: A 222 ARG cc_start: 0.7636 (mpp80) cc_final: 0.7145 (mpp80) REVERT: A 272 VAL cc_start: 0.7139 (OUTLIER) cc_final: 0.6809 (p) REVERT: B 10 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7269 (mtmm) REVERT: B 195 HIS cc_start: 0.7496 (t-170) cc_final: 0.7079 (t-170) REVERT: B 249 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7018 (tt) REVERT: B 255 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7010 (p0) REVERT: B 285 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7203 (pt) REVERT: C 234 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: D 47 GLU cc_start: 0.6868 (mp0) cc_final: 0.6620 (mt-10) REVERT: E 189 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7992 (mt) REVERT: E 234 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7330 (mm-30) outliers start: 67 outliers final: 47 residues processed: 184 average time/residue: 0.1831 time to fit residues: 48.4511 Evaluate side-chains 192 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 133 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 201 LEU 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 39 LEU 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 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 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 284 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 139 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 0.0980 chunk 106 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.205257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.159801 restraints weight = 10414.466| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.23 r_work: 0.3568 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9226 Z= 0.113 Angle : 0.535 7.932 12486 Z= 0.277 Chirality : 0.042 0.161 1400 Planarity : 0.003 0.042 1580 Dihedral : 4.082 21.552 1236 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 6.43 % Allowed : 25.00 % 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: 0.14 (0.25), residues: 1131 helix: 1.82 (0.27), residues: 380 sheet: -0.34 (0.30), residues: 270 loop : -1.04 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 332 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE A 38 TYR 0.016 0.001 TYR B 302 ARG 0.007 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 424) hydrogen bonds : angle 4.43204 ( 1215) SS BOND : bond 0.00586 ( 5) SS BOND : angle 1.09172 ( 10) covalent geometry : bond 0.00250 ( 9220) covalent geometry : angle 0.53453 (12476) Misc. bond : bond 0.00108 ( 1) *********************** 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 197 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 134 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6583 (tt) REVERT: A 102 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5744 (tp) REVERT: A 104 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5270 (mt) REVERT: A 112 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7017 (tt0) REVERT: A 120 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8075 (t) REVERT: A 187 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6913 (pt0) REVERT: A 201 LEU cc_start: 0.4966 (OUTLIER) cc_final: 0.4295 (tp) REVERT: A 222 ARG cc_start: 0.7620 (mpp80) cc_final: 0.7142 (mpp80) REVERT: A 272 VAL cc_start: 0.6974 (OUTLIER) cc_final: 0.6649 (p) REVERT: B 10 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7188 (mtmm) REVERT: B 32 ARG cc_start: 0.8025 (ptp-110) cc_final: 0.7673 (mtm110) REVERT: B 195 HIS cc_start: 0.7523 (t-170) cc_final: 0.7106 (t-170) REVERT: B 209 LYS cc_start: 0.8302 (pttm) cc_final: 0.7934 (ptpt) REVERT: B 249 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7069 (tt) REVERT: B 255 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.6978 (p0) REVERT: B 324 THR cc_start: 0.6259 (m) cc_final: 0.5930 (m) REVERT: C 234 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: C 332 TRP cc_start: 0.8115 (m-10) cc_final: 0.7856 (m-10) REVERT: E 189 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7856 (mt) REVERT: E 234 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7287 (mm-30) outliers start: 63 outliers final: 45 residues processed: 178 average time/residue: 0.1826 time to fit residues: 46.7759 Evaluate side-chains 189 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 119 THR 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 201 LEU 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 39 LEU 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 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 0.0050 chunk 110 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.203686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.159116 restraints weight = 10325.624| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.19 r_work: 0.3534 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9226 Z= 0.119 Angle : 0.543 8.279 12486 Z= 0.281 Chirality : 0.042 0.164 1400 Planarity : 0.004 0.042 1580 Dihedral : 4.102 21.942 1236 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 6.43 % Allowed : 24.59 % Favored : 68.98 % 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: 0.13 (0.25), residues: 1131 helix: 1.82 (0.27), residues: 380 sheet: -0.35 (0.29), residues: 269 loop : -1.05 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 38 TYR 0.018 0.001 TYR B 302 ARG 0.007 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 424) hydrogen bonds : angle 4.44121 ( 1215) SS BOND : bond 0.00636 ( 5) SS BOND : angle 1.18717 ( 10) covalent geometry : bond 0.00269 ( 9220) covalent geometry : angle 0.54184 (12476) Misc. bond : bond 0.00107 ( 1) *********************** 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 198 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 135 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.5902 (tp) REVERT: A 112 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: A 120 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.8156 (t) REVERT: A 187 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6899 (pt0) REVERT: A 201 LEU cc_start: 0.5125 (OUTLIER) cc_final: 0.4381 (tp) REVERT: A 222 ARG cc_start: 0.7657 (mpp80) cc_final: 0.7147 (mpp80) REVERT: A 272 VAL cc_start: 0.7032 (OUTLIER) cc_final: 0.6687 (p) REVERT: B 10 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7253 (mtmm) REVERT: B 32 ARG cc_start: 0.8019 (ptp-110) cc_final: 0.7648 (mtm110) REVERT: B 33 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: B 195 HIS cc_start: 0.7577 (t-170) cc_final: 0.7192 (t-170) REVERT: B 209 LYS cc_start: 0.8282 (pttm) cc_final: 0.7873 (ptpt) REVERT: B 249 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7094 (tt) REVERT: B 255 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7052 (p0) REVERT: C 234 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8503 (m-80) REVERT: C 332 TRP cc_start: 0.8088 (m-10) cc_final: 0.7850 (m-10) REVERT: E 18 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7182 (ttm170) REVERT: E 189 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.8009 (mt) REVERT: E 234 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7473 (mm-30) outliers start: 63 outliers final: 44 residues processed: 180 average time/residue: 0.1964 time to fit residues: 50.5240 Evaluate side-chains 189 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 131 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 119 THR 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 201 LEU 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 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 146 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 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 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 62 ASP 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 58 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.205383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.165288 restraints weight = 10388.537| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 3.06 r_work: 0.3509 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9226 Z= 0.122 Angle : 0.561 9.755 12486 Z= 0.288 Chirality : 0.043 0.245 1400 Planarity : 0.004 0.043 1580 Dihedral : 4.112 21.880 1236 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 6.33 % Allowed : 24.39 % Favored : 69.29 % 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: 0.11 (0.25), residues: 1131 helix: 1.79 (0.27), residues: 381 sheet: -0.38 (0.29), residues: 270 loop : -1.04 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 0.006 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 424) hydrogen bonds : angle 4.46143 ( 1215) SS BOND : bond 0.00567 ( 5) SS BOND : angle 1.28109 ( 10) covalent geometry : bond 0.00278 ( 9220) covalent geometry : angle 0.55999 (12476) Misc. bond : bond 0.00086 ( 1) ********************** 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 194 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 132 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6587 (tt) REVERT: A 102 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.5845 (tp) REVERT: A 112 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: A 120 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8130 (t) REVERT: A 187 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6946 (pt0) REVERT: A 201 LEU cc_start: 0.5049 (OUTLIER) cc_final: 0.4325 (tp) REVERT: A 222 ARG cc_start: 0.7647 (mpp80) cc_final: 0.7167 (mpp80) REVERT: A 272 VAL cc_start: 0.6998 (OUTLIER) cc_final: 0.6651 (p) REVERT: B 10 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7198 (mtmm) REVERT: B 32 ARG cc_start: 0.7936 (ptp-110) cc_final: 0.7589 (mtm110) REVERT: B 33 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: B 195 HIS cc_start: 0.7609 (t-170) cc_final: 0.7195 (t-170) REVERT: B 209 LYS cc_start: 0.8301 (pttm) cc_final: 0.7920 (ptpt) REVERT: B 249 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7118 (tt) REVERT: B 255 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7016 (p0) REVERT: C 44 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6748 (mp10) REVERT: C 234 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: C 316 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8278 (p) REVERT: C 332 TRP cc_start: 0.8060 (m-10) cc_final: 0.7805 (m-10) REVERT: E 18 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7283 (ttm170) REVERT: E 189 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7917 (mt) REVERT: E 234 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7313 (mm-30) outliers start: 62 outliers final: 44 residues processed: 175 average time/residue: 0.1850 time to fit residues: 46.5874 Evaluate side-chains 191 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 130 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 LEU 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 119 THR 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 201 LEU 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 295 THR 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 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 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 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 62 ASP 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: 0.9980 chunk 39 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.205463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.166084 restraints weight = 10378.245| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 3.03 r_work: 0.3486 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9226 Z= 0.121 Angle : 0.567 9.960 12486 Z= 0.292 Chirality : 0.043 0.212 1400 Planarity : 0.004 0.043 1580 Dihedral : 4.119 21.867 1236 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 6.33 % Allowed : 24.90 % 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: 0.13 (0.25), residues: 1131 helix: 1.82 (0.27), residues: 381 sheet: -0.40 (0.29), residues: 270 loop : -1.03 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 188 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 38 TYR 0.020 0.001 TYR B 302 ARG 0.006 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 424) hydrogen bonds : angle 4.46690 ( 1215) SS BOND : bond 0.00664 ( 5) SS BOND : angle 2.14331 ( 10) covalent geometry : bond 0.00277 ( 9220) covalent geometry : angle 0.56437 (12476) Misc. bond : bond 0.00082 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5127.99 seconds wall clock time: 89 minutes 32.11 seconds (5372.11 seconds total)