Starting phenix.real_space_refine on Sun Jul 27 02:47:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h2g_34437/07_2025/8h2g_34437.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h2g_34437/07_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_34437/07_2025/8h2g_34437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h2g_34437/07_2025/8h2g_34437.map" model { file = "/net/cci-nas-00/data/ceres_data/8h2g_34437/07_2025/8h2g_34437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h2g_34437/07_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-5711/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: 5.27, per 1000 atoms: 0.58 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: 2.37 Conformation dependent library (CDL) restraints added in 1.0 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: 1.17 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: 2.38 Time building geometry restraints manager: 2.77 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: 0.570 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.680 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- 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 : 0.923 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: 0.2281 time to fit residues: 49.4138 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 : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 38 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 131 HIS A 171 ASN A 223 HIS B 322 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.197083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.158326 restraints weight = 10216.228| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.61 r_work: 0.3384 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 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 : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.6748 (OUTLIER) cc_final: 0.6442 (m) REVERT: A 112 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: A 120 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8208 (t) REVERT: A 187 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6686 (pt0) REVERT: A 272 VAL cc_start: 0.7045 (OUTLIER) cc_final: 0.6800 (p) REVERT: B 255 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.6986 (p0) REVERT: B 285 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7313 (pt) REVERT: C 44 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6766 (mp10) REVERT: C 51 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8241 (mt) REVERT: C 251 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8030 (mtt-85) outliers start: 75 outliers final: 41 residues processed: 190 average time/residue: 0.2364 time to fit residues: 63.6871 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 : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 0.9980 chunk 86 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS A 68 ASN A 110 ASN A 223 HIS B 244 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.203437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.165751 restraints weight = 10372.071| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.58 r_work: 0.3444 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9226 Z= 0.122 Angle : 0.559 6.731 12486 Z= 0.296 Chirality : 0.042 0.154 1400 Planarity : 0.004 0.073 1580 Dihedral : 4.470 21.075 1236 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.18 % Allowed : 27.04 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1131 helix: 1.69 (0.28), residues: 378 sheet: -0.37 (0.31), residues: 267 loop : -1.15 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS C 311 PHE 0.012 0.001 PHE B 334 TYR 0.016 0.001 TYR B 302 ARG 0.010 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 424) hydrogen bonds : angle 4.89430 ( 1215) SS BOND : bond 0.00760 ( 5) SS BOND : angle 1.46592 ( 10) covalent geometry : bond 0.00263 ( 9220) covalent geometry : angle 0.55743 (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 179 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: A 120 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8041 (t) REVERT: A 187 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6655 (pt0) REVERT: A 272 VAL cc_start: 0.6934 (m) cc_final: 0.6695 (p) REVERT: A 285 MET cc_start: 0.7347 (mtt) cc_final: 0.6958 (mtt) REVERT: B 249 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7191 (tt) REVERT: C 44 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: C 234 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: C 316 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8212 (p) REVERT: E 89 GLU cc_start: 0.7306 (pp20) cc_final: 0.6897 (pp20) REVERT: E 189 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7904 (mt) outliers start: 41 outliers final: 19 residues processed: 169 average time/residue: 0.2912 time to fit residues: 72.3174 Evaluate side-chains 152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.199468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.161259 restraints weight = 10329.208| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.71 r_work: 0.3461 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9226 Z= 0.167 Angle : 0.594 7.343 12486 Z= 0.310 Chirality : 0.044 0.155 1400 Planarity : 0.004 0.077 1580 Dihedral : 4.498 22.431 1236 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 6.22 % Allowed : 25.31 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1131 helix: 1.66 (0.28), residues: 377 sheet: -0.43 (0.30), residues: 269 loop : -1.15 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 93 HIS 0.005 0.001 HIS E 35 PHE 0.018 0.002 PHE A 38 TYR 0.016 0.002 TYR B 302 ARG 0.014 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 424) hydrogen bonds : angle 4.81529 ( 1215) SS BOND : bond 0.00905 ( 5) SS BOND : angle 1.67590 ( 10) covalent geometry : bond 0.00390 ( 9220) covalent geometry : angle 0.59264 (12476) Misc. bond : bond 0.00132 ( 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 190 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 129 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7138 (tt0) REVERT: A 120 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8186 (t) REVERT: A 187 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6732 (pt0) REVERT: A 272 VAL cc_start: 0.6909 (OUTLIER) cc_final: 0.6659 (p) REVERT: B 285 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7261 (pt) REVERT: C 44 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6812 (mp10) REVERT: C 234 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8341 (m-80) REVERT: C 316 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8244 (p) REVERT: E 234 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7325 (mm-30) outliers start: 61 outliers final: 42 residues processed: 175 average time/residue: 0.2109 time to fit residues: 51.7702 Evaluate side-chains 176 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 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 190 THR 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 190 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.203516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.157169 restraints weight = 10281.000| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.28 r_work: 0.3510 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1923 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= 0.127 Angle : 0.551 9.197 12486 Z= 0.288 Chirality : 0.042 0.158 1400 Planarity : 0.004 0.041 1580 Dihedral : 4.304 22.410 1236 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.33 % Allowed : 25.20 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1131 helix: 1.72 (0.28), residues: 380 sheet: -0.36 (0.30), residues: 268 loop : -1.10 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 93 HIS 0.003 0.001 HIS C 91 PHE 0.010 0.001 PHE A 127 TYR 0.018 0.001 TYR B 302 ARG 0.008 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 424) hydrogen bonds : angle 4.61902 ( 1215) SS BOND : bond 0.00839 ( 5) SS BOND : angle 1.38335 ( 10) covalent geometry : bond 0.00289 ( 9220) covalent geometry : angle 0.54973 (12476) Misc. bond : bond 0.00160 ( 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 193 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 131 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: A 120 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8149 (t) REVERT: A 272 VAL cc_start: 0.7015 (OUTLIER) cc_final: 0.6718 (p) REVERT: B 10 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7208 (mtmm) REVERT: B 195 HIS cc_start: 0.7669 (t-170) cc_final: 0.7279 (t-170) REVERT: B 249 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7115 (tt) REVERT: C 234 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8429 (m-80) REVERT: C 316 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8275 (p) REVERT: C 336 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7850 (mp) REVERT: E 189 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7988 (mt) REVERT: E 234 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7316 (mm-30) outliers start: 62 outliers final: 41 residues processed: 176 average time/residue: 0.1901 time to fit residues: 47.8256 Evaluate side-chains 177 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 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 190 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 23 optimal weight: 0.0570 chunk 44 optimal weight: 0.4980 chunk 71 optimal weight: 0.0570 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 overall best weight: 0.2016 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.207052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.168435 restraints weight = 10261.260| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.95 r_work: 0.3554 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9226 Z= 0.102 Angle : 0.520 7.889 12486 Z= 0.272 Chirality : 0.041 0.230 1400 Planarity : 0.003 0.042 1580 Dihedral : 4.052 20.239 1236 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.61 % Allowed : 26.22 % 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: 0.16 (0.25), residues: 1131 helix: 1.84 (0.28), residues: 380 sheet: -0.28 (0.30), residues: 265 loop : -1.06 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 PHE 0.015 0.001 PHE A 38 TYR 0.018 0.001 TYR B 302 ARG 0.009 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 424) hydrogen bonds : angle 4.41988 ( 1215) SS BOND : bond 0.00411 ( 5) SS BOND : angle 0.90095 ( 10) covalent geometry : bond 0.00215 ( 9220) covalent geometry : angle 0.51967 (12476) Misc. bond : bond 0.00100 ( 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 194 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5117 (mt) REVERT: A 112 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7093 (tt0) REVERT: A 120 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8188 (t) REVERT: A 187 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6634 (pt0) REVERT: A 222 ARG cc_start: 0.7591 (mpp80) cc_final: 0.7189 (mpp80) REVERT: A 272 VAL cc_start: 0.6959 (OUTLIER) cc_final: 0.6662 (p) REVERT: B 10 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7248 (mtmm) REVERT: B 195 HIS cc_start: 0.7634 (t-170) cc_final: 0.7247 (t-170) REVERT: B 209 LYS cc_start: 0.8313 (pttm) cc_final: 0.7991 (ptpt) REVERT: B 249 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7219 (tp) REVERT: C 234 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: E 189 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7979 (mt) outliers start: 55 outliers final: 29 residues processed: 180 average time/residue: 0.1929 time to fit residues: 49.2292 Evaluate side-chains 163 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain 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 152 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 234 PHE 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 91 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 57 optimal weight: 0.0870 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 255 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.201474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.157047 restraints weight = 10412.940| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.07 r_work: 0.3556 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9226 Z= 0.166 Angle : 0.590 8.718 12486 Z= 0.305 Chirality : 0.044 0.215 1400 Planarity : 0.004 0.042 1580 Dihedral : 4.311 23.052 1236 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.20 % Allowed : 26.02 % 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: 0.07 (0.25), residues: 1131 helix: 1.71 (0.27), residues: 381 sheet: -0.34 (0.30), residues: 270 loop : -1.07 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 93 HIS 0.004 0.001 HIS C 91 PHE 0.015 0.002 PHE A 38 TYR 0.017 0.002 TYR B 302 ARG 0.007 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 424) hydrogen bonds : angle 4.59658 ( 1215) SS BOND : bond 0.00914 ( 5) SS BOND : angle 1.55657 ( 10) covalent geometry : bond 0.00394 ( 9220) covalent geometry : angle 0.58858 (12476) Misc. bond : bond 0.00101 ( 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 181 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: A 120 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8198 (t) REVERT: A 187 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6697 (pt0) REVERT: A 222 ARG cc_start: 0.7621 (mpp80) cc_final: 0.7176 (mpp80) REVERT: A 272 VAL cc_start: 0.6948 (OUTLIER) cc_final: 0.6628 (p) REVERT: B 10 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7289 (mtmm) REVERT: B 195 HIS cc_start: 0.7544 (t-170) cc_final: 0.7120 (t-170) REVERT: C 234 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: C 332 TRP cc_start: 0.8139 (m-10) cc_final: 0.7795 (m-10) REVERT: E 234 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7406 (mm-30) outliers start: 51 outliers final: 41 residues processed: 168 average time/residue: 0.1911 time to fit residues: 45.5610 Evaluate side-chains 175 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 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 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 159 THR Chi-restraints excluded: chain C residue 198 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 12 optimal weight: 0.4980 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 255 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.204275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.158850 restraints weight = 10414.895| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.25 r_work: 0.3497 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9226 Z= 0.120 Angle : 0.552 8.238 12486 Z= 0.286 Chirality : 0.043 0.236 1400 Planarity : 0.004 0.043 1580 Dihedral : 4.209 22.360 1236 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.10 % Allowed : 26.33 % 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: 0.11 (0.25), residues: 1131 helix: 1.78 (0.28), residues: 380 sheet: -0.29 (0.30), residues: 264 loop : -1.08 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 38 TYR 0.018 0.001 TYR B 302 ARG 0.007 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 424) hydrogen bonds : angle 4.52184 ( 1215) SS BOND : bond 0.00646 ( 5) SS BOND : angle 1.13652 ( 10) covalent geometry : bond 0.00270 ( 9220) covalent geometry : angle 0.55178 (12476) Misc. bond : bond 0.00084 ( 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 181 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.5845 (tp) REVERT: A 112 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7224 (tt0) REVERT: A 120 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8146 (t) REVERT: A 187 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6925 (pt0) REVERT: A 201 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4355 (tp) REVERT: A 222 ARG cc_start: 0.7648 (mpp80) cc_final: 0.7196 (mpp80) REVERT: A 272 VAL cc_start: 0.7078 (OUTLIER) cc_final: 0.6732 (p) REVERT: B 10 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7268 (mtmm) REVERT: B 195 HIS cc_start: 0.7596 (t-170) cc_final: 0.7173 (t-170) REVERT: B 249 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7096 (tt) REVERT: C 234 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8487 (m-80) REVERT: C 332 TRP cc_start: 0.8102 (m-10) cc_final: 0.7786 (m-10) REVERT: E 189 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.8014 (mt) outliers start: 50 outliers final: 36 residues processed: 169 average time/residue: 0.2357 time to fit residues: 57.8970 Evaluate side-chains 175 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 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 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 255 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.204405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.159256 restraints weight = 10297.209| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.24 r_work: 0.3563 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 0.028 9226 Z= 0.120 Angle : 0.549 8.518 12486 Z= 0.283 Chirality : 0.042 0.239 1400 Planarity : 0.004 0.042 1580 Dihedral : 4.172 22.108 1236 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.71 % Favored : 96.20 % Rotamer: Outliers : 5.61 % Allowed : 25.51 % Favored : 68.88 % 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: 0.15 (0.25), residues: 1131 helix: 1.82 (0.28), residues: 380 sheet: -0.31 (0.30), residues: 269 loop : -1.04 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 59 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE A 38 TYR 0.017 0.001 TYR B 302 ARG 0.007 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 424) hydrogen bonds : angle 4.48172 ( 1215) SS BOND : bond 0.00637 ( 5) SS BOND : angle 1.22413 ( 10) covalent geometry : bond 0.00272 ( 9220) covalent geometry : angle 0.54810 (12476) Misc. bond : bond 0.00081 ( 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 184 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 102 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.5860 (tp) REVERT: A 112 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7276 (tt0) REVERT: A 120 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8176 (t) REVERT: A 187 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.6917 (pt0) REVERT: A 201 LEU cc_start: 0.5174 (OUTLIER) cc_final: 0.4342 (tp) REVERT: A 222 ARG cc_start: 0.7645 (mpp80) cc_final: 0.7175 (mpp80) REVERT: A 272 VAL cc_start: 0.7092 (OUTLIER) cc_final: 0.6740 (p) REVERT: B 10 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7291 (mtmm) REVERT: B 32 ARG cc_start: 0.7970 (ptp-110) cc_final: 0.7595 (mtm110) REVERT: B 195 HIS cc_start: 0.7524 (t-170) cc_final: 0.7049 (t-170) REVERT: B 249 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7166 (tt) REVERT: C 234 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8502 (m-80) REVERT: C 332 TRP cc_start: 0.8133 (m-10) cc_final: 0.7790 (m-10) REVERT: E 189 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8012 (mt) REVERT: E 234 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7374 (mm-30) outliers start: 55 outliers final: 40 residues processed: 173 average time/residue: 0.1872 time to fit residues: 46.7098 Evaluate side-chains 177 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 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 78 THR Chi-restraints excluded: chain E residue 91 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 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 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: 0.8980 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 255 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.203090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.165561 restraints weight = 10390.660| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.68 r_work: 0.3439 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9226 Z= 0.153 Angle : 0.597 10.262 12486 Z= 0.305 Chirality : 0.044 0.231 1400 Planarity : 0.004 0.041 1580 Dihedral : 4.275 22.915 1236 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.98 % Favored : 95.93 % Rotamer: Outliers : 5.51 % Allowed : 25.51 % 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: 0.05 (0.25), residues: 1131 helix: 1.70 (0.27), residues: 381 sheet: -0.36 (0.30), residues: 269 loop : -1.08 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 188 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.002 PHE E 212 TYR 0.021 0.002 TYR B 302 ARG 0.007 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 424) hydrogen bonds : angle 4.58213 ( 1215) SS BOND : bond 0.00830 ( 5) SS BOND : angle 1.62028 ( 10) covalent geometry : bond 0.00360 ( 9220) covalent geometry : angle 0.59594 (12476) Misc. bond : bond 0.00066 ( 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 180 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 126 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 102 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.5835 (tp) REVERT: A 112 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7222 (tt0) REVERT: A 120 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8187 (t) REVERT: A 187 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6926 (pt0) REVERT: A 222 ARG cc_start: 0.7573 (mpp80) cc_final: 0.7128 (mpp80) REVERT: A 272 VAL cc_start: 0.6965 (OUTLIER) cc_final: 0.6622 (p) REVERT: B 10 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7229 (mtmm) REVERT: B 32 ARG cc_start: 0.7964 (ptp-110) cc_final: 0.7679 (mtm110) REVERT: B 195 HIS cc_start: 0.7724 (t-170) cc_final: 0.7303 (t-170) REVERT: B 249 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7259 (tt) REVERT: C 44 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6770 (mp10) REVERT: C 234 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: E 18 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7083 (ttm170) REVERT: E 189 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7951 (mt) REVERT: E 234 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7269 (mm-30) outliers start: 54 outliers final: 42 residues processed: 170 average time/residue: 0.2020 time to fit residues: 48.6302 Evaluate side-chains 177 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 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 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 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 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 18 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE 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 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: 0.2980 chunk 39 optimal weight: 0.0010 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 255 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.204631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.166261 restraints weight = 10345.242| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.99 r_work: 0.3497 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9226 Z= 0.114 Angle : 0.557 10.161 12486 Z= 0.285 Chirality : 0.042 0.213 1400 Planarity : 0.004 0.041 1580 Dihedral : 4.148 21.778 1236 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 5.00 % Allowed : 26.12 % Favored : 68.88 % 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: 0.12 (0.25), residues: 1131 helix: 1.79 (0.28), residues: 380 sheet: -0.31 (0.30), residues: 263 loop : -1.06 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 188 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE A 232 TYR 0.020 0.001 TYR B 302 ARG 0.006 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 424) hydrogen bonds : angle 4.49434 ( 1215) SS BOND : bond 0.00562 ( 5) SS BOND : angle 1.18124 ( 10) covalent geometry : bond 0.00252 ( 9220) covalent geometry : angle 0.55609 (12476) Misc. bond : bond 0.00066 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5829.62 seconds wall clock time: 104 minutes 41.19 seconds (6281.19 seconds total)