Starting phenix.real_space_refine on Fri Aug 22 18:43:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uo1_42424/08_2025/8uo1_42424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uo1_42424/08_2025/8uo1_42424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uo1_42424/08_2025/8uo1_42424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uo1_42424/08_2025/8uo1_42424.map" model { file = "/net/cci-nas-00/data/ceres_data/8uo1_42424/08_2025/8uo1_42424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uo1_42424/08_2025/8uo1_42424.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.020 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 4405 2.51 5 N 1222 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6915 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2242 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 10, 'TRANS': 323} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLU:plan': 25, 'ASP:plan': 18, 'GLN:plan1': 10, 'ARG:plan': 13, 'ASN:plan1': 10, 'PHE:plan': 5, 'TYR:plan': 4, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 361 Chain: "B" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2405 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 7, 'ARG:plan': 7, 'GLU:plan': 6, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 135 Chain: "G" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 344 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1876 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 407 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 9, 'GLN:plan1': 8, 'TYR:plan': 2, 'ASP:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 213 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.56, per 1000 atoms: 0.23 Number of scatterers: 6915 At special positions: 0 Unit cell: (84.1669, 134.493, 99.7855, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 3 15.00 Mg 1 11.99 O 1248 8.00 N 1222 7.00 C 4405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 307.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 49.5% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.802A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.657A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 removed outlier: 3.756A pdb=" N ASP A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.780A pdb=" N TYR A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 196 through 200 removed outlier: 3.666A pdb=" N CYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 200' Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.649A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.688A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.059A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.534A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.677A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.734A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.762A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.605A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.575A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.521A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 96 removed outlier: 3.940A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.668A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.865A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 238 removed outlier: 4.916A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.702A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.966A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.210A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.760A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 326 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 9.482A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.894A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.252A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.605A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.033A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.805A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.565A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277 removed outlier: 3.504A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1080 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: 0.79 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1211 1.32 - 1.45: 1893 1.45 - 1.57: 3893 1.57 - 1.69: 6 1.69 - 1.82: 49 Bond restraints: 7052 Sorted by residual: bond pdb=" C ILE A 207 " pdb=" N PHE A 208 " ideal model delta sigma weight residual 1.330 1.442 -0.112 1.46e-02 4.69e+03 5.91e+01 bond pdb=" CA LYS A 338 " pdb=" C LYS A 338 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.30e-02 5.92e+03 4.31e+01 bond pdb=" CA VAL A 334 " pdb=" C VAL A 334 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.27e-02 6.20e+03 2.55e+01 bond pdb=" CA ASP A 331 " pdb=" C ASP A 331 " ideal model delta sigma weight residual 1.527 1.480 0.047 1.02e-02 9.61e+03 2.12e+01 bond pdb=" CA ALA A 337 " pdb=" C ALA A 337 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.30e-02 5.92e+03 2.12e+01 ... (remaining 7047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 9457 2.77 - 5.54: 187 5.54 - 8.30: 23 8.30 - 11.07: 7 11.07 - 13.84: 3 Bond angle restraints: 9677 Sorted by residual: angle pdb=" N PRO A 143 " pdb=" CA PRO A 143 " pdb=" C PRO A 143 " ideal model delta sigma weight residual 110.70 124.54 -13.84 1.22e+00 6.72e-01 1.29e+02 angle pdb=" N GLU A 344 " pdb=" CA GLU A 344 " pdb=" C GLU A 344 " ideal model delta sigma weight residual 111.28 102.95 8.33 1.09e+00 8.42e-01 5.84e+01 angle pdb=" C PRO A 143 " pdb=" CA PRO A 143 " pdb=" CB PRO A 143 " ideal model delta sigma weight residual 110.92 103.19 7.73 1.22e+00 6.72e-01 4.02e+01 angle pdb=" N VAL A 334 " pdb=" CA VAL A 334 " pdb=" C VAL A 334 " ideal model delta sigma weight residual 110.62 104.23 6.39 1.02e+00 9.61e-01 3.92e+01 angle pdb=" N ILE A 341 " pdb=" CA ILE A 341 " pdb=" C ILE A 341 " ideal model delta sigma weight residual 110.62 104.57 6.05 1.02e+00 9.61e-01 3.52e+01 ... (remaining 9672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.04: 3971 30.04 - 60.09: 89 60.09 - 90.13: 8 90.13 - 120.17: 1 120.17 - 150.21: 2 Dihedral angle restraints: 4071 sinusoidal: 1134 harmonic: 2937 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual 93.00 -179.65 -87.35 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -140.52 -150.21 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -27.42 132.01 1 2.00e+01 2.50e-03 4.01e+01 ... (remaining 4068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 988 0.071 - 0.142: 154 0.142 - 0.214: 30 0.214 - 0.285: 2 0.285 - 0.356: 1 Chirality restraints: 1175 Sorted by residual: chirality pdb=" CA TYR A 339 " pdb=" N TYR A 339 " pdb=" C TYR A 339 " pdb=" CB TYR A 339 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CA LEU A 63 " pdb=" N LEU A 63 " pdb=" C LEU A 63 " pdb=" CB LEU A 63 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE A 95 " pdb=" N ILE A 95 " pdb=" C ILE A 95 " pdb=" CB ILE A 95 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1172 not shown) Planarity restraints: 1233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 138 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C PRO A 138 " 0.045 2.00e-02 2.50e+03 pdb=" O PRO A 138 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 139 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 256 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C VAL A 256 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL A 256 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 257 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 262 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" C GLN A 262 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN A 262 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 263 " -0.015 2.00e-02 2.50e+03 ... (remaining 1230 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1207 2.77 - 3.30: 6662 3.30 - 3.83: 10672 3.83 - 4.37: 11467 4.37 - 4.90: 20707 Nonbonded interactions: 50715 Sorted by model distance: nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.233 3.120 nonbonded pdb=" O GLN A 59 " pdb=" CG2 ILE A 62 " model vdw 2.236 3.460 nonbonded pdb=" NE2 HIS B 142 " pdb=" OG SER B 161 " model vdw 2.288 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.310 3.040 nonbonded pdb=" N GLU A 370 " pdb=" OE1 GLU A 370 " model vdw 2.332 3.120 ... (remaining 50710 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 group one per residue 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: 2.240 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.100 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.006 0.112 7053 Z= 0.465 Angle : 0.918 13.842 9679 Z= 0.632 Chirality : 0.056 0.356 1175 Planarity : 0.004 0.031 1233 Dihedral : 13.475 150.214 2154 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.18 % Allowed : 0.55 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.26), residues: 986 helix: 1.97 (0.24), residues: 439 sheet: -0.49 (0.43), residues: 154 loop : -0.71 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.020 0.001 TYR A 339 PHE 0.012 0.001 PHE B 234 TRP 0.008 0.001 TRP R 105 HIS 0.006 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00638 ( 7052) covalent geometry : angle 0.91722 ( 9677) SS BOND : bond 0.00236 ( 1) SS BOND : angle 2.62280 ( 2) hydrogen bonds : bond 0.24166 ( 370) hydrogen bonds : angle 6.70051 ( 1080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.261 Fit side-chains REVERT: A 208 PHE cc_start: 0.7817 (m-80) cc_final: 0.7460 (m-80) REVERT: A 264 ASN cc_start: 0.8027 (m-40) cc_final: 0.7805 (t0) REVERT: B 59 TYR cc_start: 0.8716 (m-80) cc_final: 0.8415 (m-80) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.0475 time to fit residues: 8.6341 Evaluate side-chains 94 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 294 GLN G 44 HIS R 93 HIS R 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.123979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098588 restraints weight = 13243.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101245 restraints weight = 7486.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103059 restraints weight = 5256.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.104259 restraints weight = 4178.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105024 restraints weight = 3592.610| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7053 Z= 0.208 Angle : 0.570 6.757 9679 Z= 0.316 Chirality : 0.044 0.145 1175 Planarity : 0.004 0.036 1233 Dihedral : 7.539 148.973 1085 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.05 % Allowed : 9.21 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.27), residues: 986 helix: 2.09 (0.25), residues: 451 sheet: -0.82 (0.41), residues: 166 loop : -0.99 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.017 0.002 TYR A 253 PHE 0.013 0.002 PHE B 241 TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 7052) covalent geometry : angle 0.56909 ( 9677) SS BOND : bond 0.00048 ( 1) SS BOND : angle 2.16145 ( 2) hydrogen bonds : bond 0.05768 ( 370) hydrogen bonds : angle 4.63618 ( 1080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8891 (m-30) cc_final: 0.8358 (m-30) REVERT: R 312 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8224 (t0) outliers start: 22 outliers final: 20 residues processed: 107 average time/residue: 0.0597 time to fit residues: 9.3228 Evaluate side-chains 107 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 312 ASN Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 30.0000 chunk 83 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN G 44 HIS R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.126514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100688 restraints weight = 12719.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103545 restraints weight = 7100.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105484 restraints weight = 4934.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106839 restraints weight = 3888.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107573 restraints weight = 3296.330| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7053 Z= 0.105 Angle : 0.463 6.304 9679 Z= 0.255 Chirality : 0.040 0.144 1175 Planarity : 0.003 0.033 1233 Dihedral : 7.274 153.483 1085 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.50 % Allowed : 13.26 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.27), residues: 986 helix: 2.26 (0.24), residues: 459 sheet: -0.79 (0.41), residues: 163 loop : -0.97 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.025 0.001 TYR A 253 PHE 0.008 0.001 PHE R 282 TRP 0.007 0.001 TRP A 277 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 7052) covalent geometry : angle 0.46271 ( 9677) SS BOND : bond 0.00276 ( 1) SS BOND : angle 1.45973 ( 2) hydrogen bonds : bond 0.03879 ( 370) hydrogen bonds : angle 3.95525 ( 1080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8849 (m-40) cc_final: 0.8647 (m-40) outliers start: 19 outliers final: 10 residues processed: 110 average time/residue: 0.0514 time to fit residues: 8.6975 Evaluate side-chains 99 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 12 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN G 44 HIS R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098161 restraints weight = 13002.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.100917 restraints weight = 7316.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102795 restraints weight = 5102.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103928 restraints weight = 4042.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104900 restraints weight = 3479.330| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7053 Z= 0.142 Angle : 0.488 6.282 9679 Z= 0.269 Chirality : 0.041 0.145 1175 Planarity : 0.003 0.039 1233 Dihedral : 7.226 155.698 1085 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.60 % Allowed : 15.10 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.27), residues: 986 helix: 2.38 (0.24), residues: 457 sheet: -0.77 (0.43), residues: 153 loop : -1.05 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.018 0.001 TYR A 253 PHE 0.012 0.001 PHE B 241 TRP 0.007 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7052) covalent geometry : angle 0.48776 ( 9677) SS BOND : bond 0.00151 ( 1) SS BOND : angle 1.61825 ( 2) hydrogen bonds : bond 0.04217 ( 370) hydrogen bonds : angle 3.90921 ( 1080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.190 Fit side-chains REVERT: A 19 GLN cc_start: 0.8770 (tt0) cc_final: 0.8416 (tt0) REVERT: R 312 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7907 (t0) outliers start: 25 outliers final: 21 residues processed: 100 average time/residue: 0.0540 time to fit residues: 8.1031 Evaluate side-chains 106 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 312 ASN Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 84 optimal weight: 0.0010 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.5908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 75 GLN B 156 GLN G 44 HIS R 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100678 restraints weight = 12846.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103529 restraints weight = 7155.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105475 restraints weight = 4970.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.106650 restraints weight = 3910.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107700 restraints weight = 3348.318| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7053 Z= 0.094 Angle : 0.447 6.397 9679 Z= 0.244 Chirality : 0.040 0.131 1175 Planarity : 0.003 0.055 1233 Dihedral : 7.126 158.447 1085 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.79 % Allowed : 16.02 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.27), residues: 986 helix: 2.40 (0.24), residues: 465 sheet: -0.74 (0.42), residues: 158 loop : -1.00 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.023 0.001 TYR A 253 PHE 0.007 0.001 PHE B 241 TRP 0.009 0.001 TRP R 313 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 7052) covalent geometry : angle 0.44615 ( 9677) SS BOND : bond 0.00246 ( 1) SS BOND : angle 1.46049 ( 2) hydrogen bonds : bond 0.03219 ( 370) hydrogen bonds : angle 3.60202 ( 1080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: R 312 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7787 (t0) outliers start: 26 outliers final: 19 residues processed: 106 average time/residue: 0.0610 time to fit residues: 9.7321 Evaluate side-chains 104 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 312 ASN Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 70 optimal weight: 0.0170 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 294 GLN G 44 HIS R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101397 restraints weight = 12903.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.104278 restraints weight = 7165.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106197 restraints weight = 4982.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107585 restraints weight = 3917.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108397 restraints weight = 3318.661| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7053 Z= 0.091 Angle : 0.458 9.294 9679 Z= 0.242 Chirality : 0.040 0.133 1175 Planarity : 0.003 0.030 1233 Dihedral : 7.052 159.661 1085 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.95 % Allowed : 18.78 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.27), residues: 986 helix: 2.51 (0.24), residues: 467 sheet: -0.65 (0.42), residues: 159 loop : -0.95 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.024 0.001 TYR A 253 PHE 0.009 0.001 PHE A 315 TRP 0.010 0.001 TRP R 313 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 7052) covalent geometry : angle 0.45733 ( 9677) SS BOND : bond 0.00212 ( 1) SS BOND : angle 1.44069 ( 2) hydrogen bonds : bond 0.02989 ( 370) hydrogen bonds : angle 3.50028 ( 1080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.239 Fit side-chains REVERT: A 19 GLN cc_start: 0.8691 (tt0) cc_final: 0.8259 (tt0) outliers start: 16 outliers final: 15 residues processed: 92 average time/residue: 0.0509 time to fit residues: 7.1412 Evaluate side-chains 98 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 86 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN G 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100832 restraints weight = 12866.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103648 restraints weight = 7233.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105591 restraints weight = 5050.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106769 restraints weight = 3977.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107808 restraints weight = 3407.432| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7053 Z= 0.095 Angle : 0.458 8.068 9679 Z= 0.242 Chirality : 0.040 0.135 1175 Planarity : 0.003 0.031 1233 Dihedral : 7.021 160.207 1085 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.13 % Allowed : 18.23 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.27), residues: 986 helix: 2.61 (0.24), residues: 467 sheet: -0.57 (0.43), residues: 154 loop : -0.94 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.025 0.001 TYR A 253 PHE 0.009 0.001 PHE B 241 TRP 0.006 0.001 TRP R 99 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 7052) covalent geometry : angle 0.45792 ( 9677) SS BOND : bond 0.00178 ( 1) SS BOND : angle 1.33984 ( 2) hydrogen bonds : bond 0.03059 ( 370) hydrogen bonds : angle 3.47167 ( 1080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.297 Fit side-chains REVERT: A 19 GLN cc_start: 0.8689 (tt0) cc_final: 0.8243 (tt0) REVERT: A 378 ASP cc_start: 0.8477 (m-30) cc_final: 0.7988 (m-30) outliers start: 17 outliers final: 16 residues processed: 94 average time/residue: 0.0621 time to fit residues: 8.8313 Evaluate side-chains 99 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS R 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098182 restraints weight = 13087.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.100899 restraints weight = 7424.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102599 restraints weight = 5214.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.103982 restraints weight = 4181.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104787 restraints weight = 3556.936| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7053 Z= 0.139 Angle : 0.491 7.871 9679 Z= 0.263 Chirality : 0.041 0.142 1175 Planarity : 0.003 0.042 1233 Dihedral : 7.120 159.161 1085 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.68 % Allowed : 17.86 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.27), residues: 986 helix: 2.65 (0.25), residues: 465 sheet: -0.71 (0.43), residues: 154 loop : -1.07 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.023 0.001 TYR A 253 PHE 0.012 0.001 PHE B 241 TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7052) covalent geometry : angle 0.49079 ( 9677) SS BOND : bond 0.00161 ( 1) SS BOND : angle 1.41769 ( 2) hydrogen bonds : bond 0.03780 ( 370) hydrogen bonds : angle 3.63995 ( 1080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.283 Fit side-chains REVERT: A 19 GLN cc_start: 0.8802 (tt0) cc_final: 0.8307 (tt0) REVERT: R 312 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8033 (t0) outliers start: 20 outliers final: 17 residues processed: 95 average time/residue: 0.0611 time to fit residues: 8.7817 Evaluate side-chains 101 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 312 ASN Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.6980 chunk 89 optimal weight: 0.4980 chunk 66 optimal weight: 30.0000 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 chunk 77 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099572 restraints weight = 13082.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102382 restraints weight = 7351.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104304 restraints weight = 5118.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105573 restraints weight = 4037.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106511 restraints weight = 3453.111| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7053 Z= 0.104 Angle : 0.473 7.935 9679 Z= 0.251 Chirality : 0.040 0.134 1175 Planarity : 0.003 0.032 1233 Dihedral : 7.095 160.306 1085 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.50 % Allowed : 18.23 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.27), residues: 986 helix: 2.63 (0.24), residues: 465 sheet: -0.64 (0.44), residues: 149 loop : -1.03 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.023 0.001 TYR A 253 PHE 0.009 0.001 PHE B 241 TRP 0.007 0.001 TRP R 99 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 7052) covalent geometry : angle 0.47226 ( 9677) SS BOND : bond 0.00222 ( 1) SS BOND : angle 1.38030 ( 2) hydrogen bonds : bond 0.03229 ( 370) hydrogen bonds : angle 3.50627 ( 1080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: R 312 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7969 (t0) outliers start: 19 outliers final: 17 residues processed: 97 average time/residue: 0.0621 time to fit residues: 9.0383 Evaluate side-chains 102 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 312 ASN Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN G 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.097131 restraints weight = 13011.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099804 restraints weight = 7429.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101648 restraints weight = 5260.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102715 restraints weight = 4177.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.103688 restraints weight = 3612.259| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7053 Z= 0.152 Angle : 0.513 8.136 9679 Z= 0.274 Chirality : 0.042 0.141 1175 Planarity : 0.003 0.032 1233 Dihedral : 7.178 158.901 1085 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.68 % Allowed : 18.05 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.27), residues: 986 helix: 2.63 (0.25), residues: 464 sheet: -0.76 (0.43), residues: 149 loop : -1.16 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.021 0.002 TYR A 253 PHE 0.012 0.001 PHE B 241 TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7052) covalent geometry : angle 0.51260 ( 9677) SS BOND : bond 0.00174 ( 1) SS BOND : angle 1.45996 ( 2) hydrogen bonds : bond 0.04008 ( 370) hydrogen bonds : angle 3.70834 ( 1080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.283 Fit side-chains REVERT: R 312 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8069 (t0) outliers start: 20 outliers final: 18 residues processed: 95 average time/residue: 0.0645 time to fit residues: 9.1696 Evaluate side-chains 102 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 312 ASN Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 21 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN G 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100036 restraints weight = 13029.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102864 restraints weight = 7316.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104784 restraints weight = 5087.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106009 restraints weight = 4022.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106974 restraints weight = 3447.873| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7053 Z= 0.094 Angle : 0.471 8.437 9679 Z= 0.248 Chirality : 0.040 0.131 1175 Planarity : 0.003 0.031 1233 Dihedral : 7.078 161.029 1085 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.13 % Allowed : 18.78 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.27), residues: 986 helix: 2.64 (0.24), residues: 465 sheet: -0.67 (0.44), residues: 149 loop : -1.07 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.023 0.001 TYR A 253 PHE 0.009 0.001 PHE B 241 TRP 0.007 0.001 TRP A 277 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 7052) covalent geometry : angle 0.47022 ( 9677) SS BOND : bond 0.00228 ( 1) SS BOND : angle 1.41631 ( 2) hydrogen bonds : bond 0.03021 ( 370) hydrogen bonds : angle 3.45963 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1287.26 seconds wall clock time: 22 minutes 49.80 seconds (1369.80 seconds total)