Starting phenix.real_space_refine on Tue Jan 14 16:28:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uo1_42424/01_2025/8uo1_42424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uo1_42424/01_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_42424/01_2025/8uo1_42424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uo1_42424/01_2025/8uo1_42424.map" model { file = "/net/cci-nas-00/data/ceres_data/8uo1_42424/01_2025/8uo1_42424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uo1_42424/01_2025/8uo1_42424.cif" } resolution = 3.6 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= 0.020 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 5, 'GLU:plan': 25, 'ARG:plan': 13} 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: {'GLN:plan1': 7, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 13} 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, 'GLU:plan': 5, 'ARG:plan': 2, '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: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 9} 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: 4.99, per 1000 atoms: 0.72 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: 1.82 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.79 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: 1.92 Time building geometry restraints manager: 2.07 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: 1.500 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.140 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- 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 7052 Z= 0.447 Angle : 0.917 13.842 9677 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 (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: 0.78 (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 TRP 0.008 0.001 TRP R 105 HIS 0.006 0.001 HIS A 64 PHE 0.012 0.001 PHE B 234 TYR 0.020 0.001 TYR A 339 ARG 0.002 0.000 ARG A 232 *********************** 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 : 0.787 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: 0.1396 time to fit residues: 24.6977 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 : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 0.0050 overall best weight: 1.0196 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.127502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102153 restraints weight = 12893.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104901 restraints weight = 7246.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106780 restraints weight = 5066.585| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7052 Z= 0.192 Angle : 0.505 6.628 9677 Z= 0.280 Chirality : 0.041 0.138 1175 Planarity : 0.003 0.032 1233 Dihedral : 7.434 148.299 1085 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.58 % Allowed : 10.50 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.27), residues: 986 helix: 2.12 (0.24), residues: 454 sheet: -0.70 (0.41), residues: 171 loop : -0.87 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.004 0.001 HIS A 64 PHE 0.014 0.001 PHE A 340 TYR 0.018 0.001 TYR A 253 ARG 0.003 0.000 ARG G 27 *********************** 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 119 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8661 (m-80) cc_final: 0.8387 (m-80) outliers start: 14 outliers final: 13 residues processed: 110 average time/residue: 0.1458 time to fit residues: 23.2831 Evaluate side-chains 105 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 250 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain R residue 116 CYS 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 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 10 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 73 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 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 = 0.3626 r_free = 0.3626 target = 0.127107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.100897 restraints weight = 12946.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103817 restraints weight = 7256.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105745 restraints weight = 5028.134| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7052 Z= 0.147 Angle : 0.462 6.272 9677 Z= 0.254 Chirality : 0.040 0.136 1175 Planarity : 0.003 0.032 1233 Dihedral : 7.228 152.445 1085 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.31 % Allowed : 13.08 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.27), residues: 986 helix: 2.32 (0.24), residues: 459 sheet: -0.66 (0.41), residues: 171 loop : -0.91 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 313 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE B 241 TYR 0.010 0.001 TYR R 316 ARG 0.002 0.000 ARG G 27 *********************** 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 116 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: R 312 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8179 (t0) outliers start: 18 outliers final: 14 residues processed: 107 average time/residue: 0.1319 time to fit residues: 21.1292 Evaluate side-chains 107 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 250 SER Chi-restraints excluded: chain A residue 251 SER 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 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 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.0010 chunk 89 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 0.0030 overall best weight: 0.2714 ------------------------------------------------------------------------------- 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 G 44 HIS R 51 ASN R 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.103416 restraints weight = 12874.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106260 restraints weight = 7095.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.108359 restraints weight = 4933.552| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7052 Z= 0.109 Angle : 0.448 8.386 9677 Z= 0.241 Chirality : 0.039 0.130 1175 Planarity : 0.003 0.034 1233 Dihedral : 7.127 156.310 1085 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.31 % Allowed : 14.92 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 986 helix: 2.36 (0.24), residues: 466 sheet: -0.47 (0.41), residues: 169 loop : -0.89 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 313 HIS 0.002 0.000 HIS R 296 PHE 0.007 0.001 PHE R 282 TYR 0.019 0.001 TYR A 253 ARG 0.003 0.000 ARG G 27 *********************** 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 115 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 312 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8130 (t0) outliers start: 18 outliers final: 14 residues processed: 104 average time/residue: 0.1447 time to fit residues: 21.7788 Evaluate side-chains 102 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 251 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 300 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 230 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 75 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 = 0.3637 r_free = 0.3637 target = 0.127796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101972 restraints weight = 12706.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104891 restraints weight = 7099.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.106858 restraints weight = 4903.691| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7052 Z= 0.140 Angle : 0.458 7.482 9677 Z= 0.246 Chirality : 0.040 0.137 1175 Planarity : 0.003 0.030 1233 Dihedral : 7.068 157.462 1085 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.42 % Allowed : 15.10 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 986 helix: 2.49 (0.24), residues: 467 sheet: -0.53 (0.41), residues: 170 loop : -0.87 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 277 HIS 0.002 0.000 HIS R 296 PHE 0.008 0.001 PHE B 241 TYR 0.021 0.001 TYR A 253 ARG 0.002 0.000 ARG G 27 *********************** 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 115 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.789 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 21 residues processed: 103 average time/residue: 0.1331 time to fit residues: 20.5777 Evaluate side-chains 108 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 210 THR 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 234 PHE Chi-restraints excluded: chain B residue 300 LEU 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 230 LEU 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 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 67 optimal weight: 0.2980 chunk 73 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 49 optimal weight: 0.0770 chunk 26 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 0.0030 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 75 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 = 0.3653 r_free = 0.3653 target = 0.128884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103207 restraints weight = 12815.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106096 restraints weight = 7076.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.108082 restraints weight = 4879.131| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7052 Z= 0.116 Angle : 0.449 6.723 9677 Z= 0.240 Chirality : 0.039 0.132 1175 Planarity : 0.002 0.029 1233 Dihedral : 7.019 159.355 1085 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.05 % Allowed : 15.84 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 986 helix: 2.55 (0.24), residues: 467 sheet: -0.42 (0.40), residues: 176 loop : -0.81 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.003 0.000 HIS B 142 PHE 0.007 0.001 PHE B 241 TYR 0.021 0.001 TYR A 253 ARG 0.001 0.000 ARG G 27 *********************** 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 111 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 19 GLN cc_start: 0.8608 (tt0) cc_final: 0.8195 (tt0) REVERT: R 312 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8105 (t0) outliers start: 22 outliers final: 17 residues processed: 102 average time/residue: 0.1289 time to fit residues: 19.8643 Evaluate side-chains 106 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 210 THR 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 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 207 SER Chi-restraints excluded: chain R residue 230 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 156 GLN G 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097043 restraints weight = 12918.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099704 restraints weight = 7413.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101524 restraints weight = 5239.601| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7052 Z= 0.302 Angle : 0.536 6.345 9677 Z= 0.291 Chirality : 0.042 0.160 1175 Planarity : 0.003 0.033 1233 Dihedral : 7.199 157.492 1085 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.42 % Allowed : 16.21 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 986 helix: 2.49 (0.25), residues: 465 sheet: -0.65 (0.42), residues: 154 loop : -1.11 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.002 PHE B 241 TYR 0.025 0.002 TYR A 253 ARG 0.002 0.000 ARG A 356 *********************** 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 117 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: R 111 SER cc_start: 0.8497 (t) cc_final: 0.8277 (t) outliers start: 24 outliers final: 22 residues processed: 103 average time/residue: 0.1297 time to fit residues: 20.0258 Evaluate side-chains 108 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 210 THR 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 234 PHE Chi-restraints excluded: chain B residue 300 LEU 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 189 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 230 LEU 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 314 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 25 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101193 restraints weight = 12850.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104051 restraints weight = 7171.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105984 restraints weight = 4978.034| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7052 Z= 0.121 Angle : 0.461 7.509 9677 Z= 0.247 Chirality : 0.040 0.158 1175 Planarity : 0.003 0.039 1233 Dihedral : 7.110 160.300 1085 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.68 % Allowed : 17.31 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.27), residues: 986 helix: 2.57 (0.24), residues: 464 sheet: -0.70 (0.42), residues: 160 loop : -0.97 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 105 HIS 0.002 0.001 HIS B 142 PHE 0.018 0.001 PHE R 104 TYR 0.025 0.001 TYR A 253 ARG 0.006 0.000 ARG G 27 *********************** 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 112 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.749 Fit side-chains REVERT: A 19 GLN cc_start: 0.8776 (tt0) cc_final: 0.8263 (tt0) outliers start: 20 outliers final: 19 residues processed: 102 average time/residue: 0.1386 time to fit residues: 21.1828 Evaluate side-chains 104 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 234 PHE Chi-restraints excluded: chain B residue 300 LEU 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 207 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 25 optimal weight: 0.0050 chunk 86 optimal weight: 10.0000 chunk 30 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102590 restraints weight = 13017.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105469 restraints weight = 7244.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107468 restraints weight = 5045.043| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7052 Z= 0.115 Angle : 0.460 7.901 9677 Z= 0.242 Chirality : 0.040 0.157 1175 Planarity : 0.003 0.031 1233 Dihedral : 7.003 162.134 1085 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.31 % Allowed : 18.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 986 helix: 2.74 (0.24), residues: 461 sheet: -0.53 (0.42), residues: 158 loop : -0.87 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.002 0.000 HIS R 172 PHE 0.014 0.001 PHE R 104 TYR 0.021 0.001 TYR A 253 ARG 0.001 0.000 ARG B 49 *********************** 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 109 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8500 (m-30) cc_final: 0.8030 (m-30) REVERT: R 204 SER cc_start: 0.8322 (m) cc_final: 0.7988 (t) REVERT: R 312 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8323 (t0) outliers start: 18 outliers final: 14 residues processed: 99 average time/residue: 0.1303 time to fit residues: 19.3278 Evaluate side-chains 103 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 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 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 207 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.9132 > 50: distance: 35 - 124: 3.047 distance: 39 - 55: 5.547 distance: 51 - 55: 3.714 distance: 55 - 56: 6.977 distance: 56 - 57: 5.994 distance: 56 - 59: 5.811 distance: 57 - 58: 4.842 distance: 57 - 62: 3.960 distance: 59 - 60: 9.186 distance: 59 - 61: 7.611 distance: 62 - 63: 9.085 distance: 63 - 64: 6.182 distance: 63 - 66: 9.367 distance: 64 - 65: 17.371 distance: 64 - 67: 6.266 distance: 67 - 68: 8.033 distance: 68 - 69: 4.523 distance: 69 - 70: 7.927 distance: 69 - 73: 9.929 distance: 71 - 72: 7.676 distance: 73 - 74: 3.585 distance: 74 - 75: 11.358 distance: 75 - 76: 29.695 distance: 75 - 77: 12.243 distance: 77 - 78: 4.533 distance: 78 - 79: 17.802 distance: 78 - 81: 17.925 distance: 79 - 80: 14.413 distance: 79 - 82: 24.633 distance: 82 - 83: 10.654 distance: 83 - 84: 27.180 distance: 84 - 85: 30.747 distance: 84 - 86: 7.949 distance: 86 - 87: 6.128 distance: 87 - 88: 10.549 distance: 87 - 90: 8.172 distance: 88 - 97: 5.170 distance: 90 - 91: 11.177 distance: 91 - 92: 7.288 distance: 92 - 93: 7.017 distance: 93 - 94: 9.474 distance: 94 - 95: 4.430 distance: 94 - 96: 4.487 distance: 97 - 98: 4.717 distance: 98 - 99: 7.145 distance: 98 - 101: 6.890 distance: 99 - 100: 19.117 distance: 99 - 107: 15.519 distance: 101 - 102: 12.568 distance: 102 - 103: 4.198 distance: 102 - 104: 10.599 distance: 103 - 105: 6.914 distance: 105 - 106: 9.545 distance: 107 - 108: 8.691 distance: 108 - 109: 11.447 distance: 108 - 111: 9.889 distance: 109 - 110: 18.758 distance: 109 - 119: 8.764 distance: 111 - 112: 13.133 distance: 112 - 113: 5.982 distance: 112 - 114: 5.211 distance: 113 - 115: 9.460 distance: 114 - 116: 9.714 distance: 115 - 117: 5.168 distance: 116 - 117: 5.495 distance: 117 - 118: 10.493 distance: 119 - 120: 5.625 distance: 120 - 121: 17.217 distance: 120 - 123: 12.496 distance: 121 - 122: 20.445 distance: 121 - 124: 17.381