Starting phenix.real_space_refine on Fri Aug 22 18:48:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gga_40000/08_2025/8gga_40000.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gga_40000/08_2025/8gga_40000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gga_40000/08_2025/8gga_40000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gga_40000/08_2025/8gga_40000.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gga_40000/08_2025/8gga_40000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gga_40000/08_2025/8gga_40000.map" } resolution = 3.5 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= 0.021 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 41 5.16 5 C 4438 2.51 5 N 1224 2.21 5 O 1289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 6995 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2318 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 488 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 10, 'ASN:plan1': 6, 'GLU:plan': 20, 'ASP:plan': 9, 'HIS:plan': 2, 'PHE:plan': 3, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 255 Chain: "B" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2454 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 6, 'ARG:plan': 7, 'GLU:plan': 6, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 113 Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 352 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 1824 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 7, 'TRANS': 261} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'TRP:plan': 3, 'PHE:plan': 4, 'GLN:plan1': 7, 'GLU:plan': 7, 'ASN:plan1': 5, 'ARG:plan': 4, 'TYR:plan': 2, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 173 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 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: 1.57, per 1000 atoms: 0.22 Number of scatterers: 6995 At special positions: 0 Unit cell: (83.2992, 135.361, 102.389, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 3 15.00 O 1289 8.00 N 1224 7.00 C 4438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.66 Conformation dependent library (CDL) restraints added in 462.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1874 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 48.5% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.871A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.642A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 111 removed outlier: 3.637A pdb=" N GLU A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 152 removed outlier: 3.540A pdb=" N GLU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.572A pdb=" N CYS A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.589A pdb=" N ILE A 235 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.196A 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: 3.747A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.976A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.602A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.743A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.542A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.987A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.693A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.634A 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: 3.750A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 4.265A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.515A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE R 133 " --> pdb=" O VAL R 129 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.526A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 172 removed outlier: 3.658A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 4.268A 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 181 through 187 Processing helix chain 'R' and resid 196 through 237 removed outlier: 3.547A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.540A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.945A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.931A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 326 removed outlier: 3.690A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 6.237A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.756A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.093A 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 62 removed outlier: 3.956A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103 removed outlier: 7.096A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.013A 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: 4.073A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.965A 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: 6.756A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.821A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.037A 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 278 removed outlier: 3.705A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 1023 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: 0.92 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2299 1.34 - 1.46: 1053 1.46 - 1.57: 3719 1.57 - 1.69: 5 1.69 - 1.81: 56 Bond restraints: 7132 Sorted by residual: bond pdb=" N THR A 204 " pdb=" CA THR A 204 " ideal model delta sigma weight residual 1.457 1.497 -0.041 1.24e-02 6.50e+03 1.08e+01 bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.65e+00 bond pdb=" N ILE A 207 " pdb=" CA ILE A 207 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.25e-02 6.40e+03 8.39e+00 bond pdb=" N SER A 205 " pdb=" CA SER A 205 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.27e+00 bond pdb=" N PHE R 133 " pdb=" CA PHE R 133 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.21e-02 6.83e+03 8.13e+00 ... (remaining 7127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 9603 2.37 - 4.74: 136 4.74 - 7.10: 13 7.10 - 9.47: 8 9.47 - 11.84: 2 Bond angle restraints: 9762 Sorted by residual: angle pdb=" C ASP A 223 " pdb=" CA ASP A 223 " pdb=" CB ASP A 223 " ideal model delta sigma weight residual 110.62 101.55 9.07 1.51e+00 4.39e-01 3.60e+01 angle pdb=" N ARG A 231 " pdb=" CA ARG A 231 " pdb=" C ARG A 231 " ideal model delta sigma weight residual 113.43 107.03 6.40 1.26e+00 6.30e-01 2.58e+01 angle pdb=" CA LEU A 203 " pdb=" C LEU A 203 " pdb=" O LEU A 203 " ideal model delta sigma weight residual 121.28 116.55 4.73 1.18e+00 7.18e-01 1.61e+01 angle pdb=" CA GLY A 206 " pdb=" C GLY A 206 " pdb=" O GLY A 206 " ideal model delta sigma weight residual 121.58 118.00 3.58 9.00e-01 1.23e+00 1.58e+01 angle pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sigma weight residual 120.50 132.34 -11.84 3.00e+00 1.11e-01 1.56e+01 ... (remaining 9757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.13: 4009 28.13 - 56.25: 127 56.25 - 84.38: 8 84.38 - 112.51: 2 112.51 - 140.64: 3 Dihedral angle restraints: 4149 sinusoidal: 1269 harmonic: 2880 Sorted by residual: dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 163.16 140.64 1 2.00e+01 2.50e-03 4.26e+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 -158.46 -132.27 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" O2G GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 177.30 -65.39 -117.31 1 2.00e+01 2.50e-03 3.50e+01 ... (remaining 4146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 892 0.047 - 0.094: 203 0.094 - 0.140: 65 0.140 - 0.187: 7 0.187 - 0.234: 2 Chirality restraints: 1169 Sorted by residual: chirality pdb=" CA ASP A 223 " pdb=" N ASP A 223 " pdb=" C ASP A 223 " pdb=" CB ASP A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA VAL A 202 " pdb=" N VAL A 202 " pdb=" C VAL A 202 " pdb=" CB VAL A 202 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ARG A 201 " pdb=" N ARG A 201 " pdb=" C ARG A 201 " pdb=" CB ARG A 201 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1166 not shown) Planarity restraints: 1247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 131 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C ARG R 131 " -0.066 2.00e-02 2.50e+03 pdb=" O ARG R 131 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR R 132 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 198 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C LEU A 198 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 198 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 199 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO R 168 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.026 5.00e-02 4.00e+02 ... (remaining 1244 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 942 2.75 - 3.29: 6582 3.29 - 3.83: 10783 3.83 - 4.36: 11692 4.36 - 4.90: 21588 Nonbonded interactions: 51587 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.215 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.312 3.040 nonbonded pdb=" ND2 ASN R 51 " pdb=" O ALA R 76 " model vdw 2.355 3.120 nonbonded pdb=" ND2 ASN A 23 " pdb=" OD1 ASN B 88 " model vdw 2.359 3.120 nonbonded pdb=" OD2 ASP B 212 " pdb=" NH2 ARG B 219 " model vdw 2.372 3.120 ... (remaining 51582 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: 2.400 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7132 Z= 0.224 Angle : 0.667 11.840 9762 Z= 0.378 Chirality : 0.045 0.234 1169 Planarity : 0.005 0.073 1247 Dihedral : 14.504 140.637 2275 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -0.34 (0.27), residues: 968 helix: 1.15 (0.26), residues: 416 sheet: -1.14 (0.44), residues: 163 loop : -1.29 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.012 0.001 TYR R 132 PHE 0.010 0.001 PHE B 235 TRP 0.007 0.001 TRP R 109 HIS 0.010 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7132) covalent geometry : angle 0.66732 ( 9762) hydrogen bonds : bond 0.25870 ( 353) hydrogen bonds : angle 6.88893 ( 1023) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.210 Fit side-chains REVERT: A 177 TYR cc_start: 0.7961 (t80) cc_final: 0.7056 (t80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0747 time to fit residues: 8.6983 Evaluate side-chains 64 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.0570 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121623 restraints weight = 10349.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119863 restraints weight = 9765.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121508 restraints weight = 8966.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121788 restraints weight = 6423.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122234 restraints weight = 6554.488| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7132 Z= 0.112 Angle : 0.479 5.973 9762 Z= 0.262 Chirality : 0.041 0.137 1169 Planarity : 0.003 0.032 1247 Dihedral : 8.146 125.686 1073 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.66 % Allowed : 9.45 % Favored : 89.88 % 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: 0.15 (0.27), residues: 968 helix: 1.67 (0.26), residues: 430 sheet: -0.91 (0.44), residues: 155 loop : -1.28 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.008 0.001 TYR A 163 PHE 0.014 0.001 PHE R 223 TRP 0.005 0.001 TRP R 109 HIS 0.011 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 7132) covalent geometry : angle 0.47932 ( 9762) hydrogen bonds : bond 0.04851 ( 353) hydrogen bonds : angle 4.61493 ( 1023) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.161 Fit side-chains REVERT: A 177 TYR cc_start: 0.7863 (t80) cc_final: 0.7467 (t80) outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.0635 time to fit residues: 7.0119 Evaluate side-chains 71 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain R residue 115 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 chunk 42 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 0.0770 chunk 9 optimal weight: 8.9990 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.152109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123602 restraints weight = 10285.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121995 restraints weight = 9689.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123644 restraints weight = 8929.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123929 restraints weight = 6372.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124201 restraints weight = 6630.937| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 7132 Z= 0.092 Angle : 0.430 6.273 9762 Z= 0.232 Chirality : 0.041 0.135 1169 Planarity : 0.003 0.031 1247 Dihedral : 6.972 123.684 1073 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.83 % Allowed : 11.44 % Favored : 87.73 % 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: 0.44 (0.28), residues: 968 helix: 1.96 (0.26), residues: 428 sheet: -0.59 (0.44), residues: 157 loop : -1.27 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.006 0.000 TYR R 308 PHE 0.010 0.001 PHE R 282 TRP 0.004 0.001 TRP R 109 HIS 0.009 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00176 ( 7132) covalent geometry : angle 0.42980 ( 9762) hydrogen bonds : bond 0.03580 ( 353) hydrogen bonds : angle 4.05659 ( 1023) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.179 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 75 average time/residue: 0.0603 time to fit residues: 6.7613 Evaluate side-chains 69 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain R residue 115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 0.0570 chunk 90 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121389 restraints weight = 10344.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119562 restraints weight = 8730.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121216 restraints weight = 8007.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121534 restraints weight = 5888.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121953 restraints weight = 5980.856| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7132 Z= 0.096 Angle : 0.435 6.382 9762 Z= 0.235 Chirality : 0.041 0.140 1169 Planarity : 0.003 0.031 1247 Dihedral : 6.695 123.905 1073 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.66 % Allowed : 12.77 % Favored : 86.57 % 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: 0.59 (0.28), residues: 968 helix: 2.10 (0.26), residues: 432 sheet: -0.47 (0.43), residues: 163 loop : -1.28 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 356 TYR 0.008 0.001 TYR R 308 PHE 0.011 0.001 PHE A 212 TRP 0.005 0.001 TRP B 339 HIS 0.008 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 7132) covalent geometry : angle 0.43537 ( 9762) hydrogen bonds : bond 0.03397 ( 353) hydrogen bonds : angle 3.86723 ( 1023) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.219 Fit side-chains REVERT: B 59 TYR cc_start: 0.8692 (m-80) cc_final: 0.8318 (m-80) outliers start: 4 outliers final: 3 residues processed: 70 average time/residue: 0.0573 time to fit residues: 6.1058 Evaluate side-chains 70 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain R residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117642 restraints weight = 10362.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116651 restraints weight = 9820.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118012 restraints weight = 9241.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118385 restraints weight = 6583.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118997 restraints weight = 6306.050| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7132 Z= 0.133 Angle : 0.476 6.672 9762 Z= 0.258 Chirality : 0.042 0.146 1169 Planarity : 0.003 0.033 1247 Dihedral : 6.751 124.094 1073 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.33 % Allowed : 13.76 % Favored : 84.91 % 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: 0.58 (0.28), residues: 968 helix: 2.15 (0.26), residues: 430 sheet: -0.54 (0.42), residues: 171 loop : -1.33 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.015 0.001 TYR A 177 PHE 0.014 0.001 PHE B 235 TRP 0.008 0.001 TRP B 339 HIS 0.007 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7132) covalent geometry : angle 0.47551 ( 9762) hydrogen bonds : bond 0.04093 ( 353) hydrogen bonds : angle 3.90165 ( 1023) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.277 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.0641 time to fit residues: 6.6235 Evaluate side-chains 73 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 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 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.107135 restraints weight = 10567.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.109634 restraints weight = 7185.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111179 restraints weight = 5646.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112396 restraints weight = 4857.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113067 restraints weight = 4360.393| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7132 Z= 0.176 Angle : 0.520 6.738 9762 Z= 0.281 Chirality : 0.043 0.148 1169 Planarity : 0.003 0.036 1247 Dihedral : 6.928 122.288 1073 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.49 % Allowed : 15.09 % Favored : 83.42 % 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: 0.37 (0.28), residues: 968 helix: 1.97 (0.26), residues: 431 sheet: -0.67 (0.42), residues: 170 loop : -1.42 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 280 TYR 0.016 0.001 TYR R 308 PHE 0.017 0.002 PHE B 235 TRP 0.010 0.001 TRP B 339 HIS 0.007 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 7132) covalent geometry : angle 0.51951 ( 9762) hydrogen bonds : bond 0.04611 ( 353) hydrogen bonds : angle 4.03143 ( 1023) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.276 Fit side-chains REVERT: A 16 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6958 (tm-30) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.0601 time to fit residues: 6.1406 Evaluate side-chains 70 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 282 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117362 restraints weight = 10324.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116374 restraints weight = 9780.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117647 restraints weight = 9179.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118088 restraints weight = 6597.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118643 restraints weight = 6325.930| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7132 Z= 0.116 Angle : 0.459 6.710 9762 Z= 0.248 Chirality : 0.041 0.138 1169 Planarity : 0.003 0.035 1247 Dihedral : 6.785 123.501 1073 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.82 % Allowed : 14.93 % Favored : 83.25 % 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: 0.67 (0.28), residues: 968 helix: 2.20 (0.26), residues: 423 sheet: -0.50 (0.42), residues: 172 loop : -1.18 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.011 0.001 TYR R 308 PHE 0.011 0.001 PHE B 199 TRP 0.007 0.001 TRP B 339 HIS 0.007 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7132) covalent geometry : angle 0.45885 ( 9762) hydrogen bonds : bond 0.03714 ( 353) hydrogen bonds : angle 3.85994 ( 1023) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.271 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 0.0663 time to fit residues: 6.9912 Evaluate side-chains 70 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 282 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 19 optimal weight: 0.0000 chunk 13 optimal weight: 7.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.149456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119775 restraints weight = 10471.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.118559 restraints weight = 8058.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119867 restraints weight = 7691.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120338 restraints weight = 5893.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121240 restraints weight = 5416.859| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7132 Z= 0.091 Angle : 0.439 7.690 9762 Z= 0.234 Chirality : 0.041 0.136 1169 Planarity : 0.003 0.034 1247 Dihedral : 6.601 122.424 1073 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.66 % Allowed : 15.92 % Favored : 82.42 % 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: 0.81 (0.28), residues: 968 helix: 2.30 (0.26), residues: 423 sheet: -0.35 (0.42), residues: 174 loop : -1.12 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 68 TYR 0.008 0.001 TYR R 308 PHE 0.009 0.001 PHE B 199 TRP 0.006 0.001 TRP R 109 HIS 0.007 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 7132) covalent geometry : angle 0.43937 ( 9762) hydrogen bonds : bond 0.03094 ( 353) hydrogen bonds : angle 3.70054 ( 1023) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.233 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 0.0598 time to fit residues: 6.5875 Evaluate side-chains 75 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 282 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 43 optimal weight: 0.0030 chunk 41 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.149008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119367 restraints weight = 10391.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117677 restraints weight = 8147.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118900 restraints weight = 9484.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119274 restraints weight = 6310.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120010 restraints weight = 5806.977| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7132 Z= 0.095 Angle : 0.435 6.605 9762 Z= 0.234 Chirality : 0.041 0.140 1169 Planarity : 0.003 0.034 1247 Dihedral : 6.547 120.638 1073 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.49 % Allowed : 16.42 % Favored : 82.09 % 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: 0.82 (0.28), residues: 968 helix: 2.32 (0.26), residues: 424 sheet: -0.33 (0.41), residues: 181 loop : -1.17 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 356 TYR 0.017 0.001 TYR A 177 PHE 0.010 0.001 PHE B 199 TRP 0.005 0.001 TRP R 109 HIS 0.007 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 7132) covalent geometry : angle 0.43454 ( 9762) hydrogen bonds : bond 0.03183 ( 353) hydrogen bonds : angle 3.65634 ( 1023) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.264 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.0622 time to fit residues: 6.8882 Evaluate side-chains 75 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116096 restraints weight = 10439.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114056 restraints weight = 8650.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114967 restraints weight = 9669.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115849 restraints weight = 6769.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116447 restraints weight = 6082.080| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7132 Z= 0.158 Angle : 0.502 7.594 9762 Z= 0.268 Chirality : 0.043 0.148 1169 Planarity : 0.003 0.035 1247 Dihedral : 6.694 118.192 1073 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.49 % Allowed : 16.25 % Favored : 82.26 % 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: 0.67 (0.28), residues: 968 helix: 2.21 (0.26), residues: 424 sheet: -0.43 (0.42), residues: 173 loop : -1.24 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.014 0.001 TYR R 308 PHE 0.016 0.002 PHE B 199 TRP 0.007 0.001 TRP B 339 HIS 0.006 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7132) covalent geometry : angle 0.50192 ( 9762) hydrogen bonds : bond 0.04095 ( 353) hydrogen bonds : angle 3.86690 ( 1023) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.275 Fit side-chains REVERT: A 16 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6839 (tm-30) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.0621 time to fit residues: 6.4048 Evaluate side-chains 71 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115287 restraints weight = 10424.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.114051 restraints weight = 10034.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115394 restraints weight = 9419.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115696 restraints weight = 6823.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116294 restraints weight = 6626.117| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7132 Z= 0.171 Angle : 0.517 6.777 9762 Z= 0.278 Chirality : 0.043 0.146 1169 Planarity : 0.003 0.035 1247 Dihedral : 6.818 118.445 1073 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.33 % Allowed : 16.42 % Favored : 82.26 % 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: 0.51 (0.28), residues: 968 helix: 2.08 (0.26), residues: 425 sheet: -0.57 (0.42), residues: 170 loop : -1.31 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.015 0.001 TYR R 308 PHE 0.016 0.002 PHE B 199 TRP 0.008 0.001 TRP B 339 HIS 0.006 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7132) covalent geometry : angle 0.51668 ( 9762) hydrogen bonds : bond 0.04405 ( 353) hydrogen bonds : angle 3.98479 ( 1023) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1149.84 seconds wall clock time: 20 minutes 29.98 seconds (1229.98 seconds total)