Starting phenix.real_space_refine on Fri Aug 22 18:07:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gg7_29997/08_2025/8gg7_29997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gg7_29997/08_2025/8gg7_29997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gg7_29997/08_2025/8gg7_29997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gg7_29997/08_2025/8gg7_29997.map" model { file = "/net/cci-nas-00/data/ceres_data/8gg7_29997/08_2025/8gg7_29997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gg7_29997/08_2025/8gg7_29997.cif" } resolution = 3.3 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= 0.022 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 44 5.16 5 C 4282 2.51 5 N 1155 2.21 5 O 1203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 6687 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1781 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 3 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 15, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 129 Chain: "B" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2443 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 4, 'GLU:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 98 Chain: "G" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 332 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 2083 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 284, 2069 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'TRP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 9, 'GLN:plan1': 5, 'ASN:plan1': 3, 'ARG:plan': 5, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 131 Conformer: "B" Number of residues, atoms: 284, 2069 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'TRP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 9, 'GLN:plan1': 5, 'ASN:plan1': 3, 'ARG:plan': 5, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 131 bond proxies already assigned to first conformer: 2105 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP R 286 " occ=0.62 ... (26 atoms not shown) pdb=" CH2BTRP R 286 " occ=0.38 Time building chain proxies: 2.13, per 1000 atoms: 0.32 Number of scatterers: 6687 At special positions: 0 Unit cell: (84.1669, 134.493, 98.0501, 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 44 16.00 P 3 15.00 O 1203 8.00 N 1155 7.00 C 4282 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: 0.55 Conformation dependent library (CDL) restraints added in 353.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 49.9% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 4.005A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 65 removed outlier: 3.763A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.915A 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: 3.805A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.901A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.768A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.752A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.538A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.650A 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 'B' and resid 128 through 132 removed outlier: 3.686A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.774A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.564A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.696A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.898A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.595A pdb=" N TYR R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.685A 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: 3.616A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.542A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.511A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 4.365A 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 208 Processing helix chain 'R' and resid 208 through 238 removed outlier: 3.744A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 287 removed outlier: 3.799A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 3.599A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.509A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 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: 6.154A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.433A 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: 6.703A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.823A 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: 3.791A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.731A 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 105 removed outlier: 7.114A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.795A 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: 6.941A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.701A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.673A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.010A 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 277 339 hydrogen bonds defined for protein. 982 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: 0.88 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2153 1.34 - 1.46: 1379 1.46 - 1.58: 3237 1.58 - 1.69: 5 1.69 - 1.81: 60 Bond restraints: 6834 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.569 -0.046 2.00e-02 2.50e+03 5.29e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.440 -0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" CA TRP R 32 " pdb=" C TRP R 32 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.30e-02 5.92e+03 4.33e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.561 -0.041 2.00e-02 2.50e+03 4.28e+00 ... (remaining 6829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 9156 1.40 - 2.81: 135 2.81 - 4.21: 36 4.21 - 5.61: 13 5.61 - 7.02: 1 Bond angle restraints: 9341 Sorted by residual: angle pdb=" N GLY R 37 " pdb=" CA GLY R 37 " pdb=" C GLY R 37 " ideal model delta sigma weight residual 112.64 116.97 -4.33 1.21e+00 6.83e-01 1.28e+01 angle pdb=" C VAL R 39 " pdb=" CA VAL R 39 " pdb=" CB VAL R 39 " ideal model delta sigma weight residual 112.14 107.55 4.59 1.35e+00 5.49e-01 1.16e+01 angle pdb=" N VAL B 90 " pdb=" CA VAL B 90 " pdb=" C VAL B 90 " ideal model delta sigma weight residual 112.96 109.71 3.25 1.00e+00 1.00e+00 1.06e+01 angle pdb=" N MET R 36 " pdb=" CA MET R 36 " pdb=" C MET R 36 " ideal model delta sigma weight residual 111.28 114.09 -2.81 1.09e+00 8.42e-01 6.66e+00 angle pdb=" C MET R 36 " pdb=" N GLY R 37 " pdb=" CA GLY R 37 " ideal model delta sigma weight residual 119.99 122.79 -2.80 1.13e+00 7.83e-01 6.15e+00 ... (remaining 9336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.75: 3888 33.75 - 67.51: 69 67.51 - 101.26: 4 101.26 - 135.02: 1 135.02 - 168.77: 1 Dihedral angle restraints: 3963 sinusoidal: 1326 harmonic: 2637 Sorted by residual: dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 92.10 168.77 1 2.00e+01 2.50e-03 4.75e+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 3.08 101.51 1 2.00e+01 2.50e-03 2.88e+01 dihedral pdb=" CA MET R 36 " pdb=" C MET R 36 " pdb=" N GLY R 37 " pdb=" CA GLY R 37 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 3960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 692 0.030 - 0.059: 252 0.059 - 0.089: 102 0.089 - 0.119: 56 0.119 - 0.148: 6 Chirality restraints: 1108 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ASP B 291 " pdb=" N ASP B 291 " pdb=" C ASP B 291 " pdb=" CB ASP B 291 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1105 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 36 " 0.016 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C MET R 36 " -0.058 2.00e-02 2.50e+03 pdb=" O MET R 36 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY R 37 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO B 194 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " 0.012 2.00e-02 2.50e+03 8.93e-03 1.40e+00 pdb=" CG PHE B 234 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " 0.003 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1876 2.81 - 3.33: 6026 3.33 - 3.86: 10318 3.86 - 4.38: 11337 4.38 - 4.90: 21270 Nonbonded interactions: 50827 Sorted by model distance: nonbonded pdb=" ND2 ASN R 322 " pdb=" O HOH R 601 " model vdw 2.288 3.120 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.295 3.040 nonbonded pdb=" O ASN R 318 " pdb=" O HOH R 601 " model vdw 2.307 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.363 3.040 nonbonded pdb=" ND2 ASN A 23 " pdb=" OD1 ASN B 88 " model vdw 2.370 3.120 ... (remaining 50822 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.750 Find NCS groups from input model: 0.040 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:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.003 0.053 6834 Z= 0.155 Angle : 0.497 7.016 9341 Z= 0.274 Chirality : 0.041 0.148 1108 Planarity : 0.003 0.033 1171 Dihedral : 13.735 168.770 2251 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.16 % Allowed : 0.32 % Favored : 99.53 % 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: 0.88 (0.28), residues: 890 helix: 1.90 (0.27), residues: 379 sheet: -0.38 (0.41), residues: 174 loop : -0.32 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 231 TYR 0.020 0.001 TYR R 185 PHE 0.020 0.001 PHE B 234 TRP 0.008 0.001 TRP R 105 HIS 0.011 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6834) covalent geometry : angle 0.49680 ( 9341) hydrogen bonds : bond 0.22694 ( 339) hydrogen bonds : angle 6.25529 ( 982) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.258 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0974 time to fit residues: 11.1384 Evaluate side-chains 70 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.0570 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116494 restraints weight = 12314.951| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.47 r_work: 0.3280 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6834 Z= 0.134 Angle : 0.492 7.077 9341 Z= 0.267 Chirality : 0.042 0.134 1108 Planarity : 0.003 0.030 1171 Dihedral : 7.437 169.994 992 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.79 % Allowed : 7.11 % Favored : 92.10 % 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: 0.93 (0.28), residues: 890 helix: 2.01 (0.26), residues: 394 sheet: -0.39 (0.41), residues: 171 loop : -0.50 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.014 0.001 TYR R 185 PHE 0.014 0.001 PHE A 212 TRP 0.006 0.001 TRP R 105 HIS 0.009 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6834) covalent geometry : angle 0.49230 ( 9341) hydrogen bonds : bond 0.05907 ( 339) hydrogen bonds : angle 4.48972 ( 982) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.262 Fit side-chains REVERT: G 18 GLN cc_start: 0.8692 (tp40) cc_final: 0.8246 (tp-100) outliers start: 4 outliers final: 3 residues processed: 76 average time/residue: 0.0847 time to fit residues: 8.6210 Evaluate side-chains 70 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS 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 = 0.143573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114222 restraints weight = 9900.020| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.24 r_work: 0.3291 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6834 Z= 0.123 Angle : 0.475 7.227 9341 Z= 0.251 Chirality : 0.042 0.134 1108 Planarity : 0.003 0.029 1171 Dihedral : 7.460 171.851 992 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.11 % Allowed : 9.95 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.28), residues: 890 helix: 2.21 (0.26), residues: 390 sheet: -0.32 (0.40), residues: 171 loop : -0.52 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.013 0.001 TYR R 185 PHE 0.012 0.001 PHE R 240 TRP 0.005 0.001 TRP R 105 HIS 0.006 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6834) covalent geometry : angle 0.47470 ( 9341) hydrogen bonds : bond 0.05085 ( 339) hydrogen bonds : angle 4.13872 ( 982) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.270 Fit side-chains REVERT: G 18 GLN cc_start: 0.8538 (tp40) cc_final: 0.8112 (tp-100) outliers start: 6 outliers final: 2 residues processed: 78 average time/residue: 0.0742 time to fit residues: 7.9845 Evaluate side-chains 71 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 4.9990 chunk 77 optimal weight: 0.0770 chunk 67 optimal weight: 6.9990 chunk 9 optimal weight: 0.2980 chunk 50 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN R 296 HIS 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 = 0.146544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117408 restraints weight = 20225.893| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.98 r_work: 0.3233 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6834 Z= 0.094 Angle : 0.442 7.086 9341 Z= 0.235 Chirality : 0.041 0.131 1108 Planarity : 0.002 0.030 1171 Dihedral : 7.378 172.414 992 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.11 % Allowed : 10.74 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.28), residues: 890 helix: 2.43 (0.26), residues: 386 sheet: -0.21 (0.40), residues: 170 loop : -0.65 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.017 0.001 TYR R 185 PHE 0.010 0.001 PHE A 212 TRP 0.005 0.001 TRP B 169 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 6834) covalent geometry : angle 0.44222 ( 9341) hydrogen bonds : bond 0.03993 ( 339) hydrogen bonds : angle 3.98056 ( 982) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.193 Fit side-chains REVERT: G 18 GLN cc_start: 0.8506 (tp40) cc_final: 0.8101 (tp-100) outliers start: 6 outliers final: 2 residues processed: 78 average time/residue: 0.0646 time to fit residues: 7.0757 Evaluate side-chains 72 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 40 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 9 optimal weight: 0.0030 chunk 35 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115114 restraints weight = 15527.808| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.83 r_work: 0.3235 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6834 Z= 0.116 Angle : 0.464 7.198 9341 Z= 0.245 Chirality : 0.041 0.132 1108 Planarity : 0.003 0.029 1171 Dihedral : 7.413 172.171 992 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.63 % Allowed : 11.69 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.28), residues: 890 helix: 2.38 (0.26), residues: 387 sheet: -0.29 (0.40), residues: 169 loop : -0.55 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.014 0.001 TYR R 185 PHE 0.012 0.001 PHE B 241 TRP 0.006 0.001 TRP B 339 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6834) covalent geometry : angle 0.46432 ( 9341) hydrogen bonds : bond 0.04425 ( 339) hydrogen bonds : angle 3.99698 ( 982) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.258 Fit side-chains REVERT: G 18 GLN cc_start: 0.8590 (tp40) cc_final: 0.8185 (tp-100) REVERT: R 302 LEU cc_start: 0.8538 (mm) cc_final: 0.8314 (mm) outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 0.0820 time to fit residues: 8.0763 Evaluate side-chains 69 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain R residue 40 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 0.0060 chunk 85 optimal weight: 0.3980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116413 restraints weight = 19136.931| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.99 r_work: 0.3194 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6834 Z= 0.089 Angle : 0.435 7.045 9341 Z= 0.229 Chirality : 0.041 0.171 1108 Planarity : 0.002 0.030 1171 Dihedral : 7.380 172.336 992 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.95 % Allowed : 12.01 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.29), residues: 890 helix: 2.52 (0.26), residues: 386 sheet: -0.20 (0.41), residues: 167 loop : -0.59 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.013 0.001 TYR R 185 PHE 0.008 0.001 PHE B 241 TRP 0.005 0.001 TRP B 169 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 6834) covalent geometry : angle 0.43522 ( 9341) hydrogen bonds : bond 0.03680 ( 339) hydrogen bonds : angle 3.89450 ( 982) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.299 Fit side-chains REVERT: G 18 GLN cc_start: 0.8357 (tp40) cc_final: 0.7955 (tp-100) REVERT: R 171 MET cc_start: 0.6826 (ttp) cc_final: 0.6251 (ttm) REVERT: R 302 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8229 (mm) outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.0747 time to fit residues: 8.2403 Evaluate side-chains 76 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113175 restraints weight = 24345.598| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 5.67 r_work: 0.3081 rms_B_bonded: 5.58 restraints_weight: 2.0000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6834 Z= 0.170 Angle : 0.523 7.265 9341 Z= 0.275 Chirality : 0.043 0.139 1108 Planarity : 0.003 0.027 1171 Dihedral : 7.538 172.014 992 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.58 % Allowed : 12.32 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.28), residues: 890 helix: 2.40 (0.26), residues: 384 sheet: -0.34 (0.40), residues: 171 loop : -0.52 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.018 0.001 TYR R 185 PHE 0.015 0.002 PHE B 241 TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6834) covalent geometry : angle 0.52275 ( 9341) hydrogen bonds : bond 0.05175 ( 339) hydrogen bonds : angle 4.09283 ( 982) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.219 Fit side-chains REVERT: G 18 GLN cc_start: 0.8632 (tp40) cc_final: 0.8199 (tp-100) REVERT: R 302 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8244 (mm) outliers start: 9 outliers final: 5 residues processed: 74 average time/residue: 0.0748 time to fit residues: 7.5336 Evaluate side-chains 74 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113476 restraints weight = 9572.646| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.21 r_work: 0.3286 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6834 Z= 0.131 Angle : 0.492 7.189 9341 Z= 0.258 Chirality : 0.042 0.133 1108 Planarity : 0.003 0.030 1171 Dihedral : 7.540 172.374 992 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.11 % Allowed : 13.43 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.28), residues: 890 helix: 2.32 (0.26), residues: 390 sheet: -0.42 (0.40), residues: 169 loop : -0.58 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 131 TYR 0.016 0.001 TYR R 185 PHE 0.014 0.001 PHE R 240 TRP 0.007 0.001 TRP B 339 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6834) covalent geometry : angle 0.49247 ( 9341) hydrogen bonds : bond 0.04729 ( 339) hydrogen bonds : angle 4.04781 ( 982) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.281 Fit side-chains REVERT: G 18 GLN cc_start: 0.8570 (tp40) cc_final: 0.8130 (tp-100) REVERT: R 302 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8225 (mm) outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.0857 time to fit residues: 8.3294 Evaluate side-chains 72 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112236 restraints weight = 18924.415| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.49 r_work: 0.3194 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6834 Z= 0.149 Angle : 0.507 7.308 9341 Z= 0.267 Chirality : 0.043 0.196 1108 Planarity : 0.003 0.029 1171 Dihedral : 7.589 172.005 992 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.26 % Allowed : 13.59 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.28), residues: 890 helix: 2.21 (0.26), residues: 396 sheet: -0.50 (0.40), residues: 170 loop : -0.54 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 131 TYR 0.016 0.001 TYR R 185 PHE 0.016 0.001 PHE R 240 TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6834) covalent geometry : angle 0.50674 ( 9341) hydrogen bonds : bond 0.05020 ( 339) hydrogen bonds : angle 4.07664 ( 982) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.251 Fit side-chains REVERT: G 18 GLN cc_start: 0.8653 (tp40) cc_final: 0.8202 (tp-100) REVERT: R 302 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8252 (mm) outliers start: 7 outliers final: 5 residues processed: 74 average time/residue: 0.0898 time to fit residues: 8.7698 Evaluate side-chains 75 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 71 optimal weight: 0.0170 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114424 restraints weight = 19996.512| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.89 r_work: 0.3184 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6834 Z= 0.113 Angle : 0.476 7.422 9341 Z= 0.251 Chirality : 0.042 0.133 1108 Planarity : 0.003 0.029 1171 Dihedral : 7.518 172.035 992 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.11 % Allowed : 14.06 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.28), residues: 890 helix: 2.51 (0.26), residues: 381 sheet: -0.44 (0.40), residues: 169 loop : -0.65 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 131 TYR 0.016 0.001 TYR R 185 PHE 0.012 0.001 PHE R 240 TRP 0.006 0.001 TRP B 339 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6834) covalent geometry : angle 0.47636 ( 9341) hydrogen bonds : bond 0.04383 ( 339) hydrogen bonds : angle 4.00997 ( 982) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.245 Fit side-chains REVERT: G 18 GLN cc_start: 0.8600 (tp40) cc_final: 0.8156 (tp-100) REVERT: R 302 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8228 (mm) outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.0876 time to fit residues: 8.8729 Evaluate side-chains 74 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 0.0070 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115110 restraints weight = 19157.599| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.77 r_work: 0.3214 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6834 Z= 0.109 Angle : 0.472 7.430 9341 Z= 0.248 Chirality : 0.042 0.222 1108 Planarity : 0.003 0.029 1171 Dihedral : 7.476 171.791 992 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.95 % Allowed : 14.22 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.28), residues: 890 helix: 2.56 (0.26), residues: 381 sheet: -0.41 (0.40), residues: 167 loop : -0.69 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 131 TYR 0.018 0.001 TYR R 185 PHE 0.011 0.001 PHE B 241 TRP 0.006 0.001 TRP A 277 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6834) covalent geometry : angle 0.47186 ( 9341) hydrogen bonds : bond 0.04218 ( 339) hydrogen bonds : angle 3.96275 ( 982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1843.69 seconds wall clock time: 32 minutes 10.08 seconds (1930.08 seconds total)