Starting phenix.real_space_refine on Fri Aug 22 18:52:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gg9_29999/08_2025/8gg9_29999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gg9_29999/08_2025/8gg9_29999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gg9_29999/08_2025/8gg9_29999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gg9_29999/08_2025/8gg9_29999.map" model { file = "/net/cci-nas-00/data/ceres_data/8gg9_29999/08_2025/8gg9_29999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gg9_29999/08_2025/8gg9_29999.cif" } resolution = 3.4 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 42 5.16 5 C 4461 2.51 5 N 1226 2.21 5 O 1291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 7023 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2173 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 6, 'TRANS': 293} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 11, 'ASN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 8, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 201 Chain: "B" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2467 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 5, 'ARG:plan': 6, 'GLU:plan': 6, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 101 Chain: "G" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 355 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 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: 1981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1981 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'TRP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 10, 'GLN:plan1': 4, 'ASN:plan1': 4, 'ARG:plan': 6, 'TYR:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 155 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: 1.60, per 1000 atoms: 0.23 Number of scatterers: 7023 At special positions: 0 Unit cell: (83.2992, 136.229, 98.9178, 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 42 16.00 P 3 15.00 O 1291 8.00 N 1226 7.00 C 4461 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: 0.49 Conformation dependent library (CDL) restraints added in 324.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1850 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 49.5% alpha, 14.7% 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: 4.171A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 65 removed outlier: 3.510A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 Processing helix chain 'A' and resid 111 through 112 No H-bonds generated for 'chain 'A' and resid 111 through 112' Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.687A pdb=" N CYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.584A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.389A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.649A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.828A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.882A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.618A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.510A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.038A 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 10 through 24 removed outlier: 3.573A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.704A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.616A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.760A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 86 removed outlier: 4.000A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.586A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.670A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.905A 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: 3.621A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.582A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.780A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 326 removed outlier: 3.821A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) 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 207 through 213 removed outlier: 6.256A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.650A 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: 6.818A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.881A 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: 3.819A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.715A 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: 7.024A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.916A 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: 6.953A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.710A 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: 6.621A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.871A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277 removed outlier: 3.775A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 1056 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: 0.82 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1242 1.32 - 1.45: 1903 1.45 - 1.57: 3958 1.57 - 1.69: 4 1.69 - 1.81: 57 Bond restraints: 7164 Sorted by residual: bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.24e-02 6.50e+03 8.67e+00 bond pdb=" N ASP A 223 " pdb=" CA ASP A 223 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.21e-02 6.83e+03 8.37e+00 bond pdb=" N VAL A 202 " pdb=" CA VAL A 202 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.33e+00 bond pdb=" C2 GTP A 401 " pdb=" N3 GTP A 401 " ideal model delta sigma weight residual 1.380 1.324 0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" N LEU A 203 " pdb=" CA LEU A 203 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.34e-02 5.57e+03 6.87e+00 ... (remaining 7159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 9652 2.37 - 4.75: 120 4.75 - 7.12: 16 7.12 - 9.49: 6 9.49 - 11.87: 4 Bond angle restraints: 9798 Sorted by residual: angle pdb=" N GLY B 53 " pdb=" CA GLY B 53 " pdb=" C GLY B 53 " ideal model delta sigma weight residual 115.64 125.19 -9.55 1.46e+00 4.69e-01 4.27e+01 angle pdb=" N GLN A 227 " pdb=" CA GLN A 227 " pdb=" C GLN A 227 " ideal model delta sigma weight residual 111.07 105.47 5.60 1.07e+00 8.73e-01 2.74e+01 angle pdb=" CA GLY A 226 " pdb=" C GLY A 226 " pdb=" O GLY A 226 " ideal model delta sigma weight residual 121.57 117.35 4.22 8.70e-01 1.32e+00 2.35e+01 angle pdb=" N LYS A 233 " pdb=" CA LYS A 233 " pdb=" C LYS A 233 " ideal model delta sigma weight residual 113.17 107.78 5.39 1.26e+00 6.30e-01 1.83e+01 angle pdb=" CA GLY A 226 " pdb=" C GLY A 226 " pdb=" N GLN A 227 " ideal model delta sigma weight residual 114.98 119.67 -4.69 1.14e+00 7.69e-01 1.69e+01 ... (remaining 9793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.97: 4091 33.97 - 67.95: 68 67.95 - 101.92: 5 101.92 - 135.89: 1 135.89 - 169.86: 4 Dihedral angle restraints: 4169 sinusoidal: 1326 harmonic: 2843 Sorted by residual: 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 -65.27 169.86 1 2.00e+01 2.50e-03 4.76e+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 -96.66 165.93 1 2.00e+01 2.50e-03 4.73e+01 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 303.79 157.34 146.45 1 2.00e+01 2.50e-03 4.40e+01 ... (remaining 4166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 869 0.045 - 0.090: 221 0.090 - 0.135: 65 0.135 - 0.180: 7 0.180 - 0.226: 4 Chirality restraints: 1166 Sorted by residual: chirality pdb=" C2' GTP A 401 " pdb=" C1' GTP A 401 " pdb=" C3' GTP A 401 " pdb=" O2' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA GLN A 227 " pdb=" N GLN A 227 " pdb=" C GLN A 227 " pdb=" CB GLN A 227 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ARG A 231 " pdb=" N ARG A 231 " pdb=" C ARG A 231 " pdb=" CB ARG A 231 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 ... (remaining 1163 not shown) Planarity restraints: 1248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 201 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.89e+00 pdb=" C ARG A 201 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG A 201 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 202 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 222 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C PHE A 222 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE A 222 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 223 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 52 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C ARG B 52 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG B 52 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY B 53 " 0.010 2.00e-02 2.50e+03 ... (remaining 1245 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 562 2.74 - 3.28: 6747 3.28 - 3.82: 10871 3.82 - 4.36: 11858 4.36 - 4.90: 22147 Nonbonded interactions: 52185 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.198 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.262 3.040 nonbonded pdb=" NE2 HIS B 142 " pdb=" OG SER B 161 " model vdw 2.280 3.120 nonbonded pdb=" NE2 GLN A 213 " pdb=" OD1 ASN A 218 " model vdw 2.315 3.120 nonbonded pdb=" O LYS B 57 " pdb=" OG SER B 74 " model vdw 2.320 3.040 ... (remaining 52180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.880 Find NCS groups from input model: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 0.056 7164 Z= 0.234 Angle : 0.681 11.867 9798 Z= 0.377 Chirality : 0.045 0.226 1166 Planarity : 0.003 0.034 1248 Dihedral : 14.830 169.863 2319 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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 (0.27), residues: 955 helix: 1.59 (0.26), residues: 411 sheet: -0.33 (0.44), residues: 150 loop : -0.83 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 131 TYR 0.011 0.001 TYR R 308 PHE 0.013 0.001 PHE B 235 TRP 0.024 0.001 TRP A 234 HIS 0.007 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 7164) covalent geometry : angle 0.68068 ( 9798) hydrogen bonds : bond 0.23791 ( 361) hydrogen bonds : angle 6.91357 ( 1056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.8861 (tptt) cc_final: 0.8657 (tttp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0587 time to fit residues: 7.4055 Evaluate side-chains 72 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** R 229 GLN R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125208 restraints weight = 9988.752| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.22 r_work: 0.3315 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7164 Z= 0.133 Angle : 0.494 6.784 9798 Z= 0.269 Chirality : 0.041 0.147 1166 Planarity : 0.003 0.036 1248 Dihedral : 10.785 169.647 1061 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.64 % Allowed : 7.79 % Favored : 91.57 % 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: 0.86 (0.28), residues: 955 helix: 1.94 (0.26), residues: 441 sheet: -0.29 (0.41), residues: 171 loop : -0.75 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 131 TYR 0.009 0.001 TYR R 308 PHE 0.011 0.001 PHE B 235 TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7164) covalent geometry : angle 0.49397 ( 9798) hydrogen bonds : bond 0.05448 ( 361) hydrogen bonds : angle 4.64663 ( 1056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.171 Fit side-chains REVERT: A 16 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7185 (tm-30) outliers start: 4 outliers final: 3 residues processed: 79 average time/residue: 0.0637 time to fit residues: 7.2230 Evaluate side-chains 71 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 223 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.153717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124144 restraints weight = 9956.227| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.20 r_work: 0.3302 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7164 Z= 0.128 Angle : 0.476 6.741 9798 Z= 0.256 Chirality : 0.041 0.136 1166 Planarity : 0.003 0.036 1248 Dihedral : 10.377 165.882 1061 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.43 % Allowed : 11.13 % Favored : 87.44 % 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: 0.95 (0.28), residues: 955 helix: 2.12 (0.26), residues: 441 sheet: -0.23 (0.42), residues: 169 loop : -0.87 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 328 TYR 0.011 0.001 TYR R 308 PHE 0.012 0.001 PHE B 241 TRP 0.011 0.001 TRP A 277 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7164) covalent geometry : angle 0.47624 ( 9798) hydrogen bonds : bond 0.04453 ( 361) hydrogen bonds : angle 4.25232 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.220 Fit side-chains REVERT: A 50 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8141 (mm-30) REVERT: R 328 ARG cc_start: 0.5725 (ttp-110) cc_final: 0.5493 (ttp-110) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.0681 time to fit residues: 7.4905 Evaluate side-chains 79 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 232 LYS Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 95 optimal weight: 0.0060 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 340 ASN R 229 GLN ** R 318 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 = 0.3872 r_free = 0.3872 target = 0.155028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124018 restraints weight = 9973.726| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.22 r_work: 0.3334 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7164 Z= 0.102 Angle : 0.443 6.362 9798 Z= 0.238 Chirality : 0.040 0.131 1166 Planarity : 0.003 0.034 1248 Dihedral : 10.087 163.626 1061 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.11 % Allowed : 11.92 % Favored : 86.96 % 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: 1.10 (0.28), residues: 955 helix: 2.28 (0.26), residues: 441 sheet: -0.25 (0.42), residues: 169 loop : -0.79 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.011 0.001 TYR B 59 PHE 0.011 0.001 PHE B 241 TRP 0.011 0.001 TRP A 277 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 7164) covalent geometry : angle 0.44338 ( 9798) hydrogen bonds : bond 0.03672 ( 361) hydrogen bonds : angle 4.04058 ( 1056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.267 Fit side-chains REVERT: A 255 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7899 (mtp) outliers start: 7 outliers final: 6 residues processed: 78 average time/residue: 0.0593 time to fit residues: 6.9390 Evaluate side-chains 76 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain R residue 232 LYS Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** R 229 GLN R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.153864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122631 restraints weight = 9964.013| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.26 r_work: 0.3311 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7164 Z= 0.119 Angle : 0.458 6.447 9798 Z= 0.245 Chirality : 0.041 0.133 1166 Planarity : 0.003 0.035 1248 Dihedral : 9.930 162.355 1061 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.38 % Allowed : 12.08 % Favored : 85.53 % 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: 1.13 (0.28), residues: 955 helix: 2.32 (0.26), residues: 442 sheet: -0.22 (0.42), residues: 169 loop : -0.82 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 131 TYR 0.011 0.001 TYR B 59 PHE 0.012 0.001 PHE B 241 TRP 0.013 0.001 TRP A 277 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7164) covalent geometry : angle 0.45832 ( 9798) hydrogen bonds : bond 0.03893 ( 361) hydrogen bonds : angle 4.00261 ( 1056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.249 Fit side-chains REVERT: A 255 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7901 (mtp) REVERT: B 142 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.8289 (t70) REVERT: R 328 ARG cc_start: 0.5915 (ttp-110) cc_final: 0.5440 (ttp-110) outliers start: 15 outliers final: 10 residues processed: 82 average time/residue: 0.0661 time to fit residues: 7.6477 Evaluate side-chains 82 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 232 LYS Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** R 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.155768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124462 restraints weight = 9984.837| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.26 r_work: 0.3341 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7164 Z= 0.091 Angle : 0.429 6.184 9798 Z= 0.230 Chirality : 0.040 0.128 1166 Planarity : 0.003 0.033 1248 Dihedral : 9.752 161.149 1061 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.27 % Allowed : 13.67 % Favored : 85.06 % 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 (0.28), residues: 955 helix: 2.41 (0.25), residues: 443 sheet: -0.13 (0.43), residues: 164 loop : -0.73 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.011 0.001 TYR B 59 PHE 0.010 0.001 PHE B 241 TRP 0.012 0.001 TRP A 277 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 7164) covalent geometry : angle 0.42919 ( 9798) hydrogen bonds : bond 0.03349 ( 361) hydrogen bonds : angle 3.88683 ( 1056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.212 Fit side-chains REVERT: A 50 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8198 (mm-30) REVERT: A 255 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.7906 (mtp) REVERT: B 57 LYS cc_start: 0.8467 (pttm) cc_final: 0.8244 (pttm) REVERT: B 142 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.8308 (t70) REVERT: R 328 ARG cc_start: 0.5946 (ttp-110) cc_final: 0.5478 (ttp-110) outliers start: 8 outliers final: 5 residues processed: 77 average time/residue: 0.0608 time to fit residues: 6.6559 Evaluate side-chains 78 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 86 optimal weight: 0.0270 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- 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** R 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124662 restraints weight = 10062.716| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.18 r_work: 0.3288 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7164 Z= 0.119 Angle : 0.454 6.303 9798 Z= 0.243 Chirality : 0.041 0.128 1166 Planarity : 0.003 0.034 1248 Dihedral : 9.686 160.400 1061 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.23 % Allowed : 12.72 % Favored : 85.06 % 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: 1.29 (0.28), residues: 955 helix: 2.44 (0.26), residues: 442 sheet: -0.16 (0.42), residues: 169 loop : -0.72 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.010 0.001 TYR R 308 PHE 0.013 0.001 PHE B 241 TRP 0.014 0.001 TRP A 277 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7164) covalent geometry : angle 0.45366 ( 9798) hydrogen bonds : bond 0.03776 ( 361) hydrogen bonds : angle 3.90744 ( 1056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.168 Fit side-chains REVERT: A 255 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7858 (mtp) REVERT: B 123 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8560 (mt) REVERT: B 142 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.8406 (t70) REVERT: R 328 ARG cc_start: 0.5971 (ttp-110) cc_final: 0.5484 (ttp-110) outliers start: 14 outliers final: 9 residues processed: 79 average time/residue: 0.0529 time to fit residues: 6.0622 Evaluate side-chains 84 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** R 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.153121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.123523 restraints weight = 10066.534| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.22 r_work: 0.3283 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7164 Z= 0.131 Angle : 0.468 6.299 9798 Z= 0.251 Chirality : 0.041 0.125 1166 Planarity : 0.003 0.035 1248 Dihedral : 9.667 160.296 1061 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.23 % Allowed : 13.35 % Favored : 84.42 % 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: 1.23 (0.28), residues: 955 helix: 2.39 (0.26), residues: 442 sheet: -0.19 (0.42), residues: 169 loop : -0.76 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.011 0.001 TYR R 308 PHE 0.013 0.001 PHE B 241 TRP 0.016 0.001 TRP A 277 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7164) covalent geometry : angle 0.46819 ( 9798) hydrogen bonds : bond 0.04040 ( 361) hydrogen bonds : angle 3.95278 ( 1056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.168 Fit side-chains REVERT: A 255 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8219 (mtt) REVERT: B 123 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8566 (mt) outliers start: 14 outliers final: 8 residues processed: 78 average time/residue: 0.0587 time to fit residues: 6.5738 Evaluate side-chains 81 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 88 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 340 ASN R 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.154784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.123784 restraints weight = 10003.953| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.32 r_work: 0.3322 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7164 Z= 0.099 Angle : 0.442 5.994 9798 Z= 0.237 Chirality : 0.040 0.128 1166 Planarity : 0.003 0.034 1248 Dihedral : 9.440 158.018 1061 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.91 % Allowed : 13.83 % Favored : 84.26 % 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: 1.33 (0.28), residues: 955 helix: 2.48 (0.25), residues: 442 sheet: -0.17 (0.42), residues: 170 loop : -0.69 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 328 TYR 0.009 0.001 TYR B 59 PHE 0.011 0.001 PHE B 241 TRP 0.015 0.001 TRP A 277 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 7164) covalent geometry : angle 0.44200 ( 9798) hydrogen bonds : bond 0.03452 ( 361) hydrogen bonds : angle 3.85708 ( 1056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.204 Fit side-chains REVERT: A 255 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8179 (mtt) REVERT: B 188 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8323 (mtp) REVERT: R 328 ARG cc_start: 0.5717 (ttp-110) cc_final: 0.5343 (ttp-110) outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 0.0597 time to fit residues: 7.3186 Evaluate side-chains 84 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** R 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.153942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124283 restraints weight = 9970.445| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.16 r_work: 0.3297 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7164 Z= 0.114 Angle : 0.459 6.029 9798 Z= 0.246 Chirality : 0.041 0.126 1166 Planarity : 0.003 0.034 1248 Dihedral : 9.297 156.067 1061 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.75 % Allowed : 14.47 % Favored : 83.78 % 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: 1.30 (0.28), residues: 955 helix: 2.45 (0.26), residues: 443 sheet: -0.25 (0.42), residues: 173 loop : -0.66 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 328 TYR 0.010 0.001 TYR R 308 PHE 0.012 0.001 PHE B 241 TRP 0.017 0.001 TRP A 277 HIS 0.002 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7164) covalent geometry : angle 0.45865 ( 9798) hydrogen bonds : bond 0.03683 ( 361) hydrogen bonds : angle 3.86728 ( 1056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.198 Fit side-chains REVERT: A 255 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8179 (mtt) REVERT: R 328 ARG cc_start: 0.5737 (ttp-110) cc_final: 0.5367 (ttp-110) outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 0.0509 time to fit residues: 5.5869 Evaluate side-chains 79 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 chunk 6 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 GLN R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124299 restraints weight = 9892.673| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.30 r_work: 0.3331 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7164 Z= 0.099 Angle : 0.440 6.037 9798 Z= 0.236 Chirality : 0.040 0.127 1166 Planarity : 0.003 0.033 1248 Dihedral : 9.033 153.143 1061 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.59 % Allowed : 15.10 % Favored : 83.31 % 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: 1.42 (0.28), residues: 955 helix: 2.54 (0.25), residues: 441 sheet: -0.08 (0.43), residues: 166 loop : -0.64 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 328 TYR 0.009 0.001 TYR R 308 PHE 0.011 0.001 PHE B 241 TRP 0.026 0.001 TRP A 277 HIS 0.002 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 7164) covalent geometry : angle 0.44015 ( 9798) hydrogen bonds : bond 0.03344 ( 361) hydrogen bonds : angle 3.79380 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1567.83 seconds wall clock time: 27 minutes 29.36 seconds (1649.36 seconds total)