Starting phenix.real_space_refine on Fri Aug 22 17:54:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggf_40005/08_2025/8ggf_40005.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggf_40005/08_2025/8ggf_40005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ggf_40005/08_2025/8ggf_40005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggf_40005/08_2025/8ggf_40005.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ggf_40005/08_2025/8ggf_40005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggf_40005/08_2025/8ggf_40005.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 33 5.16 5 C 4152 2.51 5 N 1187 2.21 5 O 1232 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: 6607 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2610 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 13, 'TRANS': 345} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 9, 'ASN:plan1': 6, 'GLU:plan': 19, 'ASP:plan': 14, 'PHE:plan': 5, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 257 Chain: "B" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2435 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 8, 'GLN:plan1': 7, 'ARG:plan': 8, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 130 Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 360 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 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: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1155 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain breaks: 9 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 666 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'PHE:plan': 12, 'ASN:plan1': 8, 'GLN:plan1': 4, 'TYR:plan': 5, 'TRP:plan': 5, 'GLU:plan': 7, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 269 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: 1.76, per 1000 atoms: 0.27 Number of scatterers: 6607 At special positions: 0 Unit cell: (83.2992, 137.097, 102.389, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 3 15.00 O 1232 8.00 N 1187 7.00 C 4152 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: 0.56 Conformation dependent library (CDL) restraints added in 280.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 45.6% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.956A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 65 removed outlier: 3.639A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 113 removed outlier: 3.724A pdb=" N GLN A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 135 removed outlier: 4.069A pdb=" N ASP A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 4.035A pdb=" N HIS A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 153 " --> pdb=" O HIS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 removed outlier: 4.231A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.742A pdb=" N PHE A 178 " --> pdb=" O CYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 removed outlier: 3.907A pdb=" N ARG A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.745A pdb=" N ILE A 235 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.718A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.834A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 4.232A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.863A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 383 removed outlier: 3.969A pdb=" N ILE A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 380 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.536A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.649A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.695A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.006A 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 7 through 24 removed outlier: 3.706A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.555A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 55 removed outlier: 3.902A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 78 removed outlier: 4.183A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR R 73 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 removed outlier: 4.531A pdb=" N ALA R 91 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.335A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP R 109 " --> pdb=" O TRP R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 171 removed outlier: 3.756A 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 179 through 187 Processing helix chain 'R' and resid 201 through 229 removed outlier: 4.017A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.621A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN R 224 " --> pdb=" O SER R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 296 removed outlier: 3.739A pdb=" N ILE R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.080A pdb=" N HIS R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 314 removed outlier: 3.985A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU R 310 " --> pdb=" O GLU R 306 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU R 311 " --> pdb=" O VAL R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 322 removed outlier: 4.141A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 210 removed outlier: 6.917A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.697A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.872A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.508A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 7.040A 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 153 removed outlier: 3.778A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.761A 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: 6.825A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.714A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.582A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1382 1.33 - 1.45: 1553 1.45 - 1.57: 3738 1.57 - 1.69: 6 1.69 - 1.81: 44 Bond restraints: 6723 Sorted by residual: bond pdb=" CA ILE A 383 " pdb=" C ILE A 383 " ideal model delta sigma weight residual 1.522 1.477 0.046 1.08e-02 8.57e+03 1.80e+01 bond pdb=" N VAL R 222 " pdb=" CA VAL R 222 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N ILE R 214 " pdb=" CA ILE R 214 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.87e+00 bond pdb=" N VAL R 216 " pdb=" CA VAL R 216 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.37e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.453 -0.056 2.00e-02 2.50e+03 7.93e+00 ... (remaining 6718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 8959 2.27 - 4.54: 199 4.54 - 6.81: 21 6.81 - 9.08: 12 9.08 - 11.35: 6 Bond angle restraints: 9197 Sorted by residual: angle pdb=" N GLN A 384 " pdb=" CA GLN A 384 " pdb=" C GLN A 384 " ideal model delta sigma weight residual 111.90 100.55 11.35 1.32e+00 5.74e-01 7.40e+01 angle pdb=" N ARG A 389 " pdb=" CA ARG A 389 " pdb=" C ARG A 389 " ideal model delta sigma weight residual 111.28 102.56 8.72 1.09e+00 8.42e-01 6.39e+01 angle pdb=" N ASP A 381 " pdb=" CA ASP A 381 " pdb=" C ASP A 381 " ideal model delta sigma weight residual 111.28 118.37 -7.09 1.09e+00 8.42e-01 4.23e+01 angle pdb=" N ASN A 377 " pdb=" CA ASN A 377 " pdb=" C ASN A 377 " ideal model delta sigma weight residual 113.18 105.57 7.61 1.21e+00 6.83e-01 3.95e+01 angle pdb=" N SER R 203 " pdb=" CA SER R 203 " pdb=" C SER R 203 " ideal model delta sigma weight residual 111.28 104.54 6.74 1.09e+00 8.42e-01 3.82e+01 ... (remaining 9192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 3837 29.56 - 59.12: 90 59.12 - 88.68: 10 88.68 - 118.24: 1 118.24 - 147.80: 1 Dihedral angle restraints: 3939 sinusoidal: 1156 harmonic: 2783 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 -43.20 147.80 1 2.00e+01 2.50e-03 4.43e+01 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 260.87 169.92 90.95 1 2.00e+01 2.50e-03 2.44e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.69 16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 3936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 851 0.050 - 0.100: 178 0.100 - 0.150: 61 0.150 - 0.200: 8 0.200 - 0.250: 3 Chirality restraints: 1101 Sorted by residual: chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.72 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA LEU A 393 " pdb=" N LEU A 393 " pdb=" C LEU A 393 " pdb=" CB LEU A 393 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE R 201 " pdb=" N ILE R 201 " pdb=" C ILE R 201 " pdb=" CB ILE R 201 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1098 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 384 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C GLN A 384 " 0.059 2.00e-02 2.50e+03 pdb=" O GLN A 384 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG A 385 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 373 " 0.234 9.50e-02 1.11e+02 1.05e-01 6.74e+00 pdb=" NE ARG A 373 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 373 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 373 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 373 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 365 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C CYS A 365 " 0.031 2.00e-02 2.50e+03 pdb=" O CYS A 365 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A 366 " -0.011 2.00e-02 2.50e+03 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 200 2.70 - 3.25: 6532 3.25 - 3.80: 9419 3.80 - 4.35: 11497 4.35 - 4.90: 19270 Nonbonded interactions: 46918 Sorted by model distance: nonbonded pdb=" O ARG A 385 " pdb=" CG MET A 386 " model vdw 2.147 3.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.294 3.040 nonbonded pdb=" N SER A 51 " pdb=" O2B GTP A 401 " model vdw 2.316 3.120 nonbonded pdb=" O SER A 352 " pdb=" OG SER A 352 " model vdw 2.323 3.040 ... (remaining 46913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.470 Find NCS groups from input model: 0.040 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.005 0.056 6723 Z= 0.317 Angle : 0.795 11.354 9197 Z= 0.504 Chirality : 0.048 0.250 1101 Planarity : 0.004 0.105 1188 Dihedral : 13.583 147.797 2121 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.06 (0.27), residues: 924 helix: 1.48 (0.29), residues: 334 sheet: -0.86 (0.42), residues: 156 loop : -0.90 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 373 TYR 0.006 0.001 TYR A 360 PHE 0.022 0.001 PHE A 146 TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 6723) covalent geometry : angle 0.79467 ( 9197) hydrogen bonds : bond 0.28727 ( 289) hydrogen bonds : angle 7.09102 ( 840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7850 (tm-30) REVERT: G 48 ASP cc_start: 0.8506 (t70) cc_final: 0.8117 (t0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0647 time to fit residues: 7.5450 Evaluate side-chains 62 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 overall best weight: 1.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN A 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.127000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.094148 restraints weight = 13725.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.096668 restraints weight = 7707.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098316 restraints weight = 5511.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099238 restraints weight = 4458.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.100121 restraints weight = 3926.470| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6723 Z= 0.206 Angle : 0.589 8.657 9197 Z= 0.322 Chirality : 0.044 0.183 1101 Planarity : 0.004 0.035 1188 Dihedral : 7.642 135.957 1030 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.13 % Allowed : 10.88 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.27), residues: 924 helix: 1.19 (0.27), residues: 360 sheet: -1.04 (0.40), residues: 168 loop : -1.18 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 374 TYR 0.011 0.001 TYR G 40 PHE 0.013 0.001 PHE B 235 TRP 0.010 0.001 TRP R 158 HIS 0.009 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 6723) covalent geometry : angle 0.58927 ( 9197) hydrogen bonds : bond 0.06555 ( 289) hydrogen bonds : angle 4.95196 ( 840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.168 Fit side-chains REVERT: A 101 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7967 (tm-30) REVERT: G 48 ASP cc_start: 0.8492 (t70) cc_final: 0.8091 (t0) REVERT: R 140 LYS cc_start: 0.7894 (ptpt) cc_final: 0.7564 (pptt) outliers start: 6 outliers final: 6 residues processed: 65 average time/residue: 0.0540 time to fit residues: 5.2846 Evaluate side-chains 63 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 311 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 18 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 30.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.129236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096377 restraints weight = 13445.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.099006 restraints weight = 7574.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.100758 restraints weight = 5351.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101836 restraints weight = 4304.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102674 restraints weight = 3747.537| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6723 Z= 0.112 Angle : 0.473 5.769 9197 Z= 0.257 Chirality : 0.041 0.134 1101 Planarity : 0.003 0.030 1188 Dihedral : 6.768 123.529 1030 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.75 % Allowed : 12.76 % Favored : 86.49 % 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: -0.04 (0.28), residues: 924 helix: 1.58 (0.28), residues: 363 sheet: -0.94 (0.39), residues: 178 loop : -1.10 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 385 TYR 0.005 0.001 TYR B 124 PHE 0.012 0.001 PHE B 199 TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6723) covalent geometry : angle 0.47286 ( 9197) hydrogen bonds : bond 0.04699 ( 289) hydrogen bonds : angle 4.27771 ( 840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.148 Fit side-chains REVERT: A 101 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8036 (tm-30) REVERT: B 111 TYR cc_start: 0.8805 (m-80) cc_final: 0.8406 (m-80) REVERT: G 48 ASP cc_start: 0.8506 (t70) cc_final: 0.8103 (t0) REVERT: R 140 LYS cc_start: 0.7905 (ptpt) cc_final: 0.7586 (pptt) outliers start: 4 outliers final: 2 residues processed: 72 average time/residue: 0.0468 time to fit residues: 5.2080 Evaluate side-chains 60 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 311 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 0.0270 chunk 12 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** 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 = 0.3787 r_free = 0.3787 target = 0.129718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.096844 restraints weight = 13524.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099474 restraints weight = 7560.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101212 restraints weight = 5359.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102179 restraints weight = 4316.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102965 restraints weight = 3779.784| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6723 Z= 0.102 Angle : 0.463 7.552 9197 Z= 0.247 Chirality : 0.041 0.132 1101 Planarity : 0.003 0.031 1188 Dihedral : 6.285 115.489 1030 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.31 % Allowed : 13.13 % Favored : 85.55 % 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: 0.10 (0.28), residues: 924 helix: 1.72 (0.28), residues: 369 sheet: -0.87 (0.39), residues: 178 loop : -1.11 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 374 TYR 0.006 0.001 TYR A 339 PHE 0.010 0.001 PHE B 199 TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 6723) covalent geometry : angle 0.46347 ( 9197) hydrogen bonds : bond 0.03859 ( 289) hydrogen bonds : angle 4.01010 ( 840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.151 Fit side-chains REVERT: A 101 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8070 (tm-30) REVERT: B 78 LYS cc_start: 0.9308 (mtpp) cc_final: 0.8931 (mtpp) REVERT: G 48 ASP cc_start: 0.8458 (t70) cc_final: 0.8117 (t0) REVERT: R 140 LYS cc_start: 0.7897 (ptpt) cc_final: 0.7577 (pptt) outliers start: 7 outliers final: 3 residues processed: 73 average time/residue: 0.0483 time to fit residues: 5.3704 Evaluate side-chains 68 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 311 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 92 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096171 restraints weight = 13728.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098854 restraints weight = 7667.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100548 restraints weight = 5390.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101763 restraints weight = 4345.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102374 restraints weight = 3758.118| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6723 Z= 0.109 Angle : 0.470 9.796 9197 Z= 0.247 Chirality : 0.040 0.126 1101 Planarity : 0.003 0.029 1188 Dihedral : 6.032 109.780 1030 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.25 % Allowed : 14.63 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.28), residues: 924 helix: 1.94 (0.28), residues: 370 sheet: -0.81 (0.39), residues: 178 loop : -1.17 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.006 0.001 TYR A 339 PHE 0.018 0.001 PHE A 146 TRP 0.008 0.001 TRP R 286 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6723) covalent geometry : angle 0.47029 ( 9197) hydrogen bonds : bond 0.03742 ( 289) hydrogen bonds : angle 3.90761 ( 840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.267 Fit side-chains REVERT: B 111 TYR cc_start: 0.8817 (m-80) cc_final: 0.8407 (m-80) REVERT: B 142 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7747 (t-170) REVERT: G 48 ASP cc_start: 0.8448 (t70) cc_final: 0.7971 (t0) REVERT: R 140 LYS cc_start: 0.7919 (ptpt) cc_final: 0.7603 (pptt) outliers start: 12 outliers final: 7 residues processed: 73 average time/residue: 0.0570 time to fit residues: 6.2823 Evaluate side-chains 71 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 45 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.131196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098177 restraints weight = 13720.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.100873 restraints weight = 7733.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102659 restraints weight = 5459.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.103875 restraints weight = 4359.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104601 restraints weight = 3768.946| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6723 Z= 0.087 Angle : 0.446 7.290 9197 Z= 0.234 Chirality : 0.040 0.133 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.657 102.497 1030 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.06 % Allowed : 15.38 % Favored : 82.55 % 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: 0.38 (0.28), residues: 924 helix: 2.10 (0.28), residues: 370 sheet: -0.61 (0.39), residues: 175 loop : -1.20 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.005 0.001 TYR A 339 PHE 0.010 0.001 PHE B 199 TRP 0.008 0.001 TRP B 339 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 6723) covalent geometry : angle 0.44625 ( 9197) hydrogen bonds : bond 0.03086 ( 289) hydrogen bonds : angle 3.70941 ( 840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.274 Fit side-chains REVERT: A 118 GLU cc_start: 0.7864 (mp0) cc_final: 0.7658 (mp0) REVERT: B 142 HIS cc_start: 0.8049 (OUTLIER) cc_final: 0.7736 (t-170) REVERT: G 48 ASP cc_start: 0.8413 (t70) cc_final: 0.8149 (t0) REVERT: R 140 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7629 (pptt) outliers start: 11 outliers final: 4 residues processed: 77 average time/residue: 0.0545 time to fit residues: 6.3849 Evaluate side-chains 70 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** 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 = 0.3798 r_free = 0.3798 target = 0.130123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097321 restraints weight = 13582.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.099964 restraints weight = 7660.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.101748 restraints weight = 5437.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102770 restraints weight = 4350.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103684 restraints weight = 3786.639| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6723 Z= 0.104 Angle : 0.460 6.479 9197 Z= 0.243 Chirality : 0.040 0.125 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.630 100.472 1030 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.25 % Allowed : 15.95 % Favored : 81.80 % 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: 0.46 (0.29), residues: 924 helix: 2.13 (0.28), residues: 376 sheet: -0.55 (0.40), residues: 170 loop : -1.19 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.006 0.001 TYR A 339 PHE 0.019 0.001 PHE A 146 TRP 0.009 0.001 TRP R 286 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6723) covalent geometry : angle 0.45976 ( 9197) hydrogen bonds : bond 0.03321 ( 289) hydrogen bonds : angle 3.71637 ( 840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.263 Fit side-chains REVERT: A 118 GLU cc_start: 0.7856 (mp0) cc_final: 0.7634 (mp0) REVERT: B 142 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7775 (t-170) REVERT: R 140 LYS cc_start: 0.7927 (ptpt) cc_final: 0.7648 (pptt) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.0495 time to fit residues: 5.8770 Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 13 optimal weight: 0.0670 chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 30.0000 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** 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 = 0.3802 r_free = 0.3802 target = 0.130465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097450 restraints weight = 13638.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100114 restraints weight = 7750.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101902 restraints weight = 5465.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103093 restraints weight = 4372.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.103798 restraints weight = 3790.162| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6723 Z= 0.095 Angle : 0.451 5.979 9197 Z= 0.238 Chirality : 0.040 0.126 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.506 97.502 1030 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.25 % Allowed : 16.32 % Favored : 81.43 % 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: 0.47 (0.29), residues: 924 helix: 2.16 (0.28), residues: 376 sheet: -0.59 (0.40), residues: 175 loop : -1.17 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.005 0.001 TYR A 339 PHE 0.009 0.001 PHE B 199 TRP 0.010 0.001 TRP R 286 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 6723) covalent geometry : angle 0.45069 ( 9197) hydrogen bonds : bond 0.03139 ( 289) hydrogen bonds : angle 3.67280 ( 840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.220 Fit side-chains REVERT: A 118 GLU cc_start: 0.7861 (mp0) cc_final: 0.7640 (mp0) REVERT: B 111 TYR cc_start: 0.8795 (m-80) cc_final: 0.8441 (m-80) REVERT: B 142 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7801 (t-170) REVERT: G 48 ASP cc_start: 0.8452 (t0) cc_final: 0.7834 (t0) REVERT: R 140 LYS cc_start: 0.7939 (ptpt) cc_final: 0.7665 (pptt) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.0415 time to fit residues: 4.8935 Evaluate side-chains 76 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 32 optimal weight: 2.9990 chunk 72 optimal weight: 0.0570 chunk 83 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 45 optimal weight: 0.5980 chunk 3 optimal weight: 0.0010 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 75 optimal weight: 0.0970 overall best weight: 0.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** 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 = 0.3842 r_free = 0.3842 target = 0.133470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100419 restraints weight = 13503.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103089 restraints weight = 7665.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104915 restraints weight = 5454.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.106204 restraints weight = 4352.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107073 restraints weight = 3725.782| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6723 Z= 0.081 Angle : 0.449 5.996 9197 Z= 0.234 Chirality : 0.040 0.135 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.161 90.870 1030 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.88 % Allowed : 17.07 % Favored : 81.05 % 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: 0.57 (0.29), residues: 924 helix: 2.26 (0.28), residues: 377 sheet: -0.51 (0.40), residues: 171 loop : -1.17 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.004 0.000 TYR A 339 PHE 0.008 0.000 PHE B 199 TRP 0.009 0.001 TRP B 339 HIS 0.003 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00160 ( 6723) covalent geometry : angle 0.44862 ( 9197) hydrogen bonds : bond 0.02457 ( 289) hydrogen bonds : angle 3.47931 ( 840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7794 (mp0) cc_final: 0.7579 (mp0) REVERT: B 111 TYR cc_start: 0.8745 (m-80) cc_final: 0.8408 (m-80) REVERT: R 140 LYS cc_start: 0.7923 (ptpt) cc_final: 0.7646 (pptt) outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.0462 time to fit residues: 5.7263 Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 311 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.0050 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 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 = 0.3807 r_free = 0.3807 target = 0.131323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098235 restraints weight = 13467.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.100929 restraints weight = 7631.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102670 restraints weight = 5392.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.103894 restraints weight = 4330.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104721 restraints weight = 3735.428| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6723 Z= 0.095 Angle : 0.454 6.086 9197 Z= 0.239 Chirality : 0.040 0.123 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.209 90.722 1030 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.25 % Allowed : 17.07 % Favored : 80.68 % 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: 0.67 (0.29), residues: 924 helix: 2.34 (0.28), residues: 377 sheet: -0.42 (0.40), residues: 171 loop : -1.14 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 20 TYR 0.009 0.001 TYR B 289 PHE 0.020 0.001 PHE A 146 TRP 0.009 0.001 TRP R 286 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 6723) covalent geometry : angle 0.45422 ( 9197) hydrogen bonds : bond 0.02797 ( 289) hydrogen bonds : angle 3.51770 ( 840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7767 (mp0) cc_final: 0.7544 (mp0) REVERT: B 111 TYR cc_start: 0.8783 (m-80) cc_final: 0.8437 (m-80) REVERT: R 140 LYS cc_start: 0.7921 (ptpt) cc_final: 0.7664 (pptt) outliers start: 12 outliers final: 10 residues processed: 75 average time/residue: 0.0471 time to fit residues: 5.6776 Evaluate side-chains 76 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 311 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 80 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096212 restraints weight = 13631.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098854 restraints weight = 7665.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100583 restraints weight = 5424.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101776 restraints weight = 4356.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102441 restraints weight = 3775.560| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6723 Z= 0.123 Angle : 0.480 5.982 9197 Z= 0.254 Chirality : 0.041 0.127 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.405 92.164 1030 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.44 % Allowed : 17.07 % Favored : 80.49 % 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: 0.66 (0.29), residues: 924 helix: 2.32 (0.28), residues: 376 sheet: -0.30 (0.41), residues: 165 loop : -1.17 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.010 0.001 TYR B 289 PHE 0.010 0.001 PHE B 241 TRP 0.013 0.001 TRP R 286 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6723) covalent geometry : angle 0.47976 ( 9197) hydrogen bonds : bond 0.03381 ( 289) hydrogen bonds : angle 3.68250 ( 840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1355.06 seconds wall clock time: 23 minutes 54.64 seconds (1434.64 seconds total)