Starting phenix.real_space_refine on Tue Feb 11 20:45:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggf_40005/02_2025/8ggf_40005.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggf_40005/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggf_40005/02_2025/8ggf_40005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggf_40005/02_2025/8ggf_40005.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggf_40005/02_2025/8ggf_40005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggf_40005/02_2025/8ggf_40005.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 14, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 9} 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: {'GLN:plan1': 7, 'GLU:plan': 8, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 8} 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, 'GLU:plan': 4, 'ARG:plan': 2, '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: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 5, 'ASP:plan': 3, 'PHE:plan': 12, 'GLU:plan': 7, 'ARG:plan': 5} 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: 5.08, per 1000 atoms: 0.77 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: 1.59 Conformation dependent library (CDL) restraints added in 891.5 milliseconds 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: 0.68 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: 1.76 Time building geometry restraints manager: 1.87 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: 2.270 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.240 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- 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= 0.330 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (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 TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.022 0.001 PHE A 146 TYR 0.006 0.001 TYR A 360 ARG 0.002 0.000 ARG A 373 *********************** 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 : 0.785 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: 0.1712 time to fit residues: 19.8435 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 : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.127775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094983 restraints weight = 13475.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097497 restraints weight = 7592.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099158 restraints weight = 5408.286| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6723 Z= 0.261 Angle : 0.564 8.567 9197 Z= 0.309 Chirality : 0.043 0.182 1101 Planarity : 0.004 0.035 1188 Dihedral : 7.575 135.715 1030 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.13 % Allowed : 9.94 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.27), residues: 924 helix: 1.26 (0.27), residues: 360 sheet: -0.90 (0.40), residues: 166 loop : -1.17 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 158 HIS 0.004 0.001 HIS B 142 PHE 0.011 0.001 PHE B 199 TYR 0.010 0.001 TYR A 358 ARG 0.007 0.000 ARG A 374 *********************** 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 70 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.741 Fit side-chains REVERT: A 101 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7957 (tm-30) REVERT: G 48 ASP cc_start: 0.8516 (t70) cc_final: 0.8017 (t0) REVERT: R 140 LYS cc_start: 0.7892 (ptpt) cc_final: 0.7590 (pptt) outliers start: 6 outliers final: 6 residues processed: 68 average time/residue: 0.1525 time to fit residues: 15.4436 Evaluate side-chains 65 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 78 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 61 optimal weight: 0.0020 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 35 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.127049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.094163 restraints weight = 13643.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096720 restraints weight = 7679.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098352 restraints weight = 5476.292| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6723 Z= 0.246 Angle : 0.514 5.788 9197 Z= 0.279 Chirality : 0.042 0.129 1101 Planarity : 0.003 0.032 1188 Dihedral : 6.994 125.078 1030 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.31 % Allowed : 12.38 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.28), residues: 924 helix: 1.53 (0.28), residues: 363 sheet: -0.98 (0.39), residues: 176 loop : -1.21 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 154 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.008 0.001 TYR A 360 ARG 0.004 0.000 ARG A 374 *********************** 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 74 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 1.309 Fit side-chains REVERT: A 101 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8114 (tm-30) REVERT: B 111 TYR cc_start: 0.8870 (m-80) cc_final: 0.8478 (m-80) REVERT: R 140 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7616 (pptt) outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 0.1567 time to fit residues: 17.9991 Evaluate side-chains 62 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 149 CYS 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 41 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 chunk 6 optimal weight: 0.0000 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.129380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096465 restraints weight = 13601.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099130 restraints weight = 7667.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100853 restraints weight = 5421.996| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6723 Z= 0.134 Angle : 0.463 7.123 9197 Z= 0.249 Chirality : 0.040 0.131 1101 Planarity : 0.003 0.031 1188 Dihedral : 6.356 116.362 1030 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.50 % Allowed : 13.70 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.28), residues: 924 helix: 1.78 (0.28), residues: 363 sheet: -0.87 (0.39), residues: 178 loop : -1.14 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS A 149 PHE 0.011 0.001 PHE B 199 TYR 0.005 0.001 TYR A 147 ARG 0.003 0.000 ARG A 374 *********************** 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: 8 poor density : 66 time to evaluate : 0.754 Fit side-chains REVERT: A 101 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8164 (tm-30) REVERT: B 78 LYS cc_start: 0.9285 (mtpp) cc_final: 0.8926 (mtpp) REVERT: B 111 TYR cc_start: 0.8863 (m-80) cc_final: 0.8467 (m-80) REVERT: B 117 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8927 (tt) REVERT: B 142 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7693 (t-170) REVERT: G 48 ASP cc_start: 0.8494 (t0) cc_final: 0.7711 (t0) REVERT: R 140 LYS cc_start: 0.7914 (ptpt) cc_final: 0.7591 (pptt) outliers start: 8 outliers final: 4 residues processed: 72 average time/residue: 0.1225 time to fit residues: 13.5069 Evaluate side-chains 67 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 124 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 13 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 62 optimal weight: 0.0970 chunk 74 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 81 optimal weight: 0.2980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.130693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097868 restraints weight = 13416.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100562 restraints weight = 7515.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102334 restraints weight = 5300.339| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2292 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= 0.119 Angle : 0.442 5.747 9197 Z= 0.235 Chirality : 0.040 0.135 1101 Planarity : 0.003 0.030 1188 Dihedral : 5.841 106.849 1030 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.06 % Allowed : 14.63 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.28), residues: 924 helix: 1.95 (0.28), residues: 370 sheet: -0.63 (0.39), residues: 175 loop : -1.22 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 286 HIS 0.002 0.001 HIS B 91 PHE 0.021 0.001 PHE A 146 TYR 0.006 0.000 TYR A 339 ARG 0.004 0.000 ARG A 374 *********************** 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 80 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.758 Fit side-chains REVERT: A 118 GLU cc_start: 0.7900 (mp0) cc_final: 0.7694 (mp0) REVERT: B 78 LYS cc_start: 0.9318 (mtpp) cc_final: 0.8923 (mtpp) REVERT: B 117 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8913 (tt) REVERT: G 48 ASP cc_start: 0.8464 (t0) cc_final: 0.7661 (t0) REVERT: R 140 LYS cc_start: 0.7896 (ptpt) cc_final: 0.7594 (pptt) outliers start: 11 outliers final: 6 residues processed: 77 average time/residue: 0.1362 time to fit residues: 15.5668 Evaluate side-chains 73 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 117 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 0.0570 chunk 47 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.130595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097741 restraints weight = 13414.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100405 restraints weight = 7609.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102108 restraints weight = 5389.747| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6723 Z= 0.132 Angle : 0.440 5.758 9197 Z= 0.236 Chirality : 0.040 0.127 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.670 102.258 1030 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.63 % Allowed : 14.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.28), residues: 924 helix: 2.07 (0.28), residues: 370 sheet: -0.55 (0.39), residues: 175 loop : -1.18 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 286 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE B 292 TYR 0.012 0.001 TYR B 111 ARG 0.003 0.000 ARG A 20 *********************** 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 82 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.716 Fit side-chains REVERT: A 118 GLU cc_start: 0.7860 (mp0) cc_final: 0.7625 (mp0) REVERT: B 111 TYR cc_start: 0.8838 (m-80) cc_final: 0.8498 (m-80) REVERT: B 117 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8928 (tt) REVERT: B 142 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7800 (t-170) REVERT: G 48 ASP cc_start: 0.8485 (t0) cc_final: 0.7720 (t0) REVERT: R 140 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7643 (pptt) outliers start: 14 outliers final: 9 residues processed: 77 average time/residue: 0.1795 time to fit residues: 20.1540 Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 117 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 G residue 41 CYS Chi-restraints excluded: chain R residue 124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 18 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 0.0370 chunk 57 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 0.0870 chunk 75 optimal weight: 10.0000 overall best weight: 0.7838 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.130184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097390 restraints weight = 13419.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.100015 restraints weight = 7635.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101772 restraints weight = 5436.871| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2434 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= 0.148 Angle : 0.446 5.861 9197 Z= 0.238 Chirality : 0.040 0.125 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.594 99.586 1030 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.81 % Allowed : 16.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.28), residues: 924 helix: 2.14 (0.28), residues: 370 sheet: -0.52 (0.40), residues: 175 loop : -1.17 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 286 HIS 0.003 0.001 HIS B 142 PHE 0.020 0.001 PHE A 146 TYR 0.010 0.001 TYR B 111 ARG 0.003 0.000 ARG A 20 *********************** 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 80 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.797 Fit side-chains REVERT: A 118 GLU cc_start: 0.7849 (mp0) cc_final: 0.7593 (mp0) REVERT: B 111 TYR cc_start: 0.8856 (m-80) cc_final: 0.8455 (m-80) REVERT: B 117 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8936 (tt) REVERT: B 142 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7781 (t-170) REVERT: R 140 LYS cc_start: 0.7926 (ptpt) cc_final: 0.7654 (pptt) outliers start: 15 outliers final: 10 residues processed: 75 average time/residue: 0.1315 time to fit residues: 14.8993 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 : 0.733 ------------------------------------------------------------------------------- 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 117 LEU 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 234 PHE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 0.0050 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.131004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098147 restraints weight = 13519.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100822 restraints weight = 7633.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102506 restraints weight = 5396.805| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2553 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= 0.126 Angle : 0.437 5.888 9197 Z= 0.233 Chirality : 0.040 0.128 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.418 95.818 1030 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.44 % Allowed : 16.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 924 helix: 2.15 (0.28), residues: 376 sheet: -0.46 (0.40), residues: 175 loop : -1.15 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 286 HIS 0.002 0.000 HIS B 91 PHE 0.010 0.001 PHE B 292 TYR 0.010 0.001 TYR B 111 ARG 0.003 0.000 ARG A 20 *********************** 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: 13 poor density : 66 time to evaluate : 0.726 Fit side-chains REVERT: A 118 GLU cc_start: 0.7832 (mp0) cc_final: 0.7559 (mp0) REVERT: B 111 TYR cc_start: 0.8842 (m-80) cc_final: 0.8434 (m-80) REVERT: B 117 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8924 (tt) REVERT: B 142 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7802 (t-170) REVERT: B 234 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8639 (t80) REVERT: R 140 LYS cc_start: 0.7930 (ptpt) cc_final: 0.7657 (pptt) outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 0.1327 time to fit residues: 15.1661 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 : 0.831 ------------------------------------------------------------------------------- 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 117 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 G residue 41 CYS Chi-restraints excluded: chain R residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 92 optimal weight: 7.9990 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** B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.130397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097485 restraints weight = 13608.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.100137 restraints weight = 7708.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101783 restraints weight = 5463.392| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6723 Z= 0.148 Angle : 0.448 5.972 9197 Z= 0.238 Chirality : 0.040 0.124 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.414 94.814 1030 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.25 % Allowed : 17.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.29), residues: 924 helix: 2.22 (0.28), residues: 376 sheet: -0.49 (0.40), residues: 175 loop : -1.14 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 286 HIS 0.003 0.001 HIS B 142 PHE 0.022 0.001 PHE A 146 TYR 0.009 0.001 TYR B 111 ARG 0.002 0.000 ARG A 20 *********************** 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 77 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.725 Fit side-chains REVERT: A 118 GLU cc_start: 0.7831 (mp0) cc_final: 0.7567 (mp0) REVERT: B 111 TYR cc_start: 0.8861 (m-80) cc_final: 0.8458 (m-80) REVERT: B 117 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8930 (tt) REVERT: B 142 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7786 (t-170) REVERT: B 234 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8697 (t80) REVERT: R 140 LYS cc_start: 0.7937 (ptpt) cc_final: 0.7657 (pptt) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.1330 time to fit residues: 15.2528 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 : 0.738 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 117 LEU 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 234 PHE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 91 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 0.0570 chunk 61 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.130474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097579 restraints weight = 13672.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100228 restraints weight = 7696.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101970 restraints weight = 5454.709| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2593 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= 0.142 Angle : 0.447 5.965 9197 Z= 0.238 Chirality : 0.040 0.125 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.367 93.501 1030 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.38 % Allowed : 16.51 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.29), residues: 924 helix: 2.25 (0.28), residues: 376 sheet: -0.44 (0.40), residues: 175 loop : -1.12 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 286 HIS 0.002 0.000 HIS B 142 PHE 0.011 0.001 PHE B 292 TYR 0.009 0.001 TYR B 111 ARG 0.002 0.000 ARG A 20 ********************** 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 83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.742 Fit side-chains REVERT: A 118 GLU cc_start: 0.7833 (mp0) cc_final: 0.7561 (mp0) REVERT: B 111 TYR cc_start: 0.8854 (m-80) cc_final: 0.8454 (m-80) REVERT: B 117 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8934 (tt) REVERT: B 142 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7810 (t-170) REVERT: B 234 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8697 (t80) REVERT: R 140 LYS cc_start: 0.7942 (ptpt) cc_final: 0.7666 (pptt) outliers start: 18 outliers final: 11 residues processed: 79 average time/residue: 0.1282 time to fit residues: 15.5239 Evaluate side-chains 78 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 117 LEU 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 234 PHE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 39 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 86 optimal weight: 0.0070 chunk 12 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.128627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095840 restraints weight = 13710.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.098469 restraints weight = 7781.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.100165 restraints weight = 5491.587| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6723 Z= 0.213 Angle : 0.490 7.555 9197 Z= 0.259 Chirality : 0.042 0.180 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.550 94.161 1030 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.63 % Allowed : 17.07 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 924 helix: 2.11 (0.28), residues: 376 sheet: -0.38 (0.41), residues: 168 loop : -1.15 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 286 HIS 0.005 0.001 HIS A 149 PHE 0.010 0.001 PHE B 241 TYR 0.009 0.001 TYR B 111 ARG 0.002 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2475.89 seconds wall clock time: 45 minutes 2.85 seconds (2702.85 seconds total)