Starting phenix.real_space_refine on Tue Mar 11 20:15:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggf_40005/03_2025/8ggf_40005.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggf_40005/03_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_40005/03_2025/8ggf_40005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggf_40005/03_2025/8ggf_40005.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggf_40005/03_2025/8ggf_40005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggf_40005/03_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-5624/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: 4.69, per 1000 atoms: 0.71 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: 1.62 Conformation dependent library (CDL) restraints added in 981.9 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: 0.76 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: 1.60 Time building geometry restraints manager: 1.92 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.870 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- 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 : 0.766 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: 0.1730 time to fit residues: 20.2026 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 : 0.760 ------------------------------------------------------------------------------- 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 = 50)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094868 restraints weight = 13475.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097397 restraints weight = 7632.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099116 restraints weight = 5447.203| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.685 Fit side-chains REVERT: A 101 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7959 (tm-30) REVERT: G 48 ASP cc_start: 0.8516 (t70) cc_final: 0.8015 (t0) REVERT: R 140 LYS cc_start: 0.7892 (ptpt) cc_final: 0.7585 (pptt) outliers start: 6 outliers final: 6 residues processed: 68 average time/residue: 0.1312 time to fit residues: 13.4221 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 : 0.683 ------------------------------------------------------------------------------- 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: 0.0370 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: 0.0870 chunk 74 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.0242 ------------------------------------------------------------------------------- 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 R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.126194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.093354 restraints weight = 13708.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095885 restraints weight = 7757.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097574 restraints weight = 5511.262| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6723 Z= 0.301 Angle : 0.544 6.202 9197 Z= 0.296 Chirality : 0.043 0.143 1101 Planarity : 0.003 0.032 1188 Dihedral : 7.274 128.347 1030 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.31 % Allowed : 12.76 % Favored : 85.93 % 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: -0.24 (0.28), residues: 924 helix: 1.42 (0.28), residues: 359 sheet: -1.05 (0.40), residues: 171 loop : -1.20 (0.30), residues: 394 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 0.013 0.001 PHE B 235 TYR 0.009 0.001 TYR A 360 ARG 0.003 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 71 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.700 Fit side-chains REVERT: B 111 TYR cc_start: 0.8891 (m-80) cc_final: 0.8501 (m-80) REVERT: R 140 LYS cc_start: 0.7923 (ptpt) cc_final: 0.7607 (pptt) outliers start: 7 outliers final: 5 residues processed: 70 average time/residue: 0.1273 time to fit residues: 13.5976 Evaluate side-chains 64 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 300 LEU 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: 2.9990 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 6 optimal weight: 0.0040 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 0.0370 chunk 79 optimal weight: 1.9990 overall best weight: 0.5870 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.128984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096144 restraints weight = 13600.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.098823 restraints weight = 7647.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100576 restraints weight = 5386.317| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6723 Z= 0.140 Angle : 0.473 7.375 9197 Z= 0.255 Chirality : 0.041 0.131 1101 Planarity : 0.003 0.031 1188 Dihedral : 6.585 119.773 1030 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.50 % Allowed : 14.07 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.02 (0.28), residues: 924 helix: 1.64 (0.28), residues: 363 sheet: -0.91 (0.39), residues: 178 loop : -1.16 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS A 149 PHE 0.019 0.001 PHE A 146 TYR 0.005 0.001 TYR B 124 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 73 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.704 Fit side-chains REVERT: B 117 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8927 (tt) REVERT: B 142 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.7728 (t-170) REVERT: G 48 ASP cc_start: 0.8497 (t0) cc_final: 0.7704 (t0) REVERT: R 140 LYS cc_start: 0.7916 (ptpt) cc_final: 0.7601 (pptt) outliers start: 8 outliers final: 3 residues processed: 72 average time/residue: 0.1241 time to fit residues: 13.7950 Evaluate side-chains 64 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 13 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.129160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096330 restraints weight = 13536.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098967 restraints weight = 7628.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100676 restraints weight = 5381.134| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6723 Z= 0.151 Angle : 0.462 6.139 9197 Z= 0.248 Chirality : 0.040 0.132 1101 Planarity : 0.003 0.030 1188 Dihedral : 6.131 111.603 1030 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.88 % Allowed : 15.20 % Favored : 82.93 % 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: 0.18 (0.28), residues: 924 helix: 1.89 (0.28), residues: 363 sheet: -0.80 (0.39), residues: 178 loop : -1.15 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 286 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE B 199 TYR 0.006 0.001 TYR A 339 ARG 0.002 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 73 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.753 Fit side-chains REVERT: B 117 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8933 (tt) REVERT: G 48 ASP cc_start: 0.8489 (t0) cc_final: 0.7706 (t0) REVERT: R 140 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7620 (pptt) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 0.1263 time to fit residues: 13.6297 Evaluate side-chains 68 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 71 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 45 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.129511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.096849 restraints weight = 13426.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099424 restraints weight = 7531.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.101163 restraints weight = 5376.092| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6723 Z= 0.141 Angle : 0.450 5.546 9197 Z= 0.241 Chirality : 0.040 0.129 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.875 106.400 1030 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.44 % Allowed : 15.38 % Favored : 82.18 % 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: 0.29 (0.28), residues: 924 helix: 2.00 (0.28), residues: 368 sheet: -0.76 (0.39), residues: 178 loop : -1.14 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 286 HIS 0.002 0.001 HIS B 91 PHE 0.021 0.001 PHE A 146 TYR 0.005 0.001 TYR A 339 ARG 0.001 0.000 ARG A 374 *********************** 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 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.738 Fit side-chains REVERT: A 118 GLU cc_start: 0.7929 (mp0) cc_final: 0.7693 (mp0) REVERT: B 117 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8915 (tt) REVERT: B 142 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7793 (t-170) REVERT: G 48 ASP cc_start: 0.8497 (t0) cc_final: 0.7696 (t0) REVERT: R 140 LYS cc_start: 0.7925 (ptpt) cc_final: 0.7629 (pptt) outliers start: 13 outliers final: 7 residues processed: 72 average time/residue: 0.1333 time to fit residues: 14.4597 Evaluate side-chains 70 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 311 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 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** 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 = 0.129222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096539 restraints weight = 13444.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099159 restraints weight = 7630.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.100914 restraints weight = 5435.981| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6723 Z= 0.162 Angle : 0.457 5.742 9197 Z= 0.244 Chirality : 0.040 0.125 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.780 103.143 1030 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.19 % Allowed : 15.20 % Favored : 81.61 % 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: 0.34 (0.28), residues: 924 helix: 2.07 (0.28), residues: 368 sheet: -0.66 (0.39), residues: 175 loop : -1.21 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 286 HIS 0.003 0.001 HIS B 142 PHE 0.010 0.001 PHE B 199 TYR 0.006 0.001 TYR A 339 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: 17 poor density : 63 time to evaluate : 0.819 Fit side-chains REVERT: A 118 GLU cc_start: 0.7902 (mp0) cc_final: 0.7652 (mp0) REVERT: B 117 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8946 (tt) REVERT: B 142 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.7768 (t-170) REVERT: R 140 LYS cc_start: 0.7928 (ptpt) cc_final: 0.7647 (pptt) outliers start: 17 outliers final: 11 residues processed: 75 average time/residue: 0.1365 time to fit residues: 15.4945 Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 45 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 149 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: 5.9990 chunk 11 optimal weight: 0.0570 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.130183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097495 restraints weight = 13555.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.100158 restraints weight = 7693.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101873 restraints weight = 5448.817| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2461 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= 0.132 Angle : 0.449 5.788 9197 Z= 0.240 Chirality : 0.040 0.130 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.579 98.964 1030 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.63 % Allowed : 16.32 % 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: 0.43 (0.29), residues: 924 helix: 2.15 (0.28), residues: 369 sheet: -0.57 (0.39), residues: 175 loop : -1.18 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 286 HIS 0.002 0.000 HIS B 91 PHE 0.011 0.001 PHE B 292 TYR 0.005 0.001 TYR A 339 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 76 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.732 Fit side-chains REVERT: A 118 GLU cc_start: 0.7895 (mp0) cc_final: 0.7634 (mp0) REVERT: B 117 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8929 (tt) REVERT: B 142 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7788 (t-170) REVERT: R 140 LYS cc_start: 0.7941 (ptpt) cc_final: 0.7665 (pptt) outliers start: 14 outliers final: 9 residues processed: 73 average time/residue: 0.1141 time to fit residues: 13.1535 Evaluate side-chains 74 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 263 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.127605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094986 restraints weight = 13723.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097567 restraints weight = 7757.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099234 restraints weight = 5513.037| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6723 Z= 0.243 Angle : 0.500 6.139 9197 Z= 0.269 Chirality : 0.041 0.135 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.786 99.295 1030 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.19 % Allowed : 15.95 % Favored : 80.86 % 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: 0.32 (0.28), residues: 924 helix: 1.98 (0.28), residues: 374 sheet: -0.55 (0.40), residues: 168 loop : -1.25 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 286 HIS 0.004 0.001 HIS B 142 PHE 0.011 0.001 PHE B 235 TYR 0.007 0.001 TYR A 360 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 80 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.689 Fit side-chains REVERT: A 118 GLU cc_start: 0.7878 (mp0) cc_final: 0.7598 (mp0) REVERT: B 111 TYR cc_start: 0.8876 (m-80) cc_final: 0.8514 (m-80) REVERT: B 117 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8962 (tt) REVERT: B 142 HIS cc_start: 0.8380 (OUTLIER) cc_final: 0.7897 (t-170) REVERT: G 48 ASP cc_start: 0.8557 (t0) cc_final: 0.7921 (t0) REVERT: R 140 LYS cc_start: 0.7957 (ptpt) cc_final: 0.7678 (pptt) outliers start: 17 outliers final: 10 residues processed: 75 average time/residue: 0.1154 time to fit residues: 13.6956 Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 45 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 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 91 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.129003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096261 restraints weight = 13720.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098899 restraints weight = 7745.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100640 restraints weight = 5481.452| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6723 Z= 0.155 Angle : 0.474 6.597 9197 Z= 0.252 Chirality : 0.040 0.126 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.611 96.939 1030 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.69 % Allowed : 17.07 % Favored : 81.24 % 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: 0.43 (0.29), residues: 924 helix: 2.14 (0.28), residues: 369 sheet: -0.49 (0.40), residues: 168 loop : -1.22 (0.30), residues: 387 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 0.011 0.001 PHE B 292 TYR 0.005 0.001 TYR A 339 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 73 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.696 Fit side-chains REVERT: A 118 GLU cc_start: 0.7926 (mp0) cc_final: 0.7648 (mp0) REVERT: B 117 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8940 (tt) REVERT: B 142 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7867 (t-170) REVERT: G 48 ASP cc_start: 0.8547 (t0) cc_final: 0.7940 (t0) REVERT: R 140 LYS cc_start: 0.7960 (ptpt) cc_final: 0.7678 (pptt) outliers start: 9 outliers final: 7 residues processed: 71 average time/residue: 0.1165 time to fit residues: 12.9808 Evaluate side-chains 72 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 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 263 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 39 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 73 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.128136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.095367 restraints weight = 13709.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097962 restraints weight = 7767.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099647 restraints weight = 5540.136| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6723 Z= 0.211 Angle : 0.491 6.242 9197 Z= 0.262 Chirality : 0.041 0.128 1101 Planarity : 0.003 0.029 1188 Dihedral : 5.655 96.012 1030 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.44 % Allowed : 16.70 % Favored : 80.86 % 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: 0.35 (0.28), residues: 924 helix: 2.03 (0.28), residues: 374 sheet: -0.54 (0.40), residues: 168 loop : -1.24 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 286 HIS 0.003 0.001 HIS B 142 PHE 0.010 0.001 PHE B 199 TYR 0.006 0.001 TYR A 339 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: 2437.78 seconds wall clock time: 42 minutes 49.95 seconds (2569.95 seconds total)