Starting phenix.real_space_refine on Thu Jul 2 19:55:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7arj_11884/07_2026/7arj_11884.cif Found real_map, /net/cci-nas-00/data/ceres_data/7arj_11884/07_2026/7arj_11884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7arj_11884/07_2026/7arj_11884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7arj_11884/07_2026/7arj_11884.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7arj_11884/07_2026/7arj_11884.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7arj_11884/07_2026/7arj_11884.cif" model { file = "/net/cci-nas-00/data/ceres_data/7arj_11884/07_2026/7arj_11884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7arj_11884/07_2026/7arj_11884.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 56 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 6112 2.51 5 N 1684 2.21 5 O 1745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9601 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2965 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3159 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain: "F" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1588 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 8, 'TRANS': 216} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'ARG:plan': 5, 'GLU:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 98 Chain: "D" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1696 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 217} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "V" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 73 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.85, per 1000 atoms: 0.19 Number of scatterers: 9601 At special positions: 0 Unit cell: (83.148, 91.26, 153.114, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 6 15.00 Mg 2 11.99 O 1745 8.00 N 1684 7.00 C 6112 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 342.6 milliseconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 9 sheets defined 39.9% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'C' and resid 22 through 28 removed outlier: 3.544A pdb=" N VAL C 26 " --> pdb=" O PHE C 22 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 22 through 28' Processing helix chain 'C' and resid 28 through 57 removed outlier: 3.680A pdb=" N ILE C 32 " --> pdb=" O TRP C 28 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR C 43 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.800A pdb=" N ASP C 136 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 137 " --> pdb=" O GLN C 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 133 through 137' Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.770A pdb=" N GLN C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 252 removed outlier: 4.102A pdb=" N ASP C 251 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG C 252 " --> pdb=" O TRP C 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 248 through 252' Processing helix chain 'C' and resid 255 through 271 removed outlier: 3.776A pdb=" N ALA C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 293 removed outlier: 3.641A pdb=" N ILE C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 4.022A pdb=" N ALA C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 299 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.790A pdb=" N MET C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 removed outlier: 4.085A pdb=" N VAL C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 339 removed outlier: 3.538A pdb=" N ALA C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 379 removed outlier: 3.712A pdb=" N VAL C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 379 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 389 removed outlier: 3.625A pdb=" N ALA C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 17 removed outlier: 3.507A pdb=" N ARG E 17 " --> pdb=" O SER E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 24 removed outlier: 4.442A pdb=" N SER E 24 " --> pdb=" O GLY E 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 21 through 24' Processing helix chain 'E' and resid 25 through 59 removed outlier: 3.632A pdb=" N THR E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA E 47 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU E 52 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN E 56 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 84 removed outlier: 4.333A pdb=" N ASP E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 84' Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.513A pdb=" N ARG E 125 " --> pdb=" O GLN E 122 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU E 126 " --> pdb=" O GLU E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 128 through 132 removed outlier: 3.779A pdb=" N SER E 131 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE E 132 " --> pdb=" O LEU E 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 128 through 132' Processing helix chain 'E' and resid 151 through 159 removed outlier: 3.875A pdb=" N ALA E 155 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 removed outlier: 3.537A pdb=" N GLN E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 215 " --> pdb=" O ALA E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.775A pdb=" N GLY E 242 " --> pdb=" O ARG E 239 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU E 243 " --> pdb=" O ASP E 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 239 through 243' Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 260 through 268 removed outlier: 3.504A pdb=" N ILE E 265 " --> pdb=" O MET E 261 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET E 267 " --> pdb=" O ARG E 263 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 284 removed outlier: 3.532A pdb=" N VAL E 277 " --> pdb=" O TYR E 273 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 298 removed outlier: 3.839A pdb=" N MET E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 309 removed outlier: 4.119A pdb=" N ALA E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL E 304 " --> pdb=" O GLY E 300 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 344 removed outlier: 3.846A pdb=" N ILE E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE E 319 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E 320 " --> pdb=" O ARG E 316 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS E 333 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 357 removed outlier: 3.734A pdb=" N ILE E 348 " --> pdb=" O GLN E 344 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 355 " --> pdb=" O TRP E 351 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 395 removed outlier: 3.712A pdb=" N PHE E 381 " --> pdb=" O TRP E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'F' and resid 47 through 55 removed outlier: 3.576A pdb=" N LEU F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 removed outlier: 3.545A pdb=" N GLN F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 109 removed outlier: 3.923A pdb=" N VAL F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 115 Processing helix chain 'F' and resid 121 through 134 removed outlier: 3.516A pdb=" N LEU F 127 " --> pdb=" O ASN F 123 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET F 129 " --> pdb=" O ARG F 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 160 removed outlier: 3.823A pdb=" N GLN F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU F 160 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 184 removed outlier: 3.594A pdb=" N SER F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE F 184 " --> pdb=" O ASN F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.844A pdb=" N LEU D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.616A pdb=" N GLN D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 88' Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.987A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.767A pdb=" N ILE D 114 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 125 removed outlier: 3.584A pdb=" N SER D 124 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG D 125 " --> pdb=" O ILE D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 125' Processing helix chain 'D' and resid 180 through 184 removed outlier: 3.580A pdb=" N ILE D 184 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 removed outlier: 4.088A pdb=" N ASN D 192 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 193 " --> pdb=" O GLU D 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 189 through 193' Processing sheet with id=AA1, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.554A pdb=" N ILE C 96 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 221 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP C 222 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 224 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA C 66 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 98 through 104 removed outlier: 3.751A pdb=" N GLY C 99 " --> pdb=" O MET C 114 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 112 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN C 204 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ASN C 143 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU C 146 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR C 189 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 166 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 164 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 165 through 166 removed outlier: 8.505A pdb=" N GLN E 147 " --> pdb=" O PRO E 207 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS E 116 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA E 93 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS E 227 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY E 66 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 67 " --> pdb=" O LYS E 252 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 252 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 103 through 104 removed outlier: 3.718A pdb=" N LEU E 103 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE E 170 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'F' and resid 37 through 38 removed outlier: 6.904A pdb=" N MET F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL F 167 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N VAL F 202 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA F 169 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLY F 90 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP F 170 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE F 92 " --> pdb=" O ASP F 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 31 through 32 removed outlier: 4.131A pdb=" N GLN D 7 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE D 67 " --> pdb=" O GLN D 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 13 through 16 removed outlier: 6.898A pdb=" N LYS D 13 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL D 24 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.799A pdb=" N GLY D 90 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N MET D 38 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N THR D 203 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE D 40 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU D 216 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D 41 " --> pdb=" O LEU D 216 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 732 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: 1.06 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3105 1.34 - 1.46: 1119 1.46 - 1.57: 5423 1.57 - 1.69: 11 1.69 - 1.81: 98 Bond restraints: 9756 Sorted by residual: bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C16 Z41 V 101 " pdb=" O2 Z41 V 101 " ideal model delta sigma weight residual 1.332 1.455 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C19 Z41 V 101 " pdb=" O3 Z41 V 101 " ideal model delta sigma weight residual 1.333 1.454 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.68e+01 ... (remaining 9751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 13089 3.44 - 6.87: 114 6.87 - 10.31: 19 10.31 - 13.74: 1 13.74 - 17.18: 2 Bond angle restraints: 13225 Sorted by residual: angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 109.77 17.18 3.00e+00 1.11e-01 3.28e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 109.82 17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" C PRO F 61 " pdb=" N THR F 62 " pdb=" CA THR F 62 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C ARG D 219 " pdb=" N ASP D 220 " pdb=" CA ASP D 220 " ideal model delta sigma weight residual 121.54 128.66 -7.12 1.91e+00 2.74e-01 1.39e+01 angle pdb=" O1B ANP D 401 " pdb=" PB ANP D 401 " pdb=" O2B ANP D 401 " ideal model delta sigma weight residual 120.08 109.91 10.17 3.00e+00 1.11e-01 1.15e+01 ... (remaining 13220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.56: 5440 18.56 - 37.13: 346 37.13 - 55.69: 70 55.69 - 74.25: 16 74.25 - 92.82: 4 Dihedral angle restraints: 5876 sinusoidal: 2288 harmonic: 3588 Sorted by residual: dihedral pdb=" CA LEU E 195 " pdb=" C LEU E 195 " pdb=" N SER E 196 " pdb=" CA SER E 196 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ASP C 227 " pdb=" CB ASP C 227 " pdb=" CG ASP C 227 " pdb=" OD1 ASP C 227 " ideal model delta sinusoidal sigma weight residual -30.00 -88.20 58.20 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" O1B ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PB ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sinusoidal sigma weight residual 35.15 -57.67 92.82 1 3.00e+01 1.11e-03 1.12e+01 ... (remaining 5873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1239 0.054 - 0.109: 268 0.109 - 0.163: 44 0.163 - 0.217: 4 0.217 - 0.271: 2 Chirality restraints: 1557 Sorted by residual: chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA THR F 62 " pdb=" N THR F 62 " pdb=" C THR F 62 " pdb=" CB THR F 62 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 1554 not shown) Planarity restraints: 1679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 178 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO C 179 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 306 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO C 307 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 184 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C ILE D 184 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE D 184 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE D 185 " -0.013 2.00e-02 2.50e+03 ... (remaining 1676 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2960 2.83 - 3.35: 7556 3.35 - 3.86: 14807 3.86 - 4.38: 16681 4.38 - 4.90: 28870 Nonbonded interactions: 70874 Sorted by model distance: nonbonded pdb=" OG SER F 49 " pdb=" O1A ANP F 401 " model vdw 2.312 3.040 nonbonded pdb=" O TYR E 382 " pdb=" OG1 THR E 386 " model vdw 2.342 3.040 nonbonded pdb=" O SER E 412 " pdb=" OG SER E 412 " model vdw 2.362 3.040 nonbonded pdb=" O SER E 27 " pdb=" OG1 THR E 31 " model vdw 2.363 3.040 nonbonded pdb=" OG1 THR E 245 " pdb=" OD1 ASN E 246 " model vdw 2.368 3.040 ... (remaining 70869 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 4 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or (resid 18 through 21 and (name N or nam \ e CA or name C or name O or name CB )) or resid 22 or (resid 23 and (name N or n \ ame CA or name C or name O or name CB )) or resid 24 through 35 or (resid 36 and \ (name N or name CA or name C or name O or name CB )) or resid 37 through 93 or \ (resid 94 through 95 and (name N or name CA or name C or name O or name CB )) or \ resid 96 through 117 or (resid 118 and (name N or name CA or name C or name O o \ r name CB )) or resid 119 through 120 or (resid 121 and (name N or name CA or na \ me C or name O or name CB )) or resid 122 through 130 or (resid 131 through 132 \ and (name N or name CA or name C or name O or name CB )) or resid 133 through 13 \ 5 or (resid 136 and (name N or name CA or name C or name O or name CB )) or resi \ d 137 through 152 or (resid 153 and (name N or name CA or name C or name O or na \ me CB )) or resid 154 through 174 or (resid 175 and (name N or name CA or name C \ or name O or name CB )) or resid 176 or (resid 177 through 182 and (name N or n \ ame CA or name C or name O or name CB )) or resid 183 through 186 or (resid 187 \ and (name N or name CA or name C or name O or name CB )) or resid 188 through 19 \ 3 or (resid 194 through 195 and (name N or name CA or name C or name O or name C \ B )) or resid 196 through 209 or (resid 210 and (name N or name CA or name C or \ name O or name CB )) or resid 211 through 216 or (resid 217 and (name N or name \ CA or name C or name O or name CB )) or resid 218 or (resid 219 through 220 and \ (name N or name CA or name C or name O or name CB )) or resid 221 or (resid 222 \ through 228 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 1 through 402)) selection = (chain 'F' and (resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 or (resid 13 through 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 61 or (resid 62 and (n \ ame N or name CA or name C or name O or name CB )) or resid 63 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.940 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 0.141 9758 Z= 0.248 Angle : 0.802 17.179 13225 Z= 0.367 Chirality : 0.047 0.271 1557 Planarity : 0.005 0.071 1679 Dihedral : 13.109 92.817 3566 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.10 % Allowed : 5.24 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.75 (0.16), residues: 1250 helix: -5.01 (0.05), residues: 430 sheet: -2.33 (0.44), residues: 122 loop : -3.37 (0.17), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 211 TYR 0.008 0.001 TYR C 199 PHE 0.012 0.001 PHE C 190 TRP 0.005 0.001 TRP E 321 HIS 0.001 0.000 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.23 ( 9756) covalent geometry : angle 0.80223 / 0.37 (13225) hydrogen bonds : bond 0.34145 / 22.01 ( 254) hydrogen bonds : angle 10.87882 / 7.69 ( 732) Misc. bond : bond 0.06881 / 3.62 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 48 MET cc_start: 0.8344 (mmt) cc_final: 0.7867 (mmt) REVERT: E 97 TYR cc_start: 0.7953 (p90) cc_final: 0.7387 (p90) REVERT: E 337 ILE cc_start: 0.8057 (tt) cc_final: 0.7794 (tp) REVERT: F 69 ASN cc_start: 0.8785 (t0) cc_final: 0.8518 (t0) REVERT: F 140 ASN cc_start: 0.8811 (m110) cc_final: 0.8552 (m-40) REVERT: F 200 LEU cc_start: 0.7106 (pp) cc_final: 0.6837 (pp) REVERT: D 10 ASN cc_start: 0.6555 (t0) cc_final: 0.6347 (t0) REVERT: D 212 MET cc_start: 0.2214 (mmt) cc_final: 0.1865 (ptm) REVERT: D 218 MET cc_start: 0.7525 (tpp) cc_final: 0.7145 (tpt) outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.0853 time to fit residues: 36.2185 Evaluate side-chains 227 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.0370 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.0980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 ASN C 341 ASN E 56 ASN E 84 HIS F 53 HIS F 96 HIS F 123 ASN F 163 ASN F 192 ASN D 71 GLN D 97 HIS D 140 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.188112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137411 restraints weight = 13418.728| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.90 r_work: 0.3630 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9758 Z= 0.111 Angle : 0.576 7.298 13225 Z= 0.278 Chirality : 0.042 0.179 1557 Planarity : 0.004 0.047 1679 Dihedral : 7.261 124.090 1394 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.71 % Allowed : 14.70 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.18), residues: 1250 helix: -3.04 (0.17), residues: 449 sheet: -2.00 (0.43), residues: 143 loop : -2.79 (0.19), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 211 TYR 0.009 0.001 TYR E 258 PHE 0.009 0.001 PHE F 30 TRP 0.010 0.001 TRP E 321 HIS 0.006 0.001 HIS E 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 9756) covalent geometry : angle 0.57570 / 0.28 (13225) hydrogen bonds : bond 0.04518 / 2.82 ( 254) hydrogen bonds : angle 5.45482 / 3.97 ( 732) Misc. bond : bond 0.00027 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8329 (mtmt) REVERT: C 182 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7725 (mmm160) REVERT: C 262 MET cc_start: 0.8111 (tmm) cc_final: 0.7689 (tmm) REVERT: C 363 LEU cc_start: 0.8272 (tp) cc_final: 0.7967 (tt) REVERT: E 48 MET cc_start: 0.8807 (mmt) cc_final: 0.8291 (mmt) REVERT: E 69 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7629 (mm-30) REVERT: E 337 ILE cc_start: 0.8799 (tt) cc_final: 0.8441 (tp) REVERT: E 346 THR cc_start: 0.6516 (OUTLIER) cc_final: 0.6202 (p) REVERT: E 353 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7026 (mt-10) REVERT: F 83 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8280 (mt-10) REVERT: F 141 HIS cc_start: 0.7997 (m-70) cc_final: 0.7545 (m-70) REVERT: D 10 ASN cc_start: 0.7231 (t0) cc_final: 0.6925 (t0) REVERT: D 30 PHE cc_start: 0.8150 (t80) cc_final: 0.7695 (t80) REVERT: D 69 ASN cc_start: 0.7359 (m-40) cc_final: 0.7114 (m110) REVERT: D 136 ASP cc_start: 0.8017 (t0) cc_final: 0.7743 (t0) REVERT: D 152 GLN cc_start: 0.7255 (tp40) cc_final: 0.6433 (pm20) REVERT: D 171 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6944 (tm-30) REVERT: D 212 MET cc_start: 0.3535 (mmt) cc_final: 0.2474 (ptm) REVERT: D 218 MET cc_start: 0.7688 (tpp) cc_final: 0.7452 (tpt) outliers start: 17 outliers final: 11 residues processed: 246 average time/residue: 0.0827 time to fit residues: 28.4731 Evaluate side-chains 222 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 41 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 0.3980 chunk 122 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 HIS C 161 GLN C 317 GLN E 114 GLN E 286 ASN F 53 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.173396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122570 restraints weight = 13516.400| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.99 r_work: 0.3340 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9758 Z= 0.152 Angle : 0.614 7.267 13225 Z= 0.299 Chirality : 0.044 0.162 1557 Planarity : 0.004 0.036 1679 Dihedral : 7.270 115.680 1394 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.22 % Allowed : 16.01 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.21), residues: 1250 helix: -1.56 (0.22), residues: 463 sheet: -1.34 (0.48), residues: 124 loop : -2.37 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 139 TYR 0.013 0.001 TYR E 258 PHE 0.016 0.002 PHE F 68 TRP 0.014 0.002 TRP E 321 HIS 0.006 0.001 HIS E 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 9756) covalent geometry : angle 0.61360 / 0.30 (13225) hydrogen bonds : bond 0.04086 / 2.54 ( 254) hydrogen bonds : angle 4.59949 / 3.31 ( 732) Misc. bond : bond 0.00073 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 SER cc_start: 0.9068 (t) cc_final: 0.8825 (p) REVERT: E 69 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7820 (mm-30) REVERT: E 139 ARG cc_start: 0.8673 (mtm110) cc_final: 0.8416 (ptp90) REVERT: F 34 GLU cc_start: 0.7190 (mp0) cc_final: 0.6854 (mp0) REVERT: F 51 LEU cc_start: 0.8610 (tp) cc_final: 0.7949 (pp) REVERT: F 59 ASP cc_start: 0.8458 (t70) cc_final: 0.7938 (t0) REVERT: F 83 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8407 (mt-10) REVERT: F 106 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8358 (mp0) REVERT: F 107 ASN cc_start: 0.8566 (m-40) cc_final: 0.7985 (m110) REVERT: F 141 HIS cc_start: 0.8225 (m-70) cc_final: 0.7706 (m-70) REVERT: F 191 LEU cc_start: 0.8260 (mm) cc_final: 0.8023 (mm) REVERT: D 10 ASN cc_start: 0.7360 (t0) cc_final: 0.7056 (t0) REVERT: D 14 ARG cc_start: 0.7376 (ttp80) cc_final: 0.6953 (ttp80) REVERT: D 30 PHE cc_start: 0.8062 (t80) cc_final: 0.7837 (t80) REVERT: D 69 ASN cc_start: 0.7370 (m-40) cc_final: 0.7114 (m110) REVERT: D 218 MET cc_start: 0.7790 (tpp) cc_final: 0.7547 (tpt) outliers start: 32 outliers final: 15 residues processed: 239 average time/residue: 0.0865 time to fit residues: 28.3491 Evaluate side-chains 207 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain D residue 127 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.0170 chunk 108 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 HIS C 143 ASN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN E 122 GLN E 134 GLN F 53 HIS ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.164592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112555 restraints weight = 13635.131| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.05 r_work: 0.3204 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9758 Z= 0.201 Angle : 0.635 9.047 13225 Z= 0.315 Chirality : 0.046 0.155 1557 Planarity : 0.004 0.032 1679 Dihedral : 7.589 111.444 1394 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.22 % Allowed : 17.72 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.22), residues: 1250 helix: -1.12 (0.22), residues: 485 sheet: -1.73 (0.42), residues: 148 loop : -2.06 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 139 TYR 0.014 0.001 TYR E 322 PHE 0.013 0.002 PHE D 199 TRP 0.009 0.002 TRP C 246 HIS 0.005 0.001 HIS E 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 ( 9756) covalent geometry : angle 0.63539 / 0.32 (13225) hydrogen bonds : bond 0.04160 / 2.57 ( 254) hydrogen bonds : angle 4.56297 / 3.27 ( 732) Misc. bond : bond 0.00084 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7867 (tp30) REVERT: C 193 ASN cc_start: 0.8610 (t0) cc_final: 0.8316 (t0) REVERT: C 310 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8681 (tt) REVERT: C 339 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7645 (mp10) REVERT: E 69 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8076 (mt-10) REVERT: E 139 ARG cc_start: 0.8806 (mtm110) cc_final: 0.8511 (ptp90) REVERT: E 217 MET cc_start: 0.6495 (mmm) cc_final: 0.6188 (mtp) REVERT: E 297 ASP cc_start: 0.8301 (m-30) cc_final: 0.8089 (t0) REVERT: E 350 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: F 59 ASP cc_start: 0.8394 (t0) cc_final: 0.7943 (t0) REVERT: F 83 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8305 (mt-10) REVERT: F 141 HIS cc_start: 0.8347 (m-70) cc_final: 0.7946 (m-70) REVERT: D 10 ASN cc_start: 0.7763 (t0) cc_final: 0.7446 (t0) REVERT: D 14 ARG cc_start: 0.7372 (ttp80) cc_final: 0.7154 (ttp80) REVERT: D 30 PHE cc_start: 0.8167 (t80) cc_final: 0.7946 (t80) REVERT: D 69 ASN cc_start: 0.7191 (m-40) cc_final: 0.6959 (m110) REVERT: D 171 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7350 (tp30) REVERT: D 212 MET cc_start: 0.4651 (mmp) cc_final: 0.3788 (tpp) outliers start: 32 outliers final: 19 residues processed: 215 average time/residue: 0.0790 time to fit residues: 23.4266 Evaluate side-chains 194 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 73 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 67 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 0.0670 chunk 38 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 294 GLN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN F 123 ASN D 163 ASN V 4 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.168174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117891 restraints weight = 13475.408| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.05 r_work: 0.3268 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9758 Z= 0.098 Angle : 0.535 7.864 13225 Z= 0.262 Chirality : 0.042 0.143 1557 Planarity : 0.003 0.034 1679 Dihedral : 7.053 103.510 1394 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.02 % Allowed : 19.13 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.23), residues: 1250 helix: -0.54 (0.24), residues: 494 sheet: -1.36 (0.42), residues: 149 loop : -1.91 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 165 TYR 0.009 0.001 TYR E 258 PHE 0.011 0.001 PHE F 68 TRP 0.011 0.001 TRP C 246 HIS 0.004 0.001 HIS E 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 9756) covalent geometry : angle 0.53528 / 0.26 (13225) hydrogen bonds : bond 0.02988 / 1.82 ( 254) hydrogen bonds : angle 4.17748 / 3.00 ( 732) Misc. bond : bond 0.00044 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7825 (tp30) REVERT: C 193 ASN cc_start: 0.8529 (t0) cc_final: 0.8176 (t0) REVERT: C 262 MET cc_start: 0.8500 (tpp) cc_final: 0.7733 (ttm) REVERT: C 310 ILE cc_start: 0.8852 (tt) cc_final: 0.8638 (tt) REVERT: E 48 MET cc_start: 0.9015 (mmt) cc_final: 0.8629 (mmt) REVERT: E 69 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7680 (mm-30) REVERT: E 73 GLN cc_start: 0.7738 (pm20) cc_final: 0.7408 (pm20) REVERT: E 139 ARG cc_start: 0.8771 (mtm110) cc_final: 0.8504 (ptp90) REVERT: E 217 MET cc_start: 0.6446 (mmm) cc_final: 0.6144 (mtp) REVERT: F 51 LEU cc_start: 0.8677 (tp) cc_final: 0.7956 (pp) REVERT: F 59 ASP cc_start: 0.8395 (t0) cc_final: 0.7862 (t0) REVERT: F 141 HIS cc_start: 0.8273 (m-70) cc_final: 0.7804 (m-70) REVERT: D 10 ASN cc_start: 0.7691 (t0) cc_final: 0.7347 (t0) REVERT: D 14 ARG cc_start: 0.7464 (ttp80) cc_final: 0.7241 (ttp80) REVERT: D 106 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: D 171 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7276 (tp30) REVERT: D 212 MET cc_start: 0.4439 (mmp) cc_final: 0.3766 (tpp) REVERT: D 218 MET cc_start: 0.6983 (tpt) cc_final: 0.6010 (tpp) outliers start: 30 outliers final: 19 residues processed: 212 average time/residue: 0.0803 time to fit residues: 23.6512 Evaluate side-chains 200 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain V residue 4 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 86 optimal weight: 0.0010 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 106 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 123 optimal weight: 0.0030 chunk 22 optimal weight: 0.9980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN D 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.169586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118879 restraints weight = 13390.355| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.16 r_work: 0.3288 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9758 Z= 0.091 Angle : 0.544 8.564 13225 Z= 0.260 Chirality : 0.042 0.146 1557 Planarity : 0.003 0.043 1679 Dihedral : 6.741 96.871 1394 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.32 % Allowed : 20.34 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.24), residues: 1250 helix: -0.10 (0.24), residues: 493 sheet: -1.29 (0.43), residues: 150 loop : -1.81 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 316 TYR 0.009 0.001 TYR E 258 PHE 0.011 0.001 PHE E 319 TRP 0.011 0.001 TRP C 246 HIS 0.003 0.000 HIS E 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 ( 9756) covalent geometry : angle 0.54356 / 0.26 (13225) hydrogen bonds : bond 0.02712 / 1.64 ( 254) hydrogen bonds : angle 4.02077 / 2.88 ( 732) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7875 (tp30) REVERT: C 153 GLN cc_start: 0.8732 (pp30) cc_final: 0.8529 (pp30) REVERT: C 193 ASN cc_start: 0.8486 (t0) cc_final: 0.8133 (t0) REVERT: C 262 MET cc_start: 0.8545 (tpp) cc_final: 0.7844 (ttm) REVERT: E 69 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7699 (mm-30) REVERT: E 217 MET cc_start: 0.6510 (mmm) cc_final: 0.6230 (mtp) REVERT: F 51 LEU cc_start: 0.8711 (tp) cc_final: 0.7990 (pp) REVERT: F 59 ASP cc_start: 0.8402 (t0) cc_final: 0.7937 (t0) REVERT: F 83 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8375 (mt-10) REVERT: F 141 HIS cc_start: 0.8240 (m-70) cc_final: 0.7562 (m-70) REVERT: D 10 ASN cc_start: 0.7617 (t0) cc_final: 0.7279 (t0) REVERT: D 14 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7091 (ttp80) REVERT: D 106 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: D 171 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7323 (tp30) REVERT: D 212 MET cc_start: 0.4374 (mmp) cc_final: 0.3838 (tpp) REVERT: D 218 MET cc_start: 0.7002 (tpt) cc_final: 0.5932 (tpp) outliers start: 23 outliers final: 16 residues processed: 206 average time/residue: 0.0770 time to fit residues: 22.1477 Evaluate side-chains 197 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 163 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 122 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 100 optimal weight: 30.0000 chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.0370 overall best weight: 2.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 26 HIS ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN V 4 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.162372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.109724 restraints weight = 13492.286| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.04 r_work: 0.3170 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9758 Z= 0.197 Angle : 0.623 7.603 13225 Z= 0.306 Chirality : 0.046 0.213 1557 Planarity : 0.004 0.045 1679 Dihedral : 7.034 99.059 1394 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.82 % Allowed : 21.25 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.24), residues: 1250 helix: -0.10 (0.24), residues: 500 sheet: -1.28 (0.44), residues: 148 loop : -1.79 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 139 TYR 0.012 0.001 TYR E 322 PHE 0.013 0.002 PHE E 319 TRP 0.007 0.001 TRP E 321 HIS 0.004 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 9756) covalent geometry : angle 0.62282 / 0.31 (13225) hydrogen bonds : bond 0.03978 / 2.48 ( 254) hydrogen bonds : angle 4.24656 / 3.01 ( 732) Misc. bond : bond 0.00119 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7955 (tp30) REVERT: C 193 ASN cc_start: 0.8719 (t0) cc_final: 0.8441 (t0) REVERT: C 212 MET cc_start: 0.5041 (ptp) cc_final: 0.4467 (ptp) REVERT: E 69 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7987 (mt-10) REVERT: E 139 ARG cc_start: 0.8812 (mtm110) cc_final: 0.8557 (ptp90) REVERT: E 217 MET cc_start: 0.6765 (mmm) cc_final: 0.6353 (mtp) REVERT: F 34 GLU cc_start: 0.7594 (mp0) cc_final: 0.7356 (mp0) REVERT: F 59 ASP cc_start: 0.8279 (t0) cc_final: 0.7762 (t0) REVERT: F 83 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8398 (mt-10) REVERT: F 141 HIS cc_start: 0.8284 (m-70) cc_final: 0.7839 (m-70) REVERT: D 10 ASN cc_start: 0.7811 (t0) cc_final: 0.7455 (t0) REVERT: D 14 ARG cc_start: 0.7429 (ttp80) cc_final: 0.6803 (ttp80) REVERT: D 30 PHE cc_start: 0.8197 (t80) cc_final: 0.7850 (t80) REVERT: D 37 MET cc_start: 0.6221 (mpp) cc_final: 0.5431 (mpp) REVERT: D 171 GLU cc_start: 0.7731 (tm-30) cc_final: 0.6980 (tm-30) REVERT: D 212 MET cc_start: 0.5038 (mmp) cc_final: 0.4342 (tpp) outliers start: 28 outliers final: 20 residues processed: 200 average time/residue: 0.0836 time to fit residues: 23.2528 Evaluate side-chains 194 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 163 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 53 optimal weight: 6.9990 chunk 113 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 17 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 73 GLN E 134 GLN F 123 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.166789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115385 restraints weight = 13462.603| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.28 r_work: 0.3246 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9758 Z= 0.094 Angle : 0.559 9.173 13225 Z= 0.267 Chirality : 0.043 0.156 1557 Planarity : 0.004 0.050 1679 Dihedral : 6.714 94.864 1394 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.32 % Allowed : 21.05 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.24), residues: 1250 helix: 0.30 (0.25), residues: 495 sheet: -1.41 (0.40), residues: 174 loop : -1.68 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 139 TYR 0.009 0.001 TYR E 258 PHE 0.012 0.001 PHE E 319 TRP 0.012 0.001 TRP C 246 HIS 0.003 0.000 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.09 ( 9756) covalent geometry : angle 0.55898 / 0.27 (13225) hydrogen bonds : bond 0.02898 / 1.78 ( 254) hydrogen bonds : angle 4.01798 / 2.85 ( 732) Misc. bond : bond 0.00046 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7875 (tp30) REVERT: C 193 ASN cc_start: 0.8591 (t0) cc_final: 0.8340 (t0) REVERT: C 212 MET cc_start: 0.5423 (ptp) cc_final: 0.4941 (ptp) REVERT: C 262 MET cc_start: 0.8572 (tpp) cc_final: 0.7820 (ttm) REVERT: E 69 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7935 (mt-10) REVERT: E 139 ARG cc_start: 0.8797 (mtm110) cc_final: 0.8593 (ptp90) REVERT: E 217 MET cc_start: 0.6684 (mmm) cc_final: 0.6275 (mtp) REVERT: F 30 PHE cc_start: 0.7646 (t80) cc_final: 0.7394 (t80) REVERT: F 51 LEU cc_start: 0.8701 (tp) cc_final: 0.8028 (pp) REVERT: F 59 ASP cc_start: 0.8340 (t0) cc_final: 0.7925 (t0) REVERT: F 141 HIS cc_start: 0.8257 (m-70) cc_final: 0.7805 (m-70) REVERT: D 10 ASN cc_start: 0.7640 (t0) cc_final: 0.7291 (t0) REVERT: D 14 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7251 (ttp80) REVERT: D 171 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7214 (tp30) REVERT: D 212 MET cc_start: 0.5004 (mmp) cc_final: 0.4438 (tpp) REVERT: D 218 MET cc_start: 0.6792 (tpt) cc_final: 0.5490 (tpp) REVERT: D 220 ASP cc_start: 0.8671 (p0) cc_final: 0.8385 (p0) outliers start: 23 outliers final: 16 residues processed: 196 average time/residue: 0.0885 time to fit residues: 23.8625 Evaluate side-chains 197 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 154 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 103 optimal weight: 0.0020 chunk 78 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 123 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.166956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115855 restraints weight = 13392.531| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.98 r_work: 0.3257 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9758 Z= 0.094 Angle : 0.545 7.463 13225 Z= 0.263 Chirality : 0.042 0.157 1557 Planarity : 0.003 0.053 1679 Dihedral : 6.400 88.817 1394 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.22 % Allowed : 20.85 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.24), residues: 1250 helix: 0.51 (0.25), residues: 495 sheet: -1.15 (0.42), residues: 165 loop : -1.63 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 139 TYR 0.008 0.001 TYR E 258 PHE 0.012 0.001 PHE E 319 TRP 0.011 0.001 TRP C 246 HIS 0.003 0.000 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.09 ( 9756) covalent geometry : angle 0.54541 / 0.26 (13225) hydrogen bonds : bond 0.02758 / 1.69 ( 254) hydrogen bonds : angle 3.90884 / 2.77 ( 732) Misc. bond : bond 0.00044 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 193 ASN cc_start: 0.8521 (t0) cc_final: 0.8301 (t0) REVERT: C 212 MET cc_start: 0.5537 (ptp) cc_final: 0.5128 (ptp) REVERT: C 262 MET cc_start: 0.8461 (tpp) cc_final: 0.7704 (ttm) REVERT: E 69 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7910 (mt-10) REVERT: E 217 MET cc_start: 0.6729 (mmm) cc_final: 0.6266 (mtp) REVERT: E 228 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8031 (mpp) REVERT: F 30 PHE cc_start: 0.7666 (t80) cc_final: 0.7412 (t80) REVERT: F 34 GLU cc_start: 0.7550 (mp0) cc_final: 0.7346 (mp0) REVERT: F 51 LEU cc_start: 0.8708 (tp) cc_final: 0.8010 (pp) REVERT: F 59 ASP cc_start: 0.8360 (t0) cc_final: 0.7946 (t0) REVERT: F 83 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8506 (mt-10) REVERT: F 141 HIS cc_start: 0.8285 (m-70) cc_final: 0.7622 (m-70) REVERT: F 165 ARG cc_start: 0.8239 (mmp80) cc_final: 0.7746 (mmp80) REVERT: D 10 ASN cc_start: 0.7728 (t0) cc_final: 0.7360 (t0) REVERT: D 14 ARG cc_start: 0.7472 (ttp80) cc_final: 0.6966 (ttp80) REVERT: D 171 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7142 (tp30) REVERT: D 212 MET cc_start: 0.5147 (mmp) cc_final: 0.3928 (mmt) REVERT: D 218 MET cc_start: 0.6863 (tpt) cc_final: 0.5588 (tpp) outliers start: 22 outliers final: 16 residues processed: 200 average time/residue: 0.0912 time to fit residues: 25.3790 Evaluate side-chains 200 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 163 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 91 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 0.0870 chunk 44 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 123 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.163968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112150 restraints weight = 13389.962| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.96 r_work: 0.3215 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9758 Z= 0.140 Angle : 0.590 7.885 13225 Z= 0.286 Chirality : 0.044 0.185 1557 Planarity : 0.004 0.052 1679 Dihedral : 6.478 89.253 1394 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.11 % Allowed : 21.15 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.24), residues: 1250 helix: 0.62 (0.25), residues: 485 sheet: -1.31 (0.41), residues: 174 loop : -1.54 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 316 TYR 0.009 0.001 TYR E 322 PHE 0.011 0.001 PHE E 319 TRP 0.008 0.001 TRP C 246 HIS 0.004 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 9756) covalent geometry : angle 0.58992 / 0.29 (13225) hydrogen bonds : bond 0.03335 / 2.07 ( 254) hydrogen bonds : angle 4.02154 / 2.85 ( 732) Misc. bond : bond 0.00089 / 0.04 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 201 MET cc_start: 0.8988 (ptp) cc_final: 0.8779 (ptt) REVERT: C 262 MET cc_start: 0.8570 (tpp) cc_final: 0.7794 (ttm) REVERT: E 69 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7969 (mt-10) REVERT: E 217 MET cc_start: 0.6829 (mmm) cc_final: 0.6324 (mtp) REVERT: F 30 PHE cc_start: 0.7662 (t80) cc_final: 0.7413 (t80) REVERT: F 51 LEU cc_start: 0.8749 (tp) cc_final: 0.8054 (pp) REVERT: F 59 ASP cc_start: 0.8346 (t0) cc_final: 0.7899 (t0) REVERT: F 83 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8490 (mt-10) REVERT: F 141 HIS cc_start: 0.8324 (m-70) cc_final: 0.7648 (m-70) REVERT: F 165 ARG cc_start: 0.8253 (mmp80) cc_final: 0.7832 (mmp80) REVERT: D 10 ASN cc_start: 0.7719 (t0) cc_final: 0.7386 (t0) REVERT: D 14 ARG cc_start: 0.7559 (ttp80) cc_final: 0.7295 (ttp80) REVERT: D 171 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7020 (tm-30) REVERT: D 212 MET cc_start: 0.5137 (mmp) cc_final: 0.4019 (mmt) outliers start: 21 outliers final: 17 residues processed: 190 average time/residue: 0.0817 time to fit residues: 21.6373 Evaluate side-chains 193 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 163 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 3.9990 chunk 118 optimal weight: 0.2980 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 39 optimal weight: 0.0170 chunk 122 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 123 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.164136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112655 restraints weight = 13380.197| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.83 r_work: 0.3219 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 9758 Z= 0.164 Angle : 0.886 59.170 13225 Z= 0.492 Chirality : 0.047 0.676 1557 Planarity : 0.004 0.072 1679 Dihedral : 6.467 89.232 1394 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.81 % Allowed : 21.95 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.24), residues: 1250 helix: 0.66 (0.25), residues: 485 sheet: -1.31 (0.41), residues: 174 loop : -1.56 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 17 TYR 0.008 0.001 TYR E 322 PHE 0.012 0.001 PHE E 319 TRP 0.008 0.001 TRP C 246 HIS 0.004 0.000 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 9756) covalent geometry : angle 0.88570 / 0.49 (13225) hydrogen bonds : bond 0.03235 / 2.01 ( 254) hydrogen bonds : angle 4.02007 / 2.85 ( 732) Misc. bond : bond 0.00085 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2093.35 seconds wall clock time: 36 minutes 23.22 seconds (2183.22 seconds total)