Starting phenix.real_space_refine on Fri Feb 14 09:10:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7arj_11884/02_2025/7arj_11884.cif Found real_map, /net/cci-nas-00/data/ceres_data/7arj_11884/02_2025/7arj_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_11884/02_2025/7arj_11884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7arj_11884/02_2025/7arj_11884.map" model { file = "/net/cci-nas-00/data/ceres_data/7arj_11884/02_2025/7arj_11884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7arj_11884/02_2025/7arj_11884.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} 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, 'PHE:plan': 1, 'ASP:plan': 2} 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: 3 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.05, per 1000 atoms: 0.63 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: 2.38 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.97 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: 2.68 Time building geometry restraints manager: 2.74 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: 5478 18.56 - 37.13: 355 37.13 - 55.69: 83 55.69 - 74.25: 18 74.25 - 92.82: 4 Dihedral angle restraints: 5938 sinusoidal: 2350 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 5935 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 228 or re \ sid 401 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.790 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 9756 Z= 0.317 Angle : 0.802 17.179 13225 Z= 0.367 Chirality : 0.047 0.271 1557 Planarity : 0.005 0.071 1679 Dihedral : 13.517 92.817 3628 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP E 321 HIS 0.001 0.000 HIS F 137 PHE 0.012 0.001 PHE C 190 TYR 0.008 0.001 TYR C 199 ARG 0.002 0.000 ARG F 211 *********************** 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 : 1.160 Fit side-chains revert: symmetry clash 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: 0.7144 (tpt) outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.2578 time to fit residues: 106.3067 Evaluate side-chains 224 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 ASN C 309 GLN C 341 ASN E 56 ASN E 84 HIS E 286 ASN F 53 HIS ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN F 163 ASN F 192 ASN D 71 GLN D 97 HIS D 140 ASN D 163 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.173515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122388 restraints weight = 13300.955| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.20 r_work: 0.3349 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9756 Z= 0.309 Angle : 0.694 7.438 13225 Z= 0.344 Chirality : 0.046 0.196 1557 Planarity : 0.005 0.049 1679 Dihedral : 9.764 140.734 1456 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.42 % Allowed : 14.70 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.19), residues: 1250 helix: -3.11 (0.16), residues: 458 sheet: -1.92 (0.45), residues: 129 loop : -2.72 (0.20), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 321 HIS 0.006 0.001 HIS E 188 PHE 0.014 0.002 PHE C 280 TYR 0.015 0.002 TYR E 322 ARG 0.004 0.001 ARG F 125 *********************** 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 255 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 69 SER cc_start: 0.9069 (t) cc_final: 0.8792 (p) REVERT: C 363 LEU cc_start: 0.8252 (tp) cc_final: 0.7919 (tt) REVERT: E 69 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7946 (mt-10) REVERT: F 34 GLU cc_start: 0.7101 (mp0) cc_final: 0.6764 (mp0) REVERT: F 59 ASP cc_start: 0.8444 (t70) cc_final: 0.8019 (t0) REVERT: F 73 MET cc_start: 0.7822 (mmt) cc_final: 0.7539 (mmt) REVERT: F 83 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8402 (mt-10) REVERT: F 107 ASN cc_start: 0.8419 (m-40) cc_final: 0.7909 (m110) REVERT: F 141 HIS cc_start: 0.8267 (m-70) cc_final: 0.7892 (m-70) REVERT: F 156 ILE cc_start: 0.8915 (mt) cc_final: 0.8647 (mm) REVERT: F 212 MET cc_start: 0.6778 (mmm) cc_final: 0.6507 (mmm) REVERT: D 10 ASN cc_start: 0.7510 (t0) cc_final: 0.7190 (t0) REVERT: D 14 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7025 (ttp80) REVERT: D 30 PHE cc_start: 0.8107 (t80) cc_final: 0.7637 (t80) REVERT: D 38 MET cc_start: 0.6438 (mpp) cc_final: 0.5995 (mpp) REVERT: D 69 ASN cc_start: 0.7395 (m-40) cc_final: 0.7121 (m110) REVERT: D 152 GLN cc_start: 0.7759 (tp40) cc_final: 0.6481 (pm20) REVERT: D 163 ASN cc_start: 0.7535 (m-40) cc_final: 0.6807 (p0) REVERT: D 171 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7105 (tm-30) REVERT: D 218 MET cc_start: 0.7765 (tpp) cc_final: 0.7470 (tpt) outliers start: 24 outliers final: 14 residues processed: 246 average time/residue: 0.2339 time to fit residues: 77.9856 Evaluate side-chains 209 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 THR 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 E residue 24 SER 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 166 VAL Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 127 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 90 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 0.0570 chunk 84 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS C 161 GLN C 309 GLN E 122 GLN F 53 HIS ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN V 4 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.175746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.124361 restraints weight = 13469.419| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 3.22 r_work: 0.3365 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9756 Z= 0.131 Angle : 0.539 6.528 13225 Z= 0.259 Chirality : 0.042 0.139 1557 Planarity : 0.003 0.037 1679 Dihedral : 8.977 135.313 1456 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.01 % Allowed : 16.31 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.21), residues: 1250 helix: -1.71 (0.22), residues: 471 sheet: -1.70 (0.44), residues: 138 loop : -2.40 (0.21), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 246 HIS 0.005 0.001 HIS E 358 PHE 0.011 0.001 PHE F 30 TYR 0.011 0.001 TYR E 258 ARG 0.003 0.000 ARG E 186 *********************** 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 228 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: C 69 SER cc_start: 0.9008 (t) cc_final: 0.8721 (p) REVERT: C 141 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8244 (mtmt) REVERT: C 153 GLN cc_start: 0.8269 (pp30) cc_final: 0.7924 (pp30) REVERT: C 262 MET cc_start: 0.8288 (tmm) cc_final: 0.8063 (tpp) REVERT: E 69 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7846 (mm-30) REVERT: F 59 ASP cc_start: 0.8430 (t70) cc_final: 0.7985 (t0) REVERT: F 83 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8339 (mt-10) REVERT: F 106 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8245 (mp0) REVERT: F 107 ASN cc_start: 0.8541 (m-40) cc_final: 0.7986 (m110) REVERT: F 141 HIS cc_start: 0.8228 (m-70) cc_final: 0.7662 (m-70) REVERT: F 190 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 10 ASN cc_start: 0.7501 (t0) cc_final: 0.7183 (t0) REVERT: D 14 ARG cc_start: 0.7395 (ttp80) cc_final: 0.6952 (ttp80) REVERT: D 30 PHE cc_start: 0.8223 (t80) cc_final: 0.7653 (t80) REVERT: D 36 GLU cc_start: 0.5071 (tt0) cc_final: 0.4081 (pt0) REVERT: D 69 ASN cc_start: 0.7313 (m-40) cc_final: 0.7067 (m110) REVERT: D 152 GLN cc_start: 0.7730 (tp40) cc_final: 0.6461 (pm20) REVERT: D 163 ASN cc_start: 0.7578 (m-40) cc_final: 0.6810 (p0) REVERT: D 171 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7161 (tm-30) REVERT: D 212 MET cc_start: 0.3628 (mmp) cc_final: 0.2613 (tpp) REVERT: D 218 MET cc_start: 0.7808 (tpp) cc_final: 0.7490 (tpt) outliers start: 20 outliers final: 14 residues processed: 221 average time/residue: 0.2364 time to fit residues: 71.0851 Evaluate side-chains 213 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 205 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 91 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 47 optimal weight: 0.0570 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS C 341 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.174723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123299 restraints weight = 13346.734| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.08 r_work: 0.3366 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9756 Z= 0.133 Angle : 0.529 9.032 13225 Z= 0.254 Chirality : 0.041 0.139 1557 Planarity : 0.003 0.037 1679 Dihedral : 8.343 125.788 1456 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.62 % Allowed : 16.82 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.22), residues: 1250 helix: -0.87 (0.23), residues: 478 sheet: -1.28 (0.49), residues: 119 loop : -2.21 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 246 HIS 0.005 0.001 HIS E 358 PHE 0.007 0.001 PHE E 319 TYR 0.011 0.001 TYR E 258 ARG 0.008 0.000 ARG E 316 *********************** 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 243 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7884 (tp30) REVERT: C 69 SER cc_start: 0.9061 (t) cc_final: 0.8813 (p) REVERT: C 141 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8250 (mtmt) REVERT: C 153 GLN cc_start: 0.8307 (pp30) cc_final: 0.7975 (pp30) REVERT: C 193 ASN cc_start: 0.8343 (t0) cc_final: 0.7841 (t0) REVERT: C 201 MET cc_start: 0.8505 (ptt) cc_final: 0.8249 (ptp) REVERT: C 363 LEU cc_start: 0.8218 (tp) cc_final: 0.7837 (tt) REVERT: E 48 MET cc_start: 0.9049 (mmt) cc_final: 0.8567 (mmt) REVERT: E 69 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7787 (mm-30) REVERT: E 314 LEU cc_start: 0.8906 (tp) cc_final: 0.8625 (tp) REVERT: E 350 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: F 51 LEU cc_start: 0.8566 (tp) cc_final: 0.7938 (pp) REVERT: F 59 ASP cc_start: 0.8363 (t70) cc_final: 0.7871 (t0) REVERT: F 83 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8246 (mt-10) REVERT: F 107 ASN cc_start: 0.8508 (m-40) cc_final: 0.7930 (m110) REVERT: F 141 HIS cc_start: 0.8180 (m-70) cc_final: 0.7621 (m-70) REVERT: D 10 ASN cc_start: 0.7465 (t0) cc_final: 0.7139 (t0) REVERT: D 14 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7088 (ttp80) REVERT: D 30 PHE cc_start: 0.8180 (t80) cc_final: 0.7608 (t80) REVERT: D 36 GLU cc_start: 0.4756 (tt0) cc_final: 0.3980 (pt0) REVERT: D 69 ASN cc_start: 0.7251 (m-40) cc_final: 0.7021 (m110) REVERT: D 152 GLN cc_start: 0.7805 (tp40) cc_final: 0.6439 (pm20) REVERT: D 163 ASN cc_start: 0.7597 (m-40) cc_final: 0.6872 (p0) REVERT: D 171 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6952 (tm-30) REVERT: D 218 MET cc_start: 0.7878 (tpp) cc_final: 0.7639 (tpt) outliers start: 26 outliers final: 14 residues processed: 232 average time/residue: 0.2380 time to fit residues: 74.6427 Evaluate side-chains 221 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 LEU 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 73 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 0.0030 chunk 94 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS E 134 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.170146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118216 restraints weight = 13394.822| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.96 r_work: 0.3295 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9756 Z= 0.183 Angle : 0.561 8.403 13225 Z= 0.270 Chirality : 0.043 0.169 1557 Planarity : 0.003 0.029 1679 Dihedral : 8.268 122.668 1456 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.02 % Allowed : 17.82 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.23), residues: 1250 helix: -0.52 (0.24), residues: 493 sheet: -1.19 (0.47), residues: 135 loop : -1.97 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 246 HIS 0.007 0.001 HIS E 358 PHE 0.013 0.001 PHE F 30 TYR 0.010 0.001 TYR E 322 ARG 0.009 0.000 ARG E 139 *********************** 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 245 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7861 (tp30) REVERT: C 69 SER cc_start: 0.9088 (t) cc_final: 0.8887 (p) REVERT: C 193 ASN cc_start: 0.8533 (t0) cc_final: 0.8176 (t0) REVERT: C 310 ILE cc_start: 0.8826 (tt) cc_final: 0.8593 (tt) REVERT: C 339 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: E 69 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7751 (mm-30) REVERT: E 123 GLU cc_start: 0.7127 (pt0) cc_final: 0.6671 (pt0) REVERT: E 139 ARG cc_start: 0.8708 (mtm110) cc_final: 0.8431 (ptp90) REVERT: E 297 ASP cc_start: 0.8141 (m-30) cc_final: 0.7898 (t0) REVERT: E 314 LEU cc_start: 0.8838 (tp) cc_final: 0.8560 (tp) REVERT: E 350 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: F 59 ASP cc_start: 0.8375 (t70) cc_final: 0.7840 (t0) REVERT: F 83 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8258 (mt-10) REVERT: F 141 HIS cc_start: 0.8202 (m-70) cc_final: 0.7600 (m-70) REVERT: F 191 LEU cc_start: 0.8166 (mm) cc_final: 0.7789 (mm) REVERT: D 10 ASN cc_start: 0.7489 (t0) cc_final: 0.7154 (t0) REVERT: D 14 ARG cc_start: 0.7459 (ttp80) cc_final: 0.7042 (ttp80) REVERT: D 30 PHE cc_start: 0.8230 (t80) cc_final: 0.7562 (t80) REVERT: D 69 ASN cc_start: 0.7233 (m-40) cc_final: 0.7004 (m110) REVERT: D 163 ASN cc_start: 0.7575 (m-40) cc_final: 0.6959 (p0) REVERT: D 171 GLU cc_start: 0.7658 (tm-30) cc_final: 0.6985 (tm-30) REVERT: D 212 MET cc_start: 0.3818 (mmp) cc_final: 0.3086 (tpp) REVERT: D 218 MET cc_start: 0.7846 (tpp) cc_final: 0.7605 (tpt) outliers start: 30 outliers final: 17 residues processed: 233 average time/residue: 0.2338 time to fit residues: 74.3429 Evaluate side-chains 210 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU 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 C residue 339 GLN Chi-restraints excluded: chain C residue 358 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 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 41 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 73 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 86 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS E 65 HIS ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 134 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.170253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119044 restraints weight = 13426.238| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.01 r_work: 0.3296 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9756 Z= 0.160 Angle : 0.551 7.481 13225 Z= 0.264 Chirality : 0.043 0.206 1557 Planarity : 0.003 0.034 1679 Dihedral : 8.069 123.171 1456 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.62 % Allowed : 19.44 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.24), residues: 1250 helix: -0.08 (0.24), residues: 484 sheet: -0.88 (0.46), residues: 141 loop : -1.87 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 246 HIS 0.007 0.001 HIS E 358 PHE 0.025 0.001 PHE F 30 TYR 0.009 0.001 TYR E 258 ARG 0.007 0.000 ARG E 139 *********************** 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 223 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7814 (tp30) REVERT: C 193 ASN cc_start: 0.8468 (t0) cc_final: 0.8108 (t0) REVERT: C 201 MET cc_start: 0.8411 (ptt) cc_final: 0.8158 (ptp) REVERT: C 310 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8589 (tt) REVERT: C 363 LEU cc_start: 0.8239 (tp) cc_final: 0.7862 (tt) REVERT: E 48 MET cc_start: 0.9002 (mmt) cc_final: 0.8614 (mmt) REVERT: E 69 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7761 (mm-30) REVERT: E 123 GLU cc_start: 0.7167 (pt0) cc_final: 0.6966 (pt0) REVERT: E 139 ARG cc_start: 0.8670 (mtm110) cc_final: 0.8427 (ptp90) REVERT: E 297 ASP cc_start: 0.8134 (m-30) cc_final: 0.7901 (t0) REVERT: E 314 LEU cc_start: 0.8874 (tp) cc_final: 0.8628 (tp) REVERT: E 350 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: F 51 LEU cc_start: 0.8447 (tp) cc_final: 0.7842 (pp) REVERT: F 59 ASP cc_start: 0.8335 (t70) cc_final: 0.7902 (t0) REVERT: F 83 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8407 (mt-10) REVERT: F 141 HIS cc_start: 0.8193 (m-70) cc_final: 0.7589 (m-70) REVERT: F 191 LEU cc_start: 0.8322 (mm) cc_final: 0.8020 (mm) REVERT: D 10 ASN cc_start: 0.7492 (t0) cc_final: 0.7159 (t0) REVERT: D 14 ARG cc_start: 0.7526 (ttp80) cc_final: 0.7097 (ttp80) REVERT: D 30 PHE cc_start: 0.8232 (t80) cc_final: 0.7572 (t80) REVERT: D 69 ASN cc_start: 0.7214 (m-40) cc_final: 0.6990 (m110) REVERT: D 163 ASN cc_start: 0.7634 (m-40) cc_final: 0.7054 (p0) REVERT: D 171 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7001 (tm-30) REVERT: D 195 GLN cc_start: 0.2014 (OUTLIER) cc_final: 0.1660 (pm20) REVERT: D 212 MET cc_start: 0.3667 (mmp) cc_final: 0.3231 (tpp) REVERT: D 218 MET cc_start: 0.7900 (tpp) cc_final: 0.7637 (tpt) outliers start: 26 outliers final: 18 residues processed: 216 average time/residue: 0.2331 time to fit residues: 68.9568 Evaluate side-chains 209 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 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 316 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 205 MET 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 41 VAL 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 73 MET Chi-restraints excluded: chain D residue 195 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 81 optimal weight: 0.0030 chunk 97 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS C 281 ASN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 69 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.166386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.114671 restraints weight = 13444.740| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.20 r_work: 0.3225 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9756 Z= 0.210 Angle : 0.566 7.838 13225 Z= 0.274 Chirality : 0.044 0.242 1557 Planarity : 0.003 0.027 1679 Dihedral : 8.303 126.465 1456 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.02 % Allowed : 19.84 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.24), residues: 1250 helix: 0.05 (0.24), residues: 494 sheet: -0.87 (0.48), residues: 129 loop : -1.79 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 246 HIS 0.005 0.001 HIS E 358 PHE 0.020 0.001 PHE F 30 TYR 0.011 0.001 TYR E 322 ARG 0.005 0.000 ARG E 139 *********************** 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 222 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7820 (tp30) REVERT: C 193 ASN cc_start: 0.8626 (t0) cc_final: 0.8300 (t0) REVERT: C 201 MET cc_start: 0.8570 (ptt) cc_final: 0.8311 (ptp) REVERT: C 310 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8668 (tt) REVERT: C 339 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7520 (mp10) REVERT: E 69 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7740 (mm-30) REVERT: E 111 ARG cc_start: 0.7387 (mmt90) cc_final: 0.7150 (mmt180) REVERT: E 123 GLU cc_start: 0.7529 (pt0) cc_final: 0.7300 (pt0) REVERT: E 139 ARG cc_start: 0.8731 (mtm110) cc_final: 0.8448 (ptp90) REVERT: E 297 ASP cc_start: 0.8297 (m-30) cc_final: 0.8072 (t0) REVERT: E 350 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: F 51 LEU cc_start: 0.8573 (tp) cc_final: 0.7938 (pp) REVERT: F 59 ASP cc_start: 0.8367 (t70) cc_final: 0.7891 (t0) REVERT: F 141 HIS cc_start: 0.8312 (m-70) cc_final: 0.7661 (m-70) REVERT: D 10 ASN cc_start: 0.7620 (t0) cc_final: 0.7274 (t0) REVERT: D 14 ARG cc_start: 0.7459 (ttp80) cc_final: 0.6827 (ttp80) REVERT: D 30 PHE cc_start: 0.8240 (t80) cc_final: 0.7591 (t80) REVERT: D 69 ASN cc_start: 0.7192 (m-40) cc_final: 0.6950 (m110) REVERT: D 163 ASN cc_start: 0.7866 (m-40) cc_final: 0.7212 (p0) REVERT: D 171 GLU cc_start: 0.7718 (tm-30) cc_final: 0.6922 (tm-30) REVERT: D 195 GLN cc_start: 0.2506 (OUTLIER) cc_final: 0.2044 (pm20) REVERT: D 218 MET cc_start: 0.7887 (tpp) cc_final: 0.7635 (tpt) outliers start: 30 outliers final: 19 residues processed: 212 average time/residue: 0.2320 time to fit residues: 67.2620 Evaluate side-chains 209 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU 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 310 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 103 LEU 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 41 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 195 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 47 optimal weight: 0.0570 chunk 80 optimal weight: 0.0060 overall best weight: 1.0716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN E 358 HIS F 87 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN F 192 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.166135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113718 restraints weight = 13550.299| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.98 r_work: 0.3242 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9756 Z= 0.183 Angle : 0.559 8.184 13225 Z= 0.269 Chirality : 0.043 0.216 1557 Planarity : 0.003 0.042 1679 Dihedral : 8.268 128.934 1456 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.22 % Allowed : 20.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.24), residues: 1250 helix: 0.31 (0.25), residues: 488 sheet: -1.12 (0.44), residues: 152 loop : -1.68 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 246 HIS 0.003 0.000 HIS D 96 PHE 0.016 0.001 PHE F 30 TYR 0.009 0.001 TYR E 322 ARG 0.007 0.000 ARG F 165 *********************** 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 221 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7845 (tp30) REVERT: C 153 GLN cc_start: 0.8744 (pp30) cc_final: 0.8481 (pp30) REVERT: C 193 ASN cc_start: 0.8581 (t0) cc_final: 0.8309 (t0) REVERT: C 310 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8664 (tt) REVERT: C 363 LEU cc_start: 0.8278 (tp) cc_final: 0.7934 (tt) REVERT: E 69 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7977 (mt-10) REVERT: E 111 ARG cc_start: 0.7389 (mmt90) cc_final: 0.7073 (mmt180) REVERT: E 139 ARG cc_start: 0.8700 (mtm110) cc_final: 0.8469 (ptp90) REVERT: E 181 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7746 (tp40) REVERT: E 228 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8047 (mpp) REVERT: E 297 ASP cc_start: 0.8284 (m-30) cc_final: 0.8068 (t0) REVERT: E 350 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: F 51 LEU cc_start: 0.8616 (tp) cc_final: 0.7863 (pp) REVERT: F 59 ASP cc_start: 0.8332 (t70) cc_final: 0.7891 (t0) REVERT: F 83 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8369 (mt-10) REVERT: F 141 HIS cc_start: 0.8306 (m-70) cc_final: 0.7660 (m-70) REVERT: F 165 ARG cc_start: 0.8213 (mmp80) cc_final: 0.7941 (mmp80) REVERT: F 191 LEU cc_start: 0.8262 (mm) cc_final: 0.7937 (mm) REVERT: D 10 ASN cc_start: 0.7631 (t0) cc_final: 0.7285 (t0) REVERT: D 14 ARG cc_start: 0.7566 (ttp80) cc_final: 0.6943 (ttp80) REVERT: D 30 PHE cc_start: 0.8216 (t80) cc_final: 0.7662 (t80) REVERT: D 69 ASN cc_start: 0.7192 (m-40) cc_final: 0.6961 (m110) REVERT: D 163 ASN cc_start: 0.7907 (m-40) cc_final: 0.7277 (p0) REVERT: D 171 GLU cc_start: 0.7814 (tm-30) cc_final: 0.6978 (tm-30) REVERT: D 195 GLN cc_start: 0.2577 (OUTLIER) cc_final: 0.2095 (pm20) REVERT: D 218 MET cc_start: 0.7873 (tpp) cc_final: 0.7621 (tpt) outliers start: 32 outliers final: 21 residues processed: 210 average time/residue: 0.2273 time to fit residues: 65.7267 Evaluate side-chains 210 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 102 VAL 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 310 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 358 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 103 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 205 MET 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 41 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 195 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 116 optimal weight: 0.0670 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.165699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.113357 restraints weight = 13271.719| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.05 r_work: 0.3237 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9756 Z= 0.174 Angle : 0.552 6.847 13225 Z= 0.266 Chirality : 0.043 0.204 1557 Planarity : 0.003 0.050 1679 Dihedral : 8.329 131.116 1456 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.62 % Allowed : 21.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.24), residues: 1250 helix: 0.44 (0.25), residues: 490 sheet: -1.07 (0.44), residues: 152 loop : -1.64 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 246 HIS 0.003 0.000 HIS D 96 PHE 0.018 0.001 PHE F 30 TYR 0.008 0.001 TYR E 322 ARG 0.006 0.000 ARG F 165 *********************** 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 216 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7855 (tp30) REVERT: C 153 GLN cc_start: 0.8756 (pp30) cc_final: 0.8487 (pp30) REVERT: C 193 ASN cc_start: 0.8543 (t0) cc_final: 0.8326 (t0) REVERT: C 201 MET cc_start: 0.8454 (ptt) cc_final: 0.8238 (ptp) REVERT: C 310 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8644 (tt) REVERT: C 363 LEU cc_start: 0.8289 (tp) cc_final: 0.7935 (tt) REVERT: E 48 MET cc_start: 0.9002 (mmt) cc_final: 0.8738 (mmp) REVERT: E 69 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7967 (mt-10) REVERT: E 71 VAL cc_start: 0.6533 (OUTLIER) cc_final: 0.6234 (p) REVERT: E 139 ARG cc_start: 0.8688 (mtm110) cc_final: 0.8467 (ptp90) REVERT: E 181 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7766 (tp40) REVERT: E 228 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8087 (mpp) REVERT: F 59 ASP cc_start: 0.8266 (t70) cc_final: 0.7877 (t0) REVERT: F 83 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8328 (mt-10) REVERT: F 141 HIS cc_start: 0.8384 (m-70) cc_final: 0.7968 (m-70) REVERT: D 10 ASN cc_start: 0.7627 (t0) cc_final: 0.7282 (t0) REVERT: D 14 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7185 (ttp80) REVERT: D 30 PHE cc_start: 0.8063 (t80) cc_final: 0.7619 (t80) REVERT: D 69 ASN cc_start: 0.7167 (m-40) cc_final: 0.6939 (m110) REVERT: D 163 ASN cc_start: 0.7817 (m-40) cc_final: 0.7446 (m-40) REVERT: D 171 GLU cc_start: 0.7743 (tm-30) cc_final: 0.6993 (tm-30) REVERT: D 195 GLN cc_start: 0.2788 (OUTLIER) cc_final: 0.2182 (pm20) REVERT: D 218 MET cc_start: 0.7833 (tpp) cc_final: 0.7567 (tpt) outliers start: 26 outliers final: 19 residues processed: 206 average time/residue: 0.2259 time to fit residues: 64.5108 Evaluate side-chains 207 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 102 VAL 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 310 ILE 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 103 LEU 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 41 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 195 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 88 optimal weight: 0.0570 chunk 10 optimal weight: 0.4980 chunk 23 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN C 281 ASN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.167172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112242 restraints weight = 13357.054| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.78 r_work: 0.3282 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9756 Z= 0.146 Angle : 0.548 7.231 13225 Z= 0.262 Chirality : 0.042 0.178 1557 Planarity : 0.003 0.054 1679 Dihedral : 8.209 131.118 1456 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.32 % Allowed : 21.55 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1250 helix: 0.62 (0.25), residues: 492 sheet: -0.98 (0.43), residues: 152 loop : -1.60 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 246 HIS 0.003 0.000 HIS D 96 PHE 0.023 0.001 PHE F 30 TYR 0.007 0.001 TYR E 258 ARG 0.006 0.000 ARG F 165 ********************** 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 215 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 GLN cc_start: 0.8747 (pp30) cc_final: 0.8528 (pp30) REVERT: C 193 ASN cc_start: 0.8644 (t0) cc_final: 0.8422 (t0) REVERT: C 201 MET cc_start: 0.8508 (ptt) cc_final: 0.8245 (ptp) REVERT: C 310 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8626 (tt) REVERT: C 363 LEU cc_start: 0.8332 (tp) cc_final: 0.7980 (tt) REVERT: E 48 MET cc_start: 0.9084 (mmt) cc_final: 0.8867 (mmp) REVERT: E 69 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8040 (mt-10) REVERT: E 71 VAL cc_start: 0.6492 (OUTLIER) cc_final: 0.6202 (p) REVERT: E 139 ARG cc_start: 0.8763 (mtm110) cc_final: 0.8544 (ptp90) REVERT: E 181 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7759 (tp40) REVERT: E 228 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8192 (mpp) REVERT: F 37 MET cc_start: 0.4490 (mmt) cc_final: 0.4261 (mmp) REVERT: F 59 ASP cc_start: 0.8297 (t70) cc_final: 0.7862 (t0) REVERT: F 83 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8419 (mt-10) REVERT: F 141 HIS cc_start: 0.8400 (m-70) cc_final: 0.7767 (m-70) REVERT: F 165 ARG cc_start: 0.8332 (mmp80) cc_final: 0.7848 (mmp80) REVERT: D 10 ASN cc_start: 0.7692 (t0) cc_final: 0.7335 (t0) REVERT: D 30 PHE cc_start: 0.8167 (t80) cc_final: 0.7771 (t80) REVERT: D 69 ASN cc_start: 0.7326 (m-40) cc_final: 0.7045 (m110) REVERT: D 163 ASN cc_start: 0.7872 (m-40) cc_final: 0.7516 (m-40) REVERT: D 171 GLU cc_start: 0.7711 (mm-30) cc_final: 0.6980 (tm-30) REVERT: D 195 GLN cc_start: 0.3216 (OUTLIER) cc_final: 0.2576 (pm20) REVERT: D 218 MET cc_start: 0.7774 (tpp) cc_final: 0.7497 (tpt) outliers start: 23 outliers final: 17 residues processed: 207 average time/residue: 0.2315 time to fit residues: 65.4156 Evaluate side-chains 207 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 102 VAL 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 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 103 LEU 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 154 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 195 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.165225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110360 restraints weight = 13332.393| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.79 r_work: 0.3251 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9756 Z= 0.169 Angle : 0.555 7.192 13225 Z= 0.266 Chirality : 0.043 0.188 1557 Planarity : 0.003 0.056 1679 Dihedral : 8.273 132.877 1456 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.42 % Allowed : 21.25 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.24), residues: 1250 helix: 0.70 (0.25), residues: 492 sheet: -0.92 (0.44), residues: 148 loop : -1.53 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 246 HIS 0.003 0.000 HIS D 96 PHE 0.019 0.001 PHE F 30 TYR 0.008 0.001 TYR E 322 ARG 0.006 0.000 ARG F 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5434.79 seconds wall clock time: 96 minutes 47.14 seconds (5807.14 seconds total)