Starting phenix.real_space_refine on Wed Sep 25 09:20:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arj_11884/09_2024/7arj_11884.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arj_11884/09_2024/7arj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arj_11884/09_2024/7arj_11884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arj_11884/09_2024/7arj_11884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arj_11884/09_2024/7arj_11884.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arj_11884/09_2024/7arj_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-5461/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: 6.41, per 1000 atoms: 0.67 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: 2.37 Conformation dependent library (CDL) restraints added in 1.2 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: 1.05 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: 2.38 Time building geometry restraints manager: 2.78 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.170 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 1.130 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: 0.2533 time to fit residues: 104.9125 Evaluate side-chains 224 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 363 LEU cc_start: 0.8155 (tp) cc_final: 0.7878 (tt) REVERT: F 34 GLU cc_start: 0.7167 (mp0) cc_final: 0.6907 (mp0) REVERT: F 59 ASP cc_start: 0.8216 (t70) cc_final: 0.7899 (t0) REVERT: F 73 MET cc_start: 0.7824 (mmt) cc_final: 0.7597 (mmt) REVERT: F 83 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7987 (mt-10) REVERT: F 107 ASN cc_start: 0.8460 (m-40) cc_final: 0.8049 (m110) REVERT: F 141 HIS cc_start: 0.7992 (m-70) cc_final: 0.7728 (m-70) REVERT: F 156 ILE cc_start: 0.9093 (mt) cc_final: 0.8798 (mm) REVERT: D 10 ASN cc_start: 0.6863 (t0) cc_final: 0.6621 (t0) REVERT: D 14 ARG cc_start: 0.7593 (ttp80) cc_final: 0.7188 (ttp80) REVERT: D 30 PHE cc_start: 0.7969 (t80) cc_final: 0.7573 (t80) REVERT: D 38 MET cc_start: 0.6349 (mpp) cc_final: 0.6019 (mpp) REVERT: D 48 LYS cc_start: 0.7881 (mtpp) cc_final: 0.7651 (mtmm) REVERT: D 152 GLN cc_start: 0.7568 (tp40) cc_final: 0.6615 (pm20) REVERT: D 163 ASN cc_start: 0.7087 (m-40) cc_final: 0.6674 (p0) REVERT: D 171 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7073 (tm-30) REVERT: D 218 MET cc_start: 0.7591 (tpp) cc_final: 0.7302 (tpt) outliers start: 24 outliers final: 14 residues processed: 246 average time/residue: 0.2290 time to fit residues: 76.5268 Evaluate side-chains 208 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 62 optimal weight: 0.0570 chunk 34 optimal weight: 10.0000 chunk 93 optimal weight: 0.0370 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9756 Z= 0.176 Angle : 0.558 6.720 13225 Z= 0.270 Chirality : 0.043 0.142 1557 Planarity : 0.003 0.038 1679 Dihedral : 8.980 121.018 1456 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.01 % Allowed : 16.52 % Favored : 81.47 % 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: -1.70 (0.22), residues: 477 sheet: -1.58 (0.46), residues: 125 loop : -2.43 (0.21), residues: 648 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 0.012 0.001 TYR E 258 ARG 0.002 0.000 ARG E 400 *********************** 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 fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 59 ASP cc_start: 0.8223 (t70) cc_final: 0.7877 (t0) REVERT: F 83 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7959 (mt-10) REVERT: F 107 ASN cc_start: 0.8507 (m-40) cc_final: 0.8010 (m110) REVERT: F 141 HIS cc_start: 0.7924 (m-70) cc_final: 0.7583 (m-70) REVERT: D 10 ASN cc_start: 0.6828 (t0) cc_final: 0.6593 (t0) REVERT: D 14 ARG cc_start: 0.7454 (ttp80) cc_final: 0.7081 (ttp80) REVERT: D 30 PHE cc_start: 0.8002 (t80) cc_final: 0.7470 (t80) REVERT: D 36 GLU cc_start: 0.4796 (tt0) cc_final: 0.4030 (pt0) REVERT: D 48 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7603 (mtmm) REVERT: D 152 GLN cc_start: 0.7688 (tp40) cc_final: 0.6674 (pm20) REVERT: D 163 ASN cc_start: 0.7183 (m-40) cc_final: 0.6723 (p0) REVERT: D 171 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7021 (tm-30) REVERT: D 212 MET cc_start: 0.2329 (mmp) cc_final: 0.2046 (tpp) outliers start: 20 outliers final: 13 residues processed: 222 average time/residue: 0.2295 time to fit residues: 68.3500 Evaluate side-chains 202 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 226 LEU 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 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 111 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.0980 chunk 119 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN E 114 GLN E 134 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9756 Z= 0.293 Angle : 0.631 9.597 13225 Z= 0.312 Chirality : 0.045 0.143 1557 Planarity : 0.003 0.034 1679 Dihedral : 8.877 117.631 1456 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.63 % Allowed : 17.42 % Favored : 78.95 % 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: -2.57 (0.22), residues: 1250 helix: -1.19 (0.23), residues: 493 sheet: -1.45 (0.45), residues: 123 loop : -2.19 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 321 HIS 0.005 0.001 HIS E 358 PHE 0.015 0.002 PHE E 319 TYR 0.015 0.001 TYR E 322 ARG 0.009 0.001 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 227 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 310 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8702 (tt) REVERT: C 335 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8093 (mm) REVERT: C 339 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: E 123 GLU cc_start: 0.6422 (pt0) cc_final: 0.6207 (pt0) REVERT: E 350 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: F 59 ASP cc_start: 0.8267 (t70) cc_final: 0.7882 (t0) REVERT: F 83 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7908 (mt-10) REVERT: F 141 HIS cc_start: 0.8030 (m-70) cc_final: 0.7739 (m-70) REVERT: D 10 ASN cc_start: 0.7001 (t0) cc_final: 0.6753 (t0) REVERT: D 48 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7853 (mtmm) REVERT: D 163 ASN cc_start: 0.7356 (m-40) cc_final: 0.7042 (p0) REVERT: D 171 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6892 (tm-30) outliers start: 36 outliers final: 15 residues processed: 217 average time/residue: 0.2200 time to fit residues: 64.9797 Evaluate side-chains 197 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 178 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 335 LEU Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 333 CYS Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 84 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 107 optimal weight: 0.0370 chunk 30 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 HIS F 69 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9756 Z= 0.147 Angle : 0.543 8.040 13225 Z= 0.265 Chirality : 0.042 0.184 1557 Planarity : 0.003 0.030 1679 Dihedral : 8.343 114.576 1456 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.72 % Allowed : 19.34 % 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: -2.03 (0.23), residues: 1250 helix: -0.60 (0.24), residues: 493 sheet: -1.28 (0.44), residues: 138 loop : -1.98 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 321 HIS 0.005 0.001 HIS E 358 PHE 0.011 0.001 PHE E 319 TYR 0.009 0.001 TYR E 258 ARG 0.006 0.000 ARG F 165 *********************** 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 217 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 190 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.7339 (tp30) cc_final: 0.7044 (tp30) REVERT: C 193 ASN cc_start: 0.7827 (t0) cc_final: 0.7560 (t0) REVERT: C 310 ILE cc_start: 0.8802 (tt) cc_final: 0.8593 (tt) REVERT: C 339 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: E 73 GLN cc_start: 0.7603 (pm20) cc_final: 0.7348 (pm20) REVERT: E 350 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: F 51 LEU cc_start: 0.8471 (tp) cc_final: 0.7822 (pp) REVERT: F 59 ASP cc_start: 0.8254 (t70) cc_final: 0.7902 (t0) REVERT: F 141 HIS cc_start: 0.7983 (m-70) cc_final: 0.7670 (m-70) REVERT: F 191 LEU cc_start: 0.8198 (mm) cc_final: 0.7884 (mm) REVERT: D 10 ASN cc_start: 0.7054 (t0) cc_final: 0.6794 (t0) REVERT: D 14 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7161 (ttp80) REVERT: D 30 PHE cc_start: 0.8107 (t80) cc_final: 0.7523 (t80) REVERT: D 48 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7807 (mtmm) REVERT: D 163 ASN cc_start: 0.7413 (m-40) cc_final: 0.7076 (p0) REVERT: D 171 GLU cc_start: 0.7433 (tm-30) cc_final: 0.6859 (tm-30) REVERT: D 218 MET cc_start: 0.6321 (tpt) cc_final: 0.5404 (tpp) outliers start: 27 outliers final: 18 residues processed: 209 average time/residue: 0.2211 time to fit residues: 63.3633 Evaluate side-chains 197 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU 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 316 VAL Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 0.2980 chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 0.0070 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 GLN F 87 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9756 Z= 0.200 Angle : 0.558 7.332 13225 Z= 0.274 Chirality : 0.043 0.216 1557 Planarity : 0.003 0.028 1679 Dihedral : 8.291 109.881 1456 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.82 % Allowed : 20.95 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.77 (0.23), residues: 1250 helix: -0.28 (0.24), residues: 500 sheet: -1.23 (0.44), residues: 138 loop : -1.93 (0.24), residues: 612 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 0.013 0.001 PHE E 319 TYR 0.009 0.001 TYR E 322 ARG 0.005 0.000 ARG E 316 *********************** 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 213 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.7461 (tp30) cc_final: 0.7214 (tp30) REVERT: C 310 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8647 (tt) REVERT: C 339 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7456 (mp10) REVERT: E 350 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: F 51 LEU cc_start: 0.8597 (tp) cc_final: 0.7954 (pp) REVERT: F 59 ASP cc_start: 0.8251 (t70) cc_final: 0.7839 (t0) REVERT: F 83 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8031 (mt-10) REVERT: F 141 HIS cc_start: 0.8038 (m-70) cc_final: 0.7690 (m-70) REVERT: D 10 ASN cc_start: 0.7117 (t0) cc_final: 0.6852 (t0) REVERT: D 14 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7300 (ttp80) REVERT: D 48 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7866 (mtmm) REVERT: D 163 ASN cc_start: 0.7421 (m-40) cc_final: 0.7094 (p0) REVERT: D 171 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6854 (tm-30) REVERT: D 195 GLN cc_start: 0.1787 (OUTLIER) cc_final: 0.1559 (pm20) outliers start: 28 outliers final: 18 residues processed: 203 average time/residue: 0.2177 time to fit residues: 61.1576 Evaluate side-chains 202 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU 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 310 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 195 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9756 Z= 0.166 Angle : 0.547 7.978 13225 Z= 0.264 Chirality : 0.043 0.189 1557 Planarity : 0.003 0.027 1679 Dihedral : 8.234 108.875 1456 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.32 % Allowed : 21.35 % Favored : 75.33 % 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: -1.41 (0.24), residues: 1250 helix: 0.20 (0.25), residues: 488 sheet: -1.26 (0.43), residues: 145 loop : -1.81 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 321 HIS 0.003 0.000 HIS D 96 PHE 0.016 0.001 PHE E 319 TYR 0.007 0.001 TYR E 258 ARG 0.005 0.000 ARG F 165 *********************** 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 220 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 201 MET cc_start: 0.7979 (ptt) cc_final: 0.7775 (ptp) REVERT: C 310 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8602 (tt) REVERT: C 339 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: F 51 LEU cc_start: 0.8542 (tp) cc_final: 0.7917 (pp) REVERT: F 59 ASP cc_start: 0.8199 (t70) cc_final: 0.7875 (t0) REVERT: F 83 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7944 (mt-10) REVERT: F 141 HIS cc_start: 0.8015 (m-70) cc_final: 0.7654 (m-70) REVERT: F 190 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8127 (tm-30) REVERT: D 10 ASN cc_start: 0.7102 (t0) cc_final: 0.6829 (t0) REVERT: D 14 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7464 (ttp80) REVERT: D 30 PHE cc_start: 0.8062 (t80) cc_final: 0.7662 (t80) REVERT: D 171 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6926 (tm-30) REVERT: D 218 MET cc_start: 0.6468 (tpt) cc_final: 0.5207 (tpp) outliers start: 33 outliers final: 23 residues processed: 209 average time/residue: 0.2200 time to fit residues: 63.2254 Evaluate side-chains 206 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 117 ILE 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 E residue 25 LEU Chi-restraints excluded: chain E residue 55 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 129 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 154 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 73 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.5872 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= 0.158 Angle : 0.540 6.868 13225 Z= 0.262 Chirality : 0.043 0.174 1557 Planarity : 0.003 0.027 1679 Dihedral : 8.261 114.810 1456 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.92 % Allowed : 21.25 % Favored : 75.83 % 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: 0.41 (0.25), residues: 489 sheet: -1.09 (0.44), residues: 144 loop : -1.79 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 321 HIS 0.003 0.000 HIS D 96 PHE 0.013 0.001 PHE E 319 TYR 0.007 0.001 TYR E 258 ARG 0.008 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 215 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 186 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 201 MET cc_start: 0.8028 (ptt) cc_final: 0.7819 (ptp) REVERT: C 310 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8542 (tt) REVERT: C 339 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7428 (mp10) REVERT: E 228 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7955 (mpp) REVERT: F 51 LEU cc_start: 0.8548 (tp) cc_final: 0.7781 (pp) REVERT: F 59 ASP cc_start: 0.8189 (t70) cc_final: 0.7812 (t0) REVERT: F 83 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7929 (mt-10) REVERT: F 141 HIS cc_start: 0.7948 (m-70) cc_final: 0.7441 (m-70) REVERT: D 10 ASN cc_start: 0.7089 (t0) cc_final: 0.6806 (t0) REVERT: D 14 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7209 (ttp80) REVERT: D 30 PHE cc_start: 0.8171 (t80) cc_final: 0.7741 (t80) REVERT: D 171 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6813 (tm-30) outliers start: 29 outliers final: 23 residues processed: 205 average time/residue: 0.2304 time to fit residues: 65.0571 Evaluate side-chains 209 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 339 GLN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 55 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 129 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 105 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 100 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6054 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= 0.196 Angle : 0.562 7.335 13225 Z= 0.273 Chirality : 0.043 0.189 1557 Planarity : 0.003 0.042 1679 Dihedral : 8.426 117.411 1456 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.02 % Allowed : 21.65 % Favored : 75.33 % 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: -1.14 (0.24), residues: 1250 helix: 0.48 (0.25), residues: 492 sheet: -1.03 (0.44), residues: 145 loop : -1.75 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 321 HIS 0.003 0.000 HIS D 96 PHE 0.013 0.001 PHE E 319 TYR 0.007 0.001 TYR E 322 ARG 0.011 0.000 ARG C 210 *********************** 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 215 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 310 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8613 (tt) REVERT: C 339 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7458 (mp10) REVERT: E 228 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7953 (mpp) REVERT: F 30 PHE cc_start: 0.7752 (t80) cc_final: 0.7424 (t80) REVERT: F 51 LEU cc_start: 0.8572 (tp) cc_final: 0.7916 (pp) REVERT: F 59 ASP cc_start: 0.8217 (t70) cc_final: 0.7884 (t0) REVERT: F 141 HIS cc_start: 0.8015 (m-70) cc_final: 0.7666 (m-70) REVERT: D 10 ASN cc_start: 0.7119 (t0) cc_final: 0.6834 (t0) REVERT: D 14 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7183 (ttp80) REVERT: D 30 PHE cc_start: 0.8149 (t80) cc_final: 0.7693 (t80) REVERT: D 163 ASN cc_start: 0.7446 (m-40) cc_final: 0.7097 (m-40) REVERT: D 171 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6834 (tm-30) outliers start: 30 outliers final: 23 residues processed: 204 average time/residue: 0.2361 time to fit residues: 66.7167 Evaluate side-chains 207 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 LEU 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 C residue 339 GLN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 55 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 129 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 154 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 73 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9756 Z= 0.185 Angle : 0.572 8.043 13225 Z= 0.279 Chirality : 0.044 0.186 1557 Planarity : 0.003 0.050 1679 Dihedral : 8.447 120.289 1456 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.82 % Allowed : 21.95 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.02 (0.24), residues: 1250 helix: 0.69 (0.25), residues: 478 sheet: -1.04 (0.43), residues: 151 loop : -1.72 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 321 HIS 0.003 0.000 HIS D 96 PHE 0.014 0.001 PHE E 319 TYR 0.007 0.001 TYR E 322 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 208 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 339 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7551 (mp10) REVERT: E 228 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7925 (mpp) REVERT: F 30 PHE cc_start: 0.7723 (t80) cc_final: 0.7398 (t80) REVERT: F 51 LEU cc_start: 0.8617 (tp) cc_final: 0.7859 (pp) REVERT: F 59 ASP cc_start: 0.8175 (t70) cc_final: 0.7792 (t0) REVERT: F 83 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8091 (mt-10) REVERT: F 141 HIS cc_start: 0.8062 (m-70) cc_final: 0.7574 (m-70) REVERT: D 10 ASN cc_start: 0.7144 (t0) cc_final: 0.6849 (t0) REVERT: D 14 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7277 (ttp80) REVERT: D 163 ASN cc_start: 0.7450 (m-40) cc_final: 0.7092 (m-40) REVERT: D 171 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6893 (tp30) outliers start: 28 outliers final: 22 residues processed: 197 average time/residue: 0.2218 time to fit residues: 60.4988 Evaluate side-chains 200 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 LEU 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 316 VAL Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 73 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN E 122 GLN F 26 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.159780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107656 restraints weight = 13291.752| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.98 r_work: 0.3153 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9756 Z= 0.297 Angle : 0.642 8.944 13225 Z= 0.315 Chirality : 0.046 0.243 1557 Planarity : 0.004 0.058 1679 Dihedral : 8.588 124.836 1456 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.82 % Allowed : 22.46 % Favored : 74.72 % 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: -1.16 (0.24), residues: 1250 helix: 0.46 (0.24), residues: 487 sheet: -1.07 (0.43), residues: 164 loop : -1.73 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 321 HIS 0.004 0.001 HIS D 96 PHE 0.016 0.002 PHE E 319 TYR 0.012 0.001 TYR E 322 ARG 0.006 0.001 ARG F 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.06 seconds wall clock time: 48 minutes 26.22 seconds (2906.22 seconds total)