Starting phenix.real_space_refine on Fri Mar 15 07:57:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arm_11887/03_2024/7arm_11887_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arm_11887/03_2024/7arm_11887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arm_11887/03_2024/7arm_11887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arm_11887/03_2024/7arm_11887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arm_11887/03_2024/7arm_11887_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arm_11887/03_2024/7arm_11887_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 6974 2.51 5 N 1931 2.21 5 O 2013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 71": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ARG 263": "NH1" <-> "NH2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F ARG 151": "NH1" <-> "NH2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "A GLU 74": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10971 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2969 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 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: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1614 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 212} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1663 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 215} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 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: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1437 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 174} 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: 6.76, per 1000 atoms: 0.62 Number of scatterers: 10971 At special positions: 0 Unit cell: (104.442, 161.226, 134.862, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 2013 8.00 N 1931 7.00 C 6974 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 - 3.50 Amino acid : False - 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: 4.57 Conformation dependent library (CDL) restraints added in 2.1 seconds 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 13 sheets defined 31.8% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'C' and resid 6 through 9 No H-bonds generated for 'chain 'C' and resid 6 through 9' Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 29 through 54 removed outlier: 3.574A pdb=" N ILE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 148 through 154 removed outlier: 3.584A pdb=" N GLN C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 254 through 292 removed outlier: 3.612A pdb=" N ALA C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.720A pdb=" N ALA C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 299 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 336 removed outlier: 4.013A pdb=" N MET C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 362 through 378 removed outlier: 3.965A pdb=" N ILE C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 388 removed outlier: 3.722A pdb=" N ARG C 386 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 10 No H-bonds generated for 'chain 'E' and resid 7 through 10' Processing helix chain 'E' and resid 22 through 58 removed outlier: 3.524A pdb=" N SER E 27 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE E 29 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER E 30 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 32 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY E 33 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA E 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU E 36 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY E 37 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA E 39 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL E 40 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE E 42 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL E 43 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY E 44 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 45 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER E 46 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 47 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET E 48 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 54 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 55 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN E 56 " --> pdb=" O ARG E 53 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN E 57 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG E 58 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 84 removed outlier: 4.014A pdb=" N ASP E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 153 through 157 removed outlier: 3.804A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 157' Processing helix chain 'E' and resid 208 through 211 No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 236 through 243 removed outlier: 3.535A pdb=" N ASP E 240 " --> pdb=" O LYS E 236 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 262 No H-bonds generated for 'chain 'E' and resid 259 through 262' Processing helix chain 'E' and resid 266 through 297 removed outlier: 4.294A pdb=" N TYR E 273 " --> pdb=" O ARG E 269 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 294 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 307 removed outlier: 3.569A pdb=" N ALA E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 335 removed outlier: 3.826A pdb=" N PHE E 319 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS E 333 " --> pdb=" O PHE E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 342 No H-bonds generated for 'chain 'E' and resid 339 through 342' Processing helix chain 'E' and resid 346 through 353 removed outlier: 3.820A pdb=" N GLU E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP E 351 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 401 removed outlier: 3.757A pdb=" N PHE E 381 " --> pdb=" O TRP E 377 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 383 " --> pdb=" O ASP E 379 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Proline residue: E 398 - end of helix removed outlier: 3.501A pdb=" N ARG E 401 " --> pdb=" O TYR E 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 54 Processing helix chain 'F' and resid 104 through 107 No H-bonds generated for 'chain 'F' and resid 104 through 107' Processing helix chain 'F' and resid 110 through 114 removed outlier: 3.651A pdb=" N ILE F 114 " --> pdb=" O MET F 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 110 through 114' Processing helix chain 'F' and resid 119 through 128 removed outlier: 3.722A pdb=" N ASN F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU F 127 " --> pdb=" O ASN F 123 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 133 No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 148 through 159 removed outlier: 3.565A pdb=" N GLN F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 190 removed outlier: 4.442A pdb=" N SER F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 184 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 3.645A pdb=" N HIS D 53 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 54 " --> pdb=" O LEU D 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 50 through 54' Processing helix chain 'D' and resid 104 through 107 No H-bonds generated for 'chain 'D' and resid 104 through 107' Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 125 through 133 removed outlier: 3.607A pdb=" N LEU D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL D 133 " --> pdb=" O MET D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 148 through 157 removed outlier: 3.611A pdb=" N GLN D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 3.541A pdb=" N ASP D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.994A pdb=" N ILE A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing sheet with id= A, first strand: chain 'C' and resid 67 through 69 Processing sheet with id= B, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.551A pdb=" N GLY C 221 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 180 through 185 removed outlier: 4.056A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET C 165 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 99 " --> pdb=" O MET C 114 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.694A pdb=" N GLU E 67 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 94 through 96 Processing sheet with id= F, first strand: chain 'E' and resid 98 through 104 removed outlier: 3.624A pdb=" N GLY E 102 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG E 111 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA E 204 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL E 118 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE E 206 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 165 through 169 removed outlier: 3.666A pdb=" N VAL E 185 " --> pdb=" O ILE E 168 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 14 through 16 Processing sheet with id= I, first strand: chain 'F' and resid 38 through 41 Processing sheet with id= J, first strand: chain 'D' and resid 39 through 41 removed outlier: 6.548A pdb=" N VAL D 201 " --> pdb=" O ILE D 40 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 17 through 19 removed outlier: 3.932A pdb=" N ALA A 18 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 23 through 25 Processing sheet with id= M, first strand: chain 'A' and resid 66 through 70 215 hydrogen bonds defined for protein. 585 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: 2.60 Time building geometry restraints manager: 4.90 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: 3604 1.34 - 1.46: 1430 1.46 - 1.57: 6026 1.57 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 11159 Sorted by residual: bond pdb=" C16 Z41 V 101 " pdb=" O2 Z41 V 101 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C19 Z41 V 101 " pdb=" O3 Z41 V 101 " ideal model delta sigma weight residual 1.333 1.455 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C ARG A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 1.334 1.387 -0.054 2.34e-02 1.83e+03 5.24e+00 bond pdb=" C GLN A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.95e+00 bond pdb=" CA THR F 62 " pdb=" CB THR F 62 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.70e+00 ... (remaining 11154 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.17: 340 107.17 - 113.88: 6319 113.88 - 120.59: 4213 120.59 - 127.30: 4118 127.30 - 134.00: 114 Bond angle restraints: 15104 Sorted by residual: angle pdb=" N ILE E 356 " pdb=" CA ILE E 356 " pdb=" C ILE E 356 " ideal model delta sigma weight residual 113.47 108.97 4.50 1.01e+00 9.80e-01 1.98e+01 angle pdb=" C PRO F 61 " pdb=" N THR F 62 " pdb=" CA THR F 62 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C GLN A 103 " pdb=" N TYR A 104 " pdb=" CA TYR A 104 " ideal model delta sigma weight residual 122.82 128.64 -5.82 1.42e+00 4.96e-01 1.68e+01 angle pdb=" C GLY F 115 " pdb=" N LYS F 116 " pdb=" CA LYS F 116 " ideal model delta sigma weight residual 122.82 127.92 -5.10 1.42e+00 4.96e-01 1.29e+01 angle pdb=" CA LEU D 160 " pdb=" CB LEU D 160 " pdb=" CG LEU D 160 " ideal model delta sigma weight residual 116.30 128.24 -11.94 3.50e+00 8.16e-02 1.16e+01 ... (remaining 15099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 6149 17.48 - 34.95: 479 34.95 - 52.43: 92 52.43 - 69.91: 19 69.91 - 87.38: 8 Dihedral angle restraints: 6747 sinusoidal: 2653 harmonic: 4094 Sorted by residual: dihedral pdb=" CA PRO E 74 " pdb=" C PRO E 74 " pdb=" N TRP E 75 " pdb=" CA TRP E 75 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG A 43 " pdb=" C ARG A 43 " pdb=" N PRO A 44 " pdb=" CA PRO A 44 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA MET C 63 " pdb=" C MET C 63 " pdb=" N PRO C 64 " pdb=" CA PRO C 64 " ideal model delta harmonic sigma weight residual 180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 6744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1207 0.042 - 0.083: 378 0.083 - 0.125: 130 0.125 - 0.166: 23 0.166 - 0.208: 4 Chirality restraints: 1742 Sorted by residual: chirality pdb=" CB ILE E 149 " pdb=" CA ILE E 149 " pdb=" CG1 ILE E 149 " pdb=" CG2 ILE E 149 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE C 178 " pdb=" CA ILE C 178 " pdb=" CG1 ILE C 178 " pdb=" CG2 ILE C 178 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CB ILE D 4 " pdb=" CA ILE D 4 " pdb=" CG1 ILE D 4 " pdb=" CG2 ILE D 4 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.41e-01 ... (remaining 1739 not shown) Planarity restraints: 1950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 178 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO C 179 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 110 " 0.037 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO D 111 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 111 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 111 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 346 " 0.036 5.00e-02 4.00e+02 5.35e-02 4.57e+00 pdb=" N PRO E 347 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 347 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 347 " 0.030 5.00e-02 4.00e+02 ... (remaining 1947 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3505 2.84 - 3.36: 8749 3.36 - 3.87: 17018 3.87 - 4.39: 19317 4.39 - 4.90: 32758 Nonbonded interactions: 81347 Sorted by model distance: nonbonded pdb=" O PRO E 74 " pdb=" OG SER E 220 " model vdw 2.328 2.440 nonbonded pdb=" O LEU F 6 " pdb=" OG SER F 31 " model vdw 2.350 2.440 nonbonded pdb=" O SER E 342 " pdb=" OG SER E 373 " model vdw 2.350 2.440 nonbonded pdb=" O ALA E 61 " pdb=" OG SER E 127 " model vdw 2.351 2.440 nonbonded pdb=" O CYS D 8 " pdb=" OG SER D 29 " model vdw 2.371 2.440 ... (remaining 81342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 3 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 or (resid 16 through 17 and (nam \ e N or name CA or name C or name O or name CB )) or resid 18 through 19 or (resi \ d 20 and (name N or name CA or name C or name O or name CB )) or resid 21 throug \ h 27 or (resid 28 and (name N or name CA or name C or name O or name CB )) or re \ sid 29 through 35 or (resid 36 and (name N or name CA or name C or name O or nam \ e CB )) or resid 37 through 47 or (resid 48 and (name N or name CA or name C or \ name O or name CB )) or resid 49 through 54 or (resid 55 and (name N or name CA \ or name C or name O or name CB )) or resid 56 through 59 or (resid 60 and (name \ N or name CA or name C or name O or name CB )) or resid 61 through 64 or (resid \ 65 and (name N or name CA or name C or name O or name CB )) or resid 66 through \ 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or resi \ d 77 through 132 or (resid 133 and (name N or name CA or name C or name O or nam \ e CB )) or resid 134 or (resid 135 and (name N or name CA or name C or name O or \ name CB )) or resid 136 through 170 or (resid 171 and (name N or name CA or nam \ e C or name O or name CB )) or resid 172 through 175 or (resid 176 through 178 a \ nd (name N or name CA or name C or name O or name CB )) or resid 179 through 211 \ or (resid 212 and (name N or name CA or name C or name O or name CB )) or resid \ 213 through 215 or (resid 216 through 217 and (name N or name CA or name C or n \ ame O or name CB )) or resid 218 through 222 or (resid 223 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'F' and (resid 3 through 164 or (resid 165 through 166 and (name N or nam \ e CA or name C or name O or name CB )) or resid 167 through 172 or (resid 173 an \ d (name N or name CA or name C or name O or name CB )) or resid 174 through 181 \ or (resid 182 and (name N or name 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 200 or (resid 201 and (name N or name CA or name C o \ r name O or name CB )) or resid 202 through 214 or (resid 215 through 217 and (n \ ame N or name CA or name C or name O or name CB )) or resid 218 through 221 or ( \ resid 222 through 223 and (name N or name CA or name C or name O or name CB )))) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 2.320 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.680 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 0.003 0.122 11159 Z= 0.215 Angle : 0.698 11.942 15104 Z= 0.355 Chirality : 0.047 0.208 1742 Planarity : 0.005 0.063 1950 Dihedral : 13.162 87.384 4109 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.17 % Allowed : 6.69 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.79 (0.14), residues: 1424 helix: -5.09 (0.05), residues: 449 sheet: -2.44 (0.36), residues: 155 loop : -3.50 (0.15), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 101 HIS 0.003 0.000 HIS A 50 PHE 0.030 0.001 PHE D 30 TYR 0.010 0.001 TYR A 104 ARG 0.002 0.000 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 371 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.7930 (mtp) cc_final: 0.7641 (mtp) REVERT: C 117 ILE cc_start: 0.8934 (pt) cc_final: 0.8727 (pt) REVERT: E 12 ARG cc_start: 0.4395 (mmp80) cc_final: 0.3681 (mmt180) REVERT: E 136 ASP cc_start: 0.7304 (t0) cc_final: 0.7097 (t0) REVERT: E 382 TYR cc_start: 0.7600 (m-10) cc_final: 0.7394 (m-10) REVERT: F 106 GLU cc_start: 0.6841 (pt0) cc_final: 0.6434 (mt-10) REVERT: F 129 MET cc_start: 0.7170 (mmm) cc_final: 0.6811 (tpp) REVERT: F 191 LEU cc_start: 0.8227 (mp) cc_final: 0.7716 (mp) REVERT: D 86 ASN cc_start: 0.6854 (p0) cc_final: 0.6267 (t0) REVERT: V 10 LEU cc_start: 0.4279 (mt) cc_final: 0.3190 (mt) REVERT: A 112 ASP cc_start: 0.5680 (m-30) cc_final: 0.4767 (t0) outliers start: 2 outliers final: 0 residues processed: 372 average time/residue: 0.2573 time to fit residues: 130.4460 Evaluate side-chains 251 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN C 76 ASN C 281 ASN C 317 GLN C 339 GLN C 364 GLN C 391 GLN E 56 ASN E 73 GLN E 140 ASN E 286 ASN E 404 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS F 207 GLN D 69 ASN D 141 HIS D 152 GLN D 204 HIS A 50 HIS A 145 GLN A 157 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11159 Z= 0.189 Angle : 0.550 10.435 15104 Z= 0.273 Chirality : 0.042 0.273 1742 Planarity : 0.004 0.052 1950 Dihedral : 4.986 54.061 1579 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.43 % Allowed : 17.29 % Favored : 80.28 % 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: -4.40 (0.17), residues: 1424 helix: -3.52 (0.15), residues: 445 sheet: -1.93 (0.39), residues: 174 loop : -2.85 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 138 HIS 0.009 0.001 HIS D 204 PHE 0.018 0.001 PHE D 68 TYR 0.012 0.001 TYR E 260 ARG 0.006 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 271 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 ARG cc_start: 0.6628 (mmp80) cc_final: 0.5287 (pmt-80) REVERT: C 63 MET cc_start: 0.8391 (tmm) cc_final: 0.8055 (tmm) REVERT: C 122 LYS cc_start: 0.8980 (tppt) cc_final: 0.8707 (tppp) REVERT: C 231 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7906 (mttm) REVERT: E 325 LEU cc_start: 0.9039 (mm) cc_final: 0.8817 (mp) REVERT: F 38 MET cc_start: 0.6459 (tpp) cc_final: 0.6241 (tpp) REVERT: F 106 GLU cc_start: 0.6866 (pt0) cc_final: 0.6471 (mt-10) REVERT: D 86 ASN cc_start: 0.6928 (p0) cc_final: 0.6388 (t0) REVERT: D 186 GLN cc_start: 0.8093 (pp30) cc_final: 0.7779 (pp30) REVERT: A 112 ASP cc_start: 0.5800 (m-30) cc_final: 0.4841 (t0) outliers start: 28 outliers final: 18 residues processed: 283 average time/residue: 0.2214 time to fit residues: 90.7207 Evaluate side-chains 247 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 229 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 152 GLN Chi-restraints excluded: chain A residue 145 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 129 optimal weight: 0.0470 chunk 139 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 128 optimal weight: 0.0070 chunk 44 optimal weight: 0.4980 chunk 103 optimal weight: 9.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN D 141 HIS A 45 ASN A 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11159 Z= 0.126 Angle : 0.498 7.740 15104 Z= 0.246 Chirality : 0.041 0.142 1742 Planarity : 0.004 0.044 1950 Dihedral : 4.555 54.232 1579 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.35 % Allowed : 20.42 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.19), residues: 1424 helix: -2.30 (0.21), residues: 443 sheet: -1.82 (0.38), residues: 180 loop : -2.61 (0.18), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 138 HIS 0.003 0.000 HIS D 96 PHE 0.024 0.001 PHE D 68 TYR 0.021 0.001 TYR E 260 ARG 0.005 0.000 ARG E 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 ARG cc_start: 0.6411 (mmp80) cc_final: 0.5412 (pmt-80) REVERT: C 63 MET cc_start: 0.8513 (tmm) cc_final: 0.8036 (tmm) REVERT: C 231 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7947 (mttm) REVERT: E 75 TRP cc_start: 0.7169 (m100) cc_final: 0.6904 (m100) REVERT: E 325 LEU cc_start: 0.9064 (mm) cc_final: 0.8824 (mp) REVERT: F 106 GLU cc_start: 0.6838 (pt0) cc_final: 0.6449 (mt-10) REVERT: F 190 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7526 (tm-30) REVERT: D 86 ASN cc_start: 0.6980 (p0) cc_final: 0.6370 (t0) REVERT: D 171 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7725 (tm-30) REVERT: A 112 ASP cc_start: 0.5856 (m-30) cc_final: 0.4830 (t0) outliers start: 27 outliers final: 20 residues processed: 250 average time/residue: 0.2274 time to fit residues: 81.4915 Evaluate side-chains 242 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 222 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 321 TRP Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 145 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 137 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN D 10 ASN D 27 ASN D 53 HIS D 141 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11159 Z= 0.364 Angle : 0.686 7.663 15104 Z= 0.347 Chirality : 0.047 0.231 1742 Planarity : 0.005 0.066 1950 Dihedral : 6.165 52.725 1579 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.69 % Allowed : 19.29 % Favored : 76.02 % 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: -3.30 (0.20), residues: 1424 helix: -2.03 (0.21), residues: 495 sheet: -1.81 (0.37), residues: 188 loop : -2.41 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 165 HIS 0.004 0.001 HIS D 96 PHE 0.024 0.002 PHE D 68 TYR 0.023 0.002 TYR E 260 ARG 0.005 0.001 ARG D 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 244 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 MET cc_start: 0.7280 (ttp) cc_final: 0.7025 (ttm) REVERT: C 231 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8306 (mttm) REVERT: E 75 TRP cc_start: 0.7236 (m100) cc_final: 0.6992 (m100) REVERT: E 286 ASN cc_start: 0.8588 (m-40) cc_final: 0.8297 (m110) REVERT: E 321 TRP cc_start: 0.8022 (OUTLIER) cc_final: 0.7814 (m-90) REVERT: E 325 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8699 (mt) REVERT: E 351 TRP cc_start: 0.8370 (t60) cc_final: 0.7859 (t60) REVERT: E 369 ASP cc_start: 0.7546 (t70) cc_final: 0.7160 (t0) REVERT: F 101 ASP cc_start: 0.8565 (p0) cc_final: 0.8249 (p0) REVERT: F 190 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7178 (tm-30) REVERT: D 38 MET cc_start: 0.5986 (mmt) cc_final: 0.5244 (mmp) REVERT: D 86 ASN cc_start: 0.7391 (p0) cc_final: 0.6741 (t0) REVERT: D 141 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6125 (m170) REVERT: D 171 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7865 (tm-30) outliers start: 54 outliers final: 31 residues processed: 276 average time/residue: 0.2128 time to fit residues: 83.9034 Evaluate side-chains 254 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 220 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 321 TRP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 145 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 117 optimal weight: 0.0470 chunk 94 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 ASN E 140 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11159 Z= 0.216 Angle : 0.571 9.751 15104 Z= 0.286 Chirality : 0.045 0.403 1742 Planarity : 0.004 0.065 1950 Dihedral : 5.755 58.656 1579 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.21 % Allowed : 22.42 % Favored : 74.37 % 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: -2.85 (0.21), residues: 1424 helix: -1.42 (0.23), residues: 495 sheet: -1.51 (0.39), residues: 172 loop : -2.34 (0.20), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 138 HIS 0.008 0.001 HIS D 141 PHE 0.019 0.001 PHE D 68 TYR 0.018 0.001 TYR E 260 ARG 0.006 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 235 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 MET cc_start: 0.7449 (ttp) cc_final: 0.7187 (ttm) REVERT: C 212 MET cc_start: 0.4887 (ttm) cc_final: 0.4380 (ttm) REVERT: C 231 LYS cc_start: 0.8511 (mmtt) cc_final: 0.8261 (mttm) REVERT: E 75 TRP cc_start: 0.7310 (m100) cc_final: 0.6943 (m100) REVERT: E 165 TRP cc_start: 0.7714 (m100) cc_final: 0.7504 (m100) REVERT: E 186 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7707 (ttp-170) REVERT: E 286 ASN cc_start: 0.8524 (m-40) cc_final: 0.8241 (m110) REVERT: E 321 TRP cc_start: 0.7601 (OUTLIER) cc_final: 0.7161 (m-90) REVERT: E 325 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8652 (mt) REVERT: E 351 TRP cc_start: 0.8302 (t60) cc_final: 0.7806 (t60) REVERT: E 369 ASP cc_start: 0.7460 (t70) cc_final: 0.7108 (t0) REVERT: F 101 ASP cc_start: 0.8542 (p0) cc_final: 0.8193 (p0) REVERT: F 128 GLU cc_start: 0.6851 (pp20) cc_final: 0.6489 (pp20) REVERT: F 190 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7228 (tm-30) REVERT: D 38 MET cc_start: 0.5732 (mmt) cc_final: 0.5097 (mmp) REVERT: D 86 ASN cc_start: 0.7399 (p0) cc_final: 0.6678 (t0) REVERT: D 171 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7775 (tm-30) REVERT: D 212 MET cc_start: 0.5784 (pmm) cc_final: 0.5539 (pmm) outliers start: 37 outliers final: 23 residues processed: 255 average time/residue: 0.2116 time to fit residues: 77.9751 Evaluate side-chains 247 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 321 TRP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11159 Z= 0.160 Angle : 0.534 9.109 15104 Z= 0.266 Chirality : 0.044 0.459 1742 Planarity : 0.004 0.059 1950 Dihedral : 5.245 58.855 1579 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.13 % Allowed : 23.11 % Favored : 73.76 % 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: -2.48 (0.21), residues: 1424 helix: -0.88 (0.24), residues: 493 sheet: -1.52 (0.38), residues: 184 loop : -2.24 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 138 HIS 0.004 0.000 HIS F 96 PHE 0.022 0.001 PHE D 68 TYR 0.018 0.001 TYR E 322 ARG 0.005 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 234 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 103 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8954 (mm) REVERT: C 165 MET cc_start: 0.7461 (ttp) cc_final: 0.7142 (ttm) REVERT: C 212 MET cc_start: 0.4689 (ttm) cc_final: 0.4151 (ttm) REVERT: C 231 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8247 (mttm) REVERT: E 75 TRP cc_start: 0.7453 (m100) cc_final: 0.6986 (m100) REVERT: E 250 TYR cc_start: 0.7744 (m-10) cc_final: 0.7318 (m-10) REVERT: E 251 ILE cc_start: 0.8648 (mm) cc_final: 0.8417 (tt) REVERT: E 286 ASN cc_start: 0.8476 (m-40) cc_final: 0.8203 (m110) REVERT: E 321 TRP cc_start: 0.7450 (OUTLIER) cc_final: 0.7140 (m-90) REVERT: E 325 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8610 (mt) REVERT: E 351 TRP cc_start: 0.8320 (t60) cc_final: 0.7830 (t60) REVERT: F 128 GLU cc_start: 0.6780 (pp20) cc_final: 0.6580 (pp20) REVERT: F 152 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8581 (mm110) REVERT: F 190 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7396 (tm-30) REVERT: F 205 ASP cc_start: 0.7853 (p0) cc_final: 0.7623 (p0) REVERT: D 38 MET cc_start: 0.5858 (mmt) cc_final: 0.5142 (mmp) REVERT: D 86 ASN cc_start: 0.7489 (p0) cc_final: 0.6694 (t0) REVERT: D 171 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7917 (tm-30) REVERT: D 212 MET cc_start: 0.5800 (pmm) cc_final: 0.5587 (pmm) REVERT: A 105 ASN cc_start: 0.2351 (OUTLIER) cc_final: 0.2029 (p0) outliers start: 36 outliers final: 22 residues processed: 250 average time/residue: 0.2094 time to fit residues: 75.7987 Evaluate side-chains 247 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 321 TRP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 105 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 8.9990 chunk 78 optimal weight: 0.0010 chunk 100 optimal weight: 0.2980 chunk 77 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 85 optimal weight: 0.0980 chunk 83 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11159 Z= 0.128 Angle : 0.533 8.868 15104 Z= 0.262 Chirality : 0.043 0.433 1742 Planarity : 0.003 0.051 1950 Dihedral : 4.986 58.474 1579 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.17 % Allowed : 25.02 % Favored : 72.81 % 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: -2.14 (0.22), residues: 1424 helix: -0.38 (0.25), residues: 472 sheet: -1.45 (0.38), residues: 185 loop : -2.14 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 138 HIS 0.004 0.000 HIS F 96 PHE 0.023 0.001 PHE D 68 TYR 0.017 0.001 TYR E 322 ARG 0.005 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 240 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 LYS cc_start: 0.8702 (mmmt) cc_final: 0.8270 (tptm) REVERT: C 165 MET cc_start: 0.7434 (ttp) cc_final: 0.7127 (ttm) REVERT: C 212 MET cc_start: 0.4795 (ttm) cc_final: 0.4204 (ttm) REVERT: C 231 LYS cc_start: 0.8470 (mmtt) cc_final: 0.8243 (mttm) REVERT: E 12 ARG cc_start: 0.8082 (mmp80) cc_final: 0.6361 (mpt180) REVERT: E 75 TRP cc_start: 0.7425 (m100) cc_final: 0.6940 (m100) REVERT: E 250 TYR cc_start: 0.7743 (m-10) cc_final: 0.7335 (m-10) REVERT: E 251 ILE cc_start: 0.8664 (mm) cc_final: 0.8409 (tt) REVERT: E 325 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8561 (mt) REVERT: E 351 TRP cc_start: 0.8216 (t60) cc_final: 0.7843 (t60) REVERT: F 84 LEU cc_start: 0.7463 (pt) cc_final: 0.7137 (pp) REVERT: F 190 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7223 (tm-30) REVERT: F 205 ASP cc_start: 0.7827 (p0) cc_final: 0.7492 (p0) REVERT: D 38 MET cc_start: 0.5956 (mmt) cc_final: 0.5291 (mmp) REVERT: D 86 ASN cc_start: 0.7472 (p0) cc_final: 0.6778 (t0) REVERT: A 105 ASN cc_start: 0.2284 (OUTLIER) cc_final: 0.1963 (p0) outliers start: 25 outliers final: 19 residues processed: 251 average time/residue: 0.2094 time to fit residues: 75.6738 Evaluate side-chains 240 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 219 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 105 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 107 optimal weight: 30.0000 chunk 124 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN D 162 ASN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11159 Z= 0.200 Angle : 0.574 8.484 15104 Z= 0.284 Chirality : 0.045 0.401 1742 Planarity : 0.004 0.052 1950 Dihedral : 5.189 57.819 1579 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.61 % Allowed : 25.20 % Favored : 72.20 % 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: -2.04 (0.22), residues: 1424 helix: -0.33 (0.25), residues: 482 sheet: -1.33 (0.39), residues: 184 loop : -2.09 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 138 HIS 0.003 0.001 HIS F 96 PHE 0.023 0.001 PHE D 68 TYR 0.016 0.001 TYR E 322 ARG 0.005 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 231 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8374 (tptm) REVERT: C 212 MET cc_start: 0.4741 (ttm) cc_final: 0.4149 (ttm) REVERT: C 231 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8262 (mttm) REVERT: E 12 ARG cc_start: 0.8227 (mmp80) cc_final: 0.7167 (mpt180) REVERT: E 75 TRP cc_start: 0.7452 (m100) cc_final: 0.6952 (m100) REVERT: E 251 ILE cc_start: 0.8810 (mm) cc_final: 0.8584 (tt) REVERT: E 286 ASN cc_start: 0.8517 (m-40) cc_final: 0.8183 (m110) REVERT: E 321 TRP cc_start: 0.7591 (OUTLIER) cc_final: 0.7345 (m-90) REVERT: E 325 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8615 (mt) REVERT: E 351 TRP cc_start: 0.8327 (t60) cc_final: 0.7881 (t60) REVERT: F 190 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7307 (tm-30) REVERT: F 205 ASP cc_start: 0.7799 (p0) cc_final: 0.7416 (p0) REVERT: D 38 MET cc_start: 0.5935 (mmt) cc_final: 0.5263 (mmp) REVERT: D 86 ASN cc_start: 0.7563 (p0) cc_final: 0.6761 (t0) REVERT: A 105 ASN cc_start: 0.2221 (OUTLIER) cc_final: 0.1903 (p0) outliers start: 30 outliers final: 22 residues processed: 242 average time/residue: 0.2081 time to fit residues: 73.4297 Evaluate side-chains 247 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 321 TRP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 105 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS D 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11159 Z= 0.400 Angle : 0.715 9.831 15104 Z= 0.361 Chirality : 0.049 0.386 1742 Planarity : 0.004 0.060 1950 Dihedral : 6.474 58.513 1579 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.13 % Allowed : 24.93 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.19 (0.22), residues: 1424 helix: -0.54 (0.24), residues: 495 sheet: -1.47 (0.37), residues: 186 loop : -2.12 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 138 HIS 0.007 0.001 HIS F 96 PHE 0.025 0.002 PHE A 90 TYR 0.017 0.002 TYR E 322 ARG 0.007 0.001 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 222 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 63 MET cc_start: 0.8419 (tmm) cc_final: 0.8143 (tmm) REVERT: C 133 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8435 (tptm) REVERT: C 212 MET cc_start: 0.4698 (ttm) cc_final: 0.4255 (ttm) REVERT: C 231 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8307 (mttm) REVERT: E 286 ASN cc_start: 0.8723 (m-40) cc_final: 0.8352 (m110) REVERT: E 321 TRP cc_start: 0.7849 (OUTLIER) cc_final: 0.7136 (m-90) REVERT: E 325 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8816 (mt) REVERT: E 369 ASP cc_start: 0.7560 (t0) cc_final: 0.7350 (t0) REVERT: F 137 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.6929 (p90) REVERT: F 190 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7289 (tm-30) REVERT: F 205 ASP cc_start: 0.7905 (p0) cc_final: 0.7480 (p0) REVERT: D 38 MET cc_start: 0.5788 (mmt) cc_final: 0.5090 (mmp) REVERT: D 86 ASN cc_start: 0.7632 (p0) cc_final: 0.7032 (t0) REVERT: A 105 ASN cc_start: 0.2623 (OUTLIER) cc_final: 0.2282 (p0) outliers start: 36 outliers final: 25 residues processed: 240 average time/residue: 0.2256 time to fit residues: 76.5968 Evaluate side-chains 246 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 217 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 321 TRP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 152 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 105 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 8.9990 chunk 63 optimal weight: 0.0060 chunk 93 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 overall best weight: 2.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11159 Z= 0.294 Angle : 0.664 9.913 15104 Z= 0.335 Chirality : 0.047 0.372 1742 Planarity : 0.004 0.052 1950 Dihedral : 6.355 56.720 1579 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.78 % Allowed : 26.15 % Favored : 71.07 % 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: -2.17 (0.22), residues: 1424 helix: -0.47 (0.24), residues: 495 sheet: -1.50 (0.38), residues: 184 loop : -2.13 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 138 HIS 0.009 0.001 HIS F 96 PHE 0.025 0.002 PHE A 90 TYR 0.018 0.001 TYR E 322 ARG 0.008 0.001 ARG D 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8415 (tptm) REVERT: C 165 MET cc_start: 0.7435 (ttp) cc_final: 0.7190 (ttm) REVERT: C 231 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8263 (mttm) REVERT: E 75 TRP cc_start: 0.7454 (m100) cc_final: 0.6880 (m100) REVERT: E 286 ASN cc_start: 0.8651 (m-40) cc_final: 0.8305 (m110) REVERT: E 321 TRP cc_start: 0.7815 (OUTLIER) cc_final: 0.7436 (m-90) REVERT: E 325 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8734 (mt) REVERT: E 351 TRP cc_start: 0.8428 (t60) cc_final: 0.8059 (t60) REVERT: E 369 ASP cc_start: 0.7610 (t0) cc_final: 0.7389 (t0) REVERT: F 54 LEU cc_start: 0.8470 (mm) cc_final: 0.7971 (mm) REVERT: F 72 PRO cc_start: 0.4481 (Cg_exo) cc_final: 0.3941 (Cg_endo) REVERT: F 137 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.6923 (p90) REVERT: F 190 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7303 (tm-30) REVERT: F 205 ASP cc_start: 0.7921 (p0) cc_final: 0.7561 (p0) REVERT: D 86 ASN cc_start: 0.7731 (p0) cc_final: 0.7054 (t0) REVERT: A 105 ASN cc_start: 0.2566 (OUTLIER) cc_final: 0.2256 (p0) REVERT: A 153 GLN cc_start: 0.6767 (pp30) cc_final: 0.6023 (mt0) outliers start: 32 outliers final: 25 residues processed: 243 average time/residue: 0.2168 time to fit residues: 75.5466 Evaluate side-chains 254 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 225 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 321 TRP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 105 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109019 restraints weight = 19062.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111294 restraints weight = 11032.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111390 restraints weight = 7388.907| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.6750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11159 Z= 0.274 Angle : 0.663 10.468 15104 Z= 0.331 Chirality : 0.047 0.378 1742 Planarity : 0.004 0.055 1950 Dihedral : 6.299 58.416 1579 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.95 % Allowed : 26.41 % Favored : 70.63 % 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: -2.08 (0.22), residues: 1424 helix: -0.32 (0.25), residues: 494 sheet: -1.65 (0.35), residues: 203 loop : -2.08 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 138 HIS 0.010 0.001 HIS F 96 PHE 0.024 0.002 PHE A 90 TYR 0.018 0.001 TYR E 322 ARG 0.006 0.000 ARG D 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2500.38 seconds wall clock time: 46 minutes 6.35 seconds (2766.35 seconds total)