Starting phenix.real_space_refine on Sun Aug 4 18:43:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arm_11887/08_2024/7arm_11887.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arm_11887/08_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_11887/08_2024/7arm_11887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arm_11887/08_2024/7arm_11887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arm_11887/08_2024/7arm_11887.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arm_11887/08_2024/7arm_11887.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 6.23, per 1000 atoms: 0.57 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: 3.62 Conformation dependent library (CDL) restraints added in 2.0 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... Secondary structure from input PDB file: 50 helices and 14 sheets defined 37.7% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'C' and resid 5 through 10 removed outlier: 4.033A pdb=" N GLY C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 26 removed outlier: 3.593A pdb=" N ARG C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 55 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 133 through 137 removed outlier: 3.864A pdb=" N LEU C 137 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 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 195 through 198 removed outlier: 3.766A pdb=" N GLY C 198 " --> pdb=" O GLU C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 248 through 252 removed outlier: 4.048A pdb=" N ASP C 251 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 252 " --> pdb=" O TRP C 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 248 through 252' Processing helix chain 'C' and resid 253 through 271 removed outlier: 3.700A pdb=" N PHE C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) 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) Processing helix chain 'C' and resid 272 through 293 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 293 through 302 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) Processing helix chain 'C' and resid 306 through 337 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) removed outlier: 3.749A pdb=" N ALA C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 348 removed outlier: 4.071A pdb=" N ILE C 347 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY C 348 " --> pdb=" O PRO C 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 344 through 348' Processing helix chain 'C' and resid 361 through 379 removed outlier: 3.569A pdb=" N VAL C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) 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 380 through 389 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 6 through 11 removed outlier: 4.060A pdb=" N LEU E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 59 removed outlier: 3.919A pdb=" N ILE E 26 " --> pdb=" O MET E 22 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E 47 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN E 56 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 85 removed outlier: 4.014A pdb=" N ASP E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.599A pdb=" N ARG E 125 " --> pdb=" O GLN E 122 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 126 " --> pdb=" O GLU E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 129 through 133 removed outlier: 3.713A pdb=" N PHE E 132 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL E 133 " --> pdb=" O PRO E 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 129 through 133' Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.647A pdb=" N ASP E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.689A pdb=" N GLN E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 208 through 212' Processing helix chain 'E' and resid 235 through 244 removed outlier: 3.759A pdb=" N ARG E 239 " --> pdb=" O ASN E 235 " (cutoff:3.500A) 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) removed outlier: 3.857A pdb=" N VAL E 244 " --> pdb=" O ASP E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 removed outlier: 3.702A pdb=" N TYR E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 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) Processing helix chain 'E' and resid 284 through 298 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) removed outlier: 3.721A pdb=" N LYS E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 308 removed outlier: 3.505A pdb=" N ILE E 302 " --> pdb=" O LYS E 298 " (cutoff:3.500A) 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 311 through 336 removed outlier: 3.622A pdb=" N ILE E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) 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 338 through 343 Processing helix chain 'E' and resid 345 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 376 through 402 removed outlier: 3.904A pdb=" N VAL E 380 " --> pdb=" O HIS E 376 " (cutoff:3.500A) 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 49 through 55 removed outlier: 3.790A pdb=" N HIS F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 4.047A pdb=" N VAL F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 115 removed outlier: 3.651A pdb=" N ILE F 114 " --> pdb=" O MET F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 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 129 through 134 Processing helix chain 'F' and resid 147 through 160 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) removed outlier: 3.643A pdb=" N LEU F 160 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 191 removed outlier: 4.664A pdb=" N ASP F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) 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) removed outlier: 4.070A pdb=" N LEU F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 55 removed outlier: 3.825A pdb=" N LEU D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 50 through 55' Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.983A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.517A pdb=" N GLY D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 removed outlier: 4.095A pdb=" N ILE D 122 " --> pdb=" O PRO D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 132 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) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.615A pdb=" N GLU D 145 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 146 " --> pdb=" O PRO D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'D' and resid 147 through 158 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 177 through 190 removed outlier: 3.674A pdb=" N ALA D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) 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) Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 205 through 209 removed outlier: 3.926A pdb=" N LEU D 208 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA D 209 " --> pdb=" O LEU D 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 209' Processing helix chain 'A' and resid 1 through 5 removed outlier: 4.311A pdb=" N SER A 4 " --> pdb=" O ASP A 1 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 5 " --> pdb=" O ALA A 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1 through 5' Processing helix chain 'A' and resid 88 through 96 removed outlier: 4.101A pdb=" N LEU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) 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) removed outlier: 3.665A pdb=" N ASN A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 96 removed outlier: 4.705A pdb=" N ARG C 92 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP C 225 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 221 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 98 through 104 removed outlier: 3.670A pdb=" N GLY C 99 " --> pdb=" O MET C 114 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N MET C 201 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 113 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL C 203 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 115 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN C 204 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ASN C 143 " --> pdb=" O ASN C 204 " (cutoff:3.500A) 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) Processing sheet with id=AA4, 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=AA5, first strand: chain 'E' and resid 91 through 96 removed outlier: 4.087A pdb=" N ALA E 93 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing sheet with id=AA6, 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: 8.110A pdb=" N ALA E 204 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLN E 114 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE E 206 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS E 116 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET E 205 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE E 149 " --> pdb=" O MET E 205 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLN E 147 " --> pdb=" O PRO E 207 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE E 150 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE E 192 " --> pdb=" O ILE E 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 14 through 16 Processing sheet with id=AA8, first strand: chain 'F' and resid 38 through 41 removed outlier: 6.309A pdb=" N MET F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR F 203 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE F 40 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE F 92 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 91 removed outlier: 5.707A pdb=" N GLY D 90 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL D 167 " --> pdb=" O LEU D 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.932A pdb=" N ALA A 18 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 31 through 35 removed outlier: 5.238A pdb=" N GLN A 33 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL A 24 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 150 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA A 142 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLN A 126 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 66 through 70 Processing sheet with id=AB5, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.274A pdb=" N ASN A 130 " --> pdb=" O HIS A 138 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 786 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: 2.56 Time building geometry restraints manager: 4.03 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: 3502 2.84 - 3.36: 8703 3.36 - 3.87: 16984 3.87 - 4.39: 19180 4.39 - 4.90: 32738 Nonbonded interactions: 81107 Sorted by model distance: nonbonded pdb=" O PRO E 74 " pdb=" OG SER E 220 " model vdw 2.328 3.040 nonbonded pdb=" O LEU F 6 " pdb=" OG SER F 31 " model vdw 2.350 3.040 nonbonded pdb=" O SER E 342 " pdb=" OG SER E 373 " model vdw 2.350 3.040 nonbonded pdb=" O ALA E 61 " pdb=" OG SER E 127 " model vdw 2.351 3.040 nonbonded pdb=" O CYS D 8 " pdb=" OG SER D 29 " model vdw 2.371 3.040 ... (remaining 81102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 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: 0.450 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.320 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.230 ------------------------------------------------------------------------------- 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= 0.223 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 : 1.263 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: 0.2445 time to fit residues: 123.5484 Evaluate side-chains 251 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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: 4.9990 chunk 107 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 111 optimal weight: 0.0670 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 128 optimal weight: 0.4980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN C 134 GLN C 281 ASN C 317 GLN C 339 GLN E 56 ASN E 73 GLN E 140 ASN E 172 ASN E 286 ASN E 404 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS D 69 ASN D 141 HIS D 152 GLN D 204 HIS ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11159 Z= 0.167 Angle : 0.570 10.786 15104 Z= 0.286 Chirality : 0.043 0.233 1742 Planarity : 0.004 0.052 1950 Dihedral : 5.060 56.912 1579 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.82 % Allowed : 16.68 % Favored : 81.49 % 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: -4.36 (0.17), residues: 1424 helix: -3.28 (0.16), residues: 463 sheet: -1.92 (0.36), residues: 187 loop : -2.95 (0.18), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 75 HIS 0.009 0.001 HIS D 204 PHE 0.019 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 308 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 287 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 ARG cc_start: 0.6404 (mmp80) cc_final: 0.5103 (pmt-80) REVERT: C 63 MET cc_start: 0.8507 (tmm) cc_final: 0.8190 (tmm) REVERT: C 75 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8282 (tp) REVERT: E 75 TRP cc_start: 0.6883 (m100) cc_final: 0.6633 (m100) REVERT: E 325 LEU cc_start: 0.8987 (mm) cc_final: 0.8625 (mt) REVERT: F 73 MET cc_start: 0.4171 (ppp) cc_final: 0.3779 (ppp) REVERT: F 106 GLU cc_start: 0.6901 (pt0) cc_final: 0.6584 (mt-10) REVERT: D 86 ASN cc_start: 0.6978 (p0) cc_final: 0.6475 (t0) REVERT: A 112 ASP cc_start: 0.5761 (m-30) cc_final: 0.4795 (t0) outliers start: 21 outliers final: 10 residues processed: 299 average time/residue: 0.2131 time to fit residues: 90.7303 Evaluate side-chains 246 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 235 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 157 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain E residue 101 THR 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 152 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 0.0030 chunk 107 optimal weight: 40.0000 chunk 87 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN E 172 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN D 10 ASN D 27 ASN D 141 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 ASN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11159 Z= 0.255 Angle : 0.620 7.107 15104 Z= 0.313 Chirality : 0.045 0.172 1742 Planarity : 0.004 0.046 1950 Dihedral : 5.263 55.760 1579 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.56 % Allowed : 19.37 % Favored : 77.06 % 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: -3.41 (0.19), residues: 1424 helix: -1.93 (0.21), residues: 481 sheet: -1.97 (0.36), residues: 189 loop : -2.60 (0.19), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 28 HIS 0.004 0.001 HIS E 188 PHE 0.024 0.002 PHE D 68 TYR 0.017 0.001 TYR C 142 ARG 0.006 0.001 ARG D 151 *********************** 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 293 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 252 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 231 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8146 (mttm) REVERT: C 299 ILE cc_start: 0.9317 (tp) cc_final: 0.9096 (tp) REVERT: C 311 MET cc_start: 0.8248 (ttt) cc_final: 0.7936 (ttt) REVERT: E 75 TRP cc_start: 0.7112 (m100) cc_final: 0.6901 (m100) REVERT: E 325 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8598 (mt) REVERT: F 106 GLU cc_start: 0.7251 (pt0) cc_final: 0.6729 (mt-10) REVERT: F 117 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7518 (mmtt) REVERT: F 129 MET cc_start: 0.7010 (tpp) cc_final: 0.6570 (tpp) REVERT: F 190 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7328 (tm-30) REVERT: D 86 ASN cc_start: 0.7226 (p0) cc_final: 0.6669 (t0) REVERT: D 141 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.5958 (m90) REVERT: D 171 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7933 (tm-30) outliers start: 41 outliers final: 24 residues processed: 271 average time/residue: 0.2110 time to fit residues: 81.8879 Evaluate side-chains 247 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 PHE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 340 LEU 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 325 LEU Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 154 VAL 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 141 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 129 optimal weight: 30.0000 chunk 137 optimal weight: 40.0000 chunk 122 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 114 optimal weight: 0.1980 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 140 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11159 Z= 0.249 Angle : 0.593 7.041 15104 Z= 0.301 Chirality : 0.045 0.350 1742 Planarity : 0.004 0.054 1950 Dihedral : 5.297 57.372 1579 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.82 % Allowed : 20.85 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.20), residues: 1424 helix: -1.24 (0.23), residues: 494 sheet: -1.87 (0.37), residues: 187 loop : -2.46 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 28 HIS 0.023 0.001 HIS D 141 PHE 0.025 0.002 PHE D 68 TYR 0.014 0.001 TYR E 260 ARG 0.004 0.000 ARG E 18 *********************** 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 280 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 236 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: C 165 MET cc_start: 0.7346 (ttp) cc_final: 0.7081 (ttm) REVERT: C 231 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8215 (mttm) REVERT: C 299 ILE cc_start: 0.9359 (tp) cc_final: 0.9132 (tp) REVERT: E 75 TRP cc_start: 0.7231 (m100) cc_final: 0.6867 (m100) REVERT: E 325 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8633 (mt) REVERT: E 328 LEU cc_start: 0.9399 (tp) cc_final: 0.9100 (tt) REVERT: F 106 GLU cc_start: 0.7306 (pt0) cc_final: 0.6926 (mp0) REVERT: F 190 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7221 (tm-30) REVERT: D 38 MET cc_start: 0.5534 (mmp) cc_final: 0.5117 (mmp) REVERT: D 86 ASN cc_start: 0.7137 (p0) cc_final: 0.6729 (t0) REVERT: D 171 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7790 (tm-30) REVERT: A 51 MET cc_start: 0.6094 (mtt) cc_final: 0.5859 (pmm) outliers start: 44 outliers final: 27 residues processed: 267 average time/residue: 0.1971 time to fit residues: 76.4628 Evaluate side-chains 244 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 ILE 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 152 SER Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 224 LEU 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 E residue 23 VAL Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 368 ILE 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 8 CYS Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain A residue 88 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 94 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN D 141 HIS D 152 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5090 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= 0.166 Angle : 0.555 8.780 15104 Z= 0.276 Chirality : 0.044 0.310 1742 Planarity : 0.004 0.052 1950 Dihedral : 5.089 57.572 1579 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.61 % Allowed : 22.94 % Favored : 74.46 % 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: -2.44 (0.21), residues: 1424 helix: -0.65 (0.24), residues: 492 sheet: -1.74 (0.37), residues: 187 loop : -2.31 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 138 HIS 0.005 0.001 HIS D 141 PHE 0.023 0.001 PHE D 68 TYR 0.007 0.001 TYR A 104 ARG 0.004 0.000 ARG D 142 *********************** 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 278 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 248 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: C 25 PHE cc_start: 0.8573 (t80) cc_final: 0.8319 (t80) REVERT: C 48 MET cc_start: 0.8131 (mtt) cc_final: 0.7844 (mtt) REVERT: C 165 MET cc_start: 0.7430 (ttp) cc_final: 0.7172 (ttm) REVERT: C 231 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8219 (mttm) REVERT: C 299 ILE cc_start: 0.9359 (tp) cc_final: 0.9128 (tp) REVERT: E 75 TRP cc_start: 0.7205 (m100) cc_final: 0.6928 (m100) REVERT: E 325 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8599 (mt) REVERT: E 328 LEU cc_start: 0.9372 (tp) cc_final: 0.9153 (tt) REVERT: E 400 ARG cc_start: 0.7264 (mtt180) cc_final: 0.6995 (ttt180) REVERT: F 106 GLU cc_start: 0.7284 (pt0) cc_final: 0.6895 (mp0) REVERT: F 190 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7131 (tm-30) REVERT: F 205 ASP cc_start: 0.7791 (p0) cc_final: 0.7478 (p0) REVERT: F 218 MET cc_start: 0.6434 (tpt) cc_final: 0.6055 (tpt) REVERT: D 38 MET cc_start: 0.5348 (mmp) cc_final: 0.4916 (mmp) REVERT: D 86 ASN cc_start: 0.7310 (p0) cc_final: 0.6785 (t0) outliers start: 30 outliers final: 18 residues processed: 264 average time/residue: 0.1996 time to fit residues: 76.4490 Evaluate side-chains 250 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 231 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 152 GLN Chi-restraints excluded: chain A residue 88 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN D 141 HIS ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11159 Z= 0.178 Angle : 0.564 8.192 15104 Z= 0.281 Chirality : 0.044 0.270 1742 Planarity : 0.004 0.052 1950 Dihedral : 5.063 58.588 1579 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.95 % Allowed : 23.81 % Favored : 73.24 % 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: -2.08 (0.21), residues: 1424 helix: -0.25 (0.24), residues: 495 sheet: -1.55 (0.37), residues: 180 loop : -2.17 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 138 HIS 0.004 0.001 HIS F 96 PHE 0.022 0.001 PHE D 68 TYR 0.020 0.001 TYR E 260 ARG 0.003 0.000 ARG D 142 *********************** 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 272 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 238 time to evaluate : 1.324 Fit side-chains REVERT: C 165 MET cc_start: 0.7431 (ttp) cc_final: 0.7175 (ttm) REVERT: C 231 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8269 (mttm) REVERT: C 299 ILE cc_start: 0.9357 (tp) cc_final: 0.9090 (tp) REVERT: C 315 MET cc_start: 0.7738 (tpp) cc_final: 0.7399 (tpp) REVERT: E 12 ARG cc_start: 0.7807 (mmp80) cc_final: 0.7392 (mmp-170) REVERT: E 63 VAL cc_start: 0.9480 (t) cc_final: 0.9187 (m) REVERT: E 75 TRP cc_start: 0.7213 (m100) cc_final: 0.6941 (m100) REVERT: E 325 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8593 (mt) REVERT: E 328 LEU cc_start: 0.9405 (tp) cc_final: 0.9189 (tt) REVERT: E 400 ARG cc_start: 0.7318 (mtt180) cc_final: 0.7065 (ttt180) REVERT: F 84 LEU cc_start: 0.7456 (pt) cc_final: 0.7123 (pp) REVERT: F 185 PHE cc_start: 0.7777 (m-80) cc_final: 0.7568 (m-80) REVERT: F 187 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6320 (mm) REVERT: F 190 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7008 (tm-30) REVERT: F 205 ASP cc_start: 0.7861 (p0) cc_final: 0.7489 (p0) REVERT: F 218 MET cc_start: 0.6501 (tpt) cc_final: 0.6270 (tpt) REVERT: D 38 MET cc_start: 0.5338 (mmp) cc_final: 0.3989 (mmt) REVERT: D 86 ASN cc_start: 0.7356 (p0) cc_final: 0.6917 (t0) REVERT: D 142 ARG cc_start: 0.7947 (mmt-90) cc_final: 0.7658 (mmt-90) REVERT: A 51 MET cc_start: 0.6097 (mtt) cc_final: 0.5791 (ttt) outliers start: 34 outliers final: 24 residues processed: 258 average time/residue: 0.2158 time to fit residues: 80.0606 Evaluate side-chains 251 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 225 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 ILE 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 187 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 288 LEU 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 E residue 129 LEU Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain A residue 88 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.0370 chunk 78 optimal weight: 0.0970 chunk 100 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 115 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 85 optimal weight: 0.0270 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 HIS F 140 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11159 Z= 0.139 Angle : 0.567 9.487 15104 Z= 0.278 Chirality : 0.044 0.282 1742 Planarity : 0.004 0.045 1950 Dihedral : 4.992 59.936 1579 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.26 % Allowed : 25.02 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.22), residues: 1424 helix: 0.27 (0.25), residues: 480 sheet: -1.63 (0.37), residues: 188 loop : -2.10 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 138 HIS 0.004 0.000 HIS F 96 PHE 0.024 0.001 PHE D 68 TYR 0.007 0.001 TYR A 104 ARG 0.002 0.000 ARG E 18 *********************** 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 283 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 257 time to evaluate : 1.128 Fit side-chains REVERT: C 63 MET cc_start: 0.8530 (tmm) cc_final: 0.8058 (tmm) REVERT: C 123 ASP cc_start: 0.7689 (t0) cc_final: 0.7483 (t0) REVERT: C 299 ILE cc_start: 0.9371 (tp) cc_final: 0.9113 (tp) REVERT: E 75 TRP cc_start: 0.7201 (m100) cc_final: 0.6901 (m100) REVERT: E 250 TYR cc_start: 0.7495 (m-10) cc_final: 0.7227 (m-10) REVERT: E 325 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8515 (mt) REVERT: E 328 LEU cc_start: 0.9372 (tp) cc_final: 0.9169 (tt) REVERT: E 366 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7240 (t80) REVERT: F 84 LEU cc_start: 0.7462 (pt) cc_final: 0.7194 (pp) REVERT: F 190 GLU cc_start: 0.7540 (tm-30) cc_final: 0.6939 (tm-30) REVERT: F 218 MET cc_start: 0.6466 (tpt) cc_final: 0.6209 (tpt) REVERT: D 38 MET cc_start: 0.5475 (mmp) cc_final: 0.4990 (tpp) REVERT: D 86 ASN cc_start: 0.7359 (p0) cc_final: 0.6880 (t0) REVERT: D 142 ARG cc_start: 0.7882 (mmt-90) cc_final: 0.7556 (mmt-90) REVERT: A 51 MET cc_start: 0.6030 (mtt) cc_final: 0.5777 (ttt) outliers start: 26 outliers final: 17 residues processed: 269 average time/residue: 0.2003 time to fit residues: 77.2201 Evaluate side-chains 256 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 237 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 224 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 366 TYR Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.0980 chunk 81 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 124 optimal weight: 0.0000 chunk 131 optimal weight: 9.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN F 140 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 HIS D 141 HIS D 162 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11159 Z= 0.154 Angle : 0.589 13.458 15104 Z= 0.288 Chirality : 0.045 0.366 1742 Planarity : 0.004 0.044 1950 Dihedral : 4.915 57.665 1579 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.43 % Allowed : 25.63 % 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: -1.58 (0.22), residues: 1424 helix: 0.50 (0.26), residues: 468 sheet: -1.48 (0.37), residues: 183 loop : -1.98 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 138 HIS 0.014 0.001 HIS D 96 PHE 0.027 0.001 PHE A 90 TYR 0.010 0.001 TYR C 382 ARG 0.003 0.000 ARG C 15 *********************** 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 268 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 240 time to evaluate : 1.293 Fit side-chains REVERT: C 123 ASP cc_start: 0.7681 (t0) cc_final: 0.7448 (t0) REVERT: C 299 ILE cc_start: 0.9360 (tp) cc_final: 0.9090 (tp) REVERT: E 75 TRP cc_start: 0.7235 (m100) cc_final: 0.6938 (m100) REVERT: E 325 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8508 (mt) REVERT: E 366 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7254 (t80) REVERT: F 84 LEU cc_start: 0.7541 (pt) cc_final: 0.7274 (pp) REVERT: F 190 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7004 (tm-30) REVERT: F 218 MET cc_start: 0.6439 (tpt) cc_final: 0.6184 (tpt) REVERT: D 38 MET cc_start: 0.5605 (mmp) cc_final: 0.5087 (tpp) REVERT: D 86 ASN cc_start: 0.7354 (p0) cc_final: 0.6865 (t0) REVERT: A 51 MET cc_start: 0.6042 (mtt) cc_final: 0.5782 (ttt) outliers start: 28 outliers final: 22 residues processed: 255 average time/residue: 0.1987 time to fit residues: 73.8375 Evaluate side-chains 255 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 224 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 366 TYR Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 143 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 39 optimal weight: 0.0970 chunk 115 optimal weight: 10.0000 chunk 120 optimal weight: 0.0050 chunk 83 optimal weight: 8.9990 chunk 134 optimal weight: 0.0270 overall best weight: 1.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS D 186 GLN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11159 Z= 0.189 Angle : 0.597 8.399 15104 Z= 0.298 Chirality : 0.045 0.275 1742 Planarity : 0.004 0.046 1950 Dihedral : 5.017 57.333 1579 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.78 % Allowed : 25.98 % Favored : 71.24 % 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: -1.61 (0.22), residues: 1424 helix: 0.29 (0.25), residues: 487 sheet: -1.41 (0.38), residues: 182 loop : -1.94 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 138 HIS 0.004 0.001 HIS F 96 PHE 0.025 0.001 PHE D 68 TYR 0.008 0.001 TYR A 104 ARG 0.003 0.000 ARG E 12 *********************** 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 267 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 235 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: E 75 TRP cc_start: 0.7222 (m100) cc_final: 0.6909 (m100) REVERT: E 325 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8549 (mt) REVERT: F 190 GLU cc_start: 0.7552 (tm-30) cc_final: 0.6949 (tm-30) REVERT: F 205 ASP cc_start: 0.7988 (p0) cc_final: 0.7704 (p0) REVERT: F 218 MET cc_start: 0.6404 (tpt) cc_final: 0.6175 (tpt) REVERT: D 38 MET cc_start: 0.5610 (mmp) cc_final: 0.5143 (tpp) REVERT: D 86 ASN cc_start: 0.7393 (p0) cc_final: 0.6901 (t0) REVERT: A 51 MET cc_start: 0.5953 (mtt) cc_final: 0.5680 (ttt) outliers start: 32 outliers final: 24 residues processed: 251 average time/residue: 0.2074 time to fit residues: 75.5886 Evaluate side-chains 257 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 232 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 153 GLN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN E 201 HIS ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN D 97 HIS ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11159 Z= 0.377 Angle : 0.744 8.824 15104 Z= 0.375 Chirality : 0.050 0.261 1742 Planarity : 0.005 0.058 1950 Dihedral : 6.073 53.541 1579 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.69 % Allowed : 26.24 % 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: -1.90 (0.22), residues: 1424 helix: -0.19 (0.24), residues: 507 sheet: -1.45 (0.37), residues: 184 loop : -2.01 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 138 HIS 0.009 0.001 HIS F 96 PHE 0.026 0.002 PHE A 90 TYR 0.014 0.002 TYR E 322 ARG 0.005 0.001 ARG D 158 ********************** 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 258 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 227 time to evaluate : 1.261 Fit side-chains REVERT: C 267 MET cc_start: 0.7937 (ttm) cc_final: 0.7591 (ttm) REVERT: E 54 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8262 (mm-30) REVERT: E 75 TRP cc_start: 0.7193 (m100) cc_final: 0.6907 (m100) REVERT: E 325 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8776 (mt) REVERT: F 190 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7056 (tm-30) REVERT: F 205 ASP cc_start: 0.8191 (p0) cc_final: 0.7937 (p0) REVERT: D 38 MET cc_start: 0.5395 (mmp) cc_final: 0.5049 (tpp) REVERT: D 86 ASN cc_start: 0.7517 (p0) cc_final: 0.6982 (t0) REVERT: A 51 MET cc_start: 0.5986 (mtt) cc_final: 0.5663 (ttt) REVERT: A 153 GLN cc_start: 0.7046 (pp30) cc_final: 0.6353 (mt0) REVERT: A 178 ASP cc_start: 0.7917 (t0) cc_final: 0.7705 (t0) outliers start: 31 outliers final: 19 residues processed: 247 average time/residue: 0.2149 time to fit residues: 76.1009 Evaluate side-chains 236 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 216 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 148 GLU Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.9504 > 50: distance: 30 - 68: 16.282 distance: 63 - 68: 18.571 distance: 68 - 69: 17.912 distance: 69 - 70: 26.818 distance: 69 - 72: 25.793 distance: 70 - 71: 46.884 distance: 70 - 75: 18.557 distance: 72 - 73: 15.134 distance: 72 - 74: 24.432 distance: 75 - 76: 18.710 distance: 76 - 77: 22.074 distance: 76 - 79: 33.135 distance: 77 - 78: 39.462 distance: 77 - 82: 22.414 distance: 79 - 80: 6.141 distance: 79 - 81: 22.869 distance: 82 - 83: 39.035 distance: 83 - 84: 21.731 distance: 83 - 86: 34.406 distance: 84 - 85: 28.700 distance: 84 - 92: 40.424 distance: 86 - 87: 25.076 distance: 87 - 88: 18.550 distance: 87 - 89: 6.382 distance: 88 - 90: 7.510 distance: 89 - 91: 16.428 distance: 90 - 91: 16.911 distance: 92 - 93: 44.186 distance: 93 - 94: 19.407 distance: 93 - 96: 15.918 distance: 94 - 95: 38.856 distance: 94 - 100: 10.678 distance: 96 - 97: 43.647 distance: 97 - 98: 7.368 distance: 100 - 101: 15.764 distance: 101 - 102: 11.334 distance: 101 - 104: 39.404 distance: 102 - 103: 3.746 distance: 102 - 108: 14.827 distance: 104 - 105: 33.514 distance: 105 - 106: 20.132 distance: 105 - 107: 35.704 distance: 108 - 109: 15.704 distance: 109 - 110: 31.002 distance: 109 - 112: 29.418 distance: 110 - 111: 53.433 distance: 110 - 117: 53.425 distance: 112 - 113: 10.810 distance: 113 - 114: 19.734 distance: 114 - 115: 11.676 distance: 114 - 116: 9.800 distance: 117 - 118: 54.755 distance: 118 - 119: 42.923 distance: 118 - 121: 8.013 distance: 119 - 120: 15.266 distance: 119 - 125: 54.369 distance: 121 - 122: 13.032 distance: 122 - 123: 10.631 distance: 122 - 124: 42.962 distance: 125 - 126: 14.978 distance: 126 - 127: 26.241 distance: 126 - 129: 43.382 distance: 127 - 128: 7.652 distance: 127 - 130: 21.980 distance: 130 - 131: 20.568 distance: 131 - 132: 19.535 distance: 131 - 134: 18.202 distance: 132 - 133: 34.280 distance: 132 - 139: 25.615 distance: 134 - 135: 33.300 distance: 135 - 136: 21.865 distance: 136 - 137: 16.477 distance: 137 - 138: 26.556 distance: 139 - 140: 11.435 distance: 140 - 141: 6.220 distance: 140 - 143: 19.704 distance: 141 - 142: 12.529 distance: 141 - 150: 22.099 distance: 143 - 144: 16.444 distance: 144 - 145: 10.377 distance: 145 - 146: 13.506 distance: 146 - 147: 5.438 distance: 147 - 148: 20.125 distance: 147 - 149: 18.654