Starting phenix.real_space_refine on Mon Apr 8 14:40:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cte_30462/04_2024/7cte_30462_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cte_30462/04_2024/7cte_30462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cte_30462/04_2024/7cte_30462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cte_30462/04_2024/7cte_30462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cte_30462/04_2024/7cte_30462_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cte_30462/04_2024/7cte_30462_updated.pdb" } resolution = 3.8 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= 0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 64 5.16 5 C 8810 2.51 5 N 2306 2.21 5 O 2513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 273": "NH1" <-> "NH2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 396": "OD1" <-> "OD2" Residue "B ASP 434": "OD1" <-> "OD2" Residue "B PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 529": "OD1" <-> "OD2" Residue "B ARG 533": "NH1" <-> "NH2" Residue "B GLU 571": "OE1" <-> "OE2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C ARG 373": "NH1" <-> "NH2" Residue "C TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 466": "OD1" <-> "OD2" Residue "C PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C GLU 578": "OE1" <-> "OE2" Residue "C TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 642": "NH1" <-> "NH2" Residue "C ARG 683": "NH1" <-> "NH2" Residue "C PHE 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ASP 197": "OD1" <-> "OD2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 337": "OD1" <-> "OD2" Residue "D PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 368": "OE1" <-> "OE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 377": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D ASP 424": "OD1" <-> "OD2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 70": "NH1" <-> "NH2" Residue "E ASP 101": "OD1" <-> "OD2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 221": "OD1" <-> "OD2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 326": "NH1" <-> "NH2" Residue "E PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 373": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13699 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2460 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 302, 2460 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4828 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 567} Chain breaks: 7 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3305 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 3 Chain: "E" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3044 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 18, 'TRANS': 354} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.28, per 1000 atoms: 0.53 Number of scatterers: 13699 At special positions: 0 Unit cell: (112.69, 121.804, 149.977, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 6 15.00 O 2513 8.00 N 2306 7.00 C 8810 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=0, symmetry=0 Time building additional restraints: 5.63 Conformation dependent library (CDL) restraints added in 2.4 seconds 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 8 sheets defined 53.1% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'B' and resid 270 through 273 No H-bonds generated for 'chain 'B' and resid 270 through 273' Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.889A pdb=" N PHE B 298 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N HIS B 299 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 304 " --> pdb=" O TRP B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 348 through 358 Processing helix chain 'B' and resid 369 through 382 removed outlier: 4.384A pdb=" N PHE B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 413 removed outlier: 3.611A pdb=" N ILE B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 435 through 438 No H-bonds generated for 'chain 'B' and resid 435 through 438' Processing helix chain 'B' and resid 455 through 460 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 486 through 502 removed outlier: 3.562A pdb=" N LEU B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 502 " --> pdb=" O TYR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 521 Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 567 through 572 Processing helix chain 'C' and resid 40 through 63 Processing helix chain 'C' and resid 65 through 82 removed outlier: 4.198A pdb=" N ASN C 68 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C 70 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP C 71 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE C 74 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 77 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 80 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 82 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.691A pdb=" N PHE C 118 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 162 removed outlier: 3.900A pdb=" N ILE C 162 " --> pdb=" O CYS C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 256 through 262 removed outlier: 4.063A pdb=" N LEU C 262 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 281 through 292 removed outlier: 4.689A pdb=" N THR C 286 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 289 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS C 291 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 292 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 322 through 338 Processing helix chain 'C' and resid 348 through 354 removed outlier: 4.299A pdb=" N ARG C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 368 Processing helix chain 'C' and resid 370 through 377 Processing helix chain 'C' and resid 381 through 387 removed outlier: 4.765A pdb=" N ALA C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 424 removed outlier: 4.130A pdb=" N GLU C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 414 " --> pdb=" O MET C 410 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL C 415 " --> pdb=" O ASN C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 441 removed outlier: 4.263A pdb=" N TYR C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 459 Processing helix chain 'C' and resid 466 through 481 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 493 through 500 Processing helix chain 'C' and resid 549 through 565 Processing helix chain 'C' and resid 570 through 573 No H-bonds generated for 'chain 'C' and resid 570 through 573' Processing helix chain 'C' and resid 585 through 592 removed outlier: 4.605A pdb=" N GLU C 590 " --> pdb=" O HIS C 586 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 605 removed outlier: 3.861A pdb=" N HIS C 601 " --> pdb=" O ARG C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 637 Processing helix chain 'C' and resid 646 through 662 Processing helix chain 'C' and resid 670 through 690 removed outlier: 3.805A pdb=" N GLU C 687 " --> pdb=" O ARG C 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 29 removed outlier: 3.803A pdb=" N GLU D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 56 removed outlier: 4.054A pdb=" N GLU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU D 50 " --> pdb=" O HIS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 107 through 117 removed outlier: 3.596A pdb=" N LYS D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 132 through 145 Processing helix chain 'D' and resid 161 through 166 removed outlier: 4.544A pdb=" N HIS D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 removed outlier: 4.962A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 223 through 234 removed outlier: 3.985A pdb=" N LYS D 228 " --> pdb=" O PRO D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.567A pdb=" N ILE D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 288 removed outlier: 3.992A pdb=" N ALA D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.632A pdb=" N MET D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS D 374 " --> pdb=" O PRO D 370 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 375 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 376 " --> pdb=" O VAL D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 417 removed outlier: 4.048A pdb=" N GLN D 416 " --> pdb=" O MET D 412 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS D 417 " --> pdb=" O ASN D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 431 Processing helix chain 'E' and resid 12 through 22 Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.917A pdb=" N THR E 53 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 80 removed outlier: 3.761A pdb=" N ILE E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 109 removed outlier: 3.744A pdb=" N LYS E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN E 108 " --> pdb=" O ARG E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 131 No H-bonds generated for 'chain 'E' and resid 128 through 131' Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 144 through 147 No H-bonds generated for 'chain 'E' and resid 144 through 147' Processing helix chain 'E' and resid 162 through 165 No H-bonds generated for 'chain 'E' and resid 162 through 165' Processing helix chain 'E' and resid 184 through 190 Processing helix chain 'E' and resid 201 through 215 removed outlier: 3.767A pdb=" N GLY E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 214 " --> pdb=" O ILE E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 243 Proline residue: E 234 - end of helix Proline residue: E 239 - end of helix Processing helix chain 'E' and resid 250 through 267 Proline residue: E 259 - end of helix removed outlier: 4.427A pdb=" N LYS E 263 " --> pdb=" O PRO E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 318 Processing helix chain 'E' and resid 324 through 327 No H-bonds generated for 'chain 'E' and resid 324 through 327' Processing helix chain 'E' and resid 359 through 369 Processing helix chain 'E' and resid 378 through 389 removed outlier: 4.334A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 422 Processing helix chain 'E' and resid 428 through 431 No H-bonds generated for 'chain 'E' and resid 428 through 431' Processing sheet with id= A, first strand: chain 'B' and resid 309 through 314 removed outlier: 5.945A pdb=" N ASN B 442 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 312 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU B 444 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR B 314 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR B 446 " --> pdb=" O TYR B 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 546 through 549 Processing sheet with id= C, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.304A pdb=" N VAL C 216 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU C 136 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE C 218 " --> pdb=" O LEU C 136 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'D' and resid 94 through 100 removed outlier: 7.577A pdb=" N VAL D 97 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE D 155 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU D 99 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE D 157 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 188 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 385 through 387 Processing sheet with id= F, first strand: chain 'E' and resid 33 through 36 removed outlier: 6.026A pdb=" N PHE E 175 " --> pdb=" O PHE E 34 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N TYR E 36 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU E 177 " --> pdb=" O TYR E 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.330A pdb=" N TYR E 121 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL E 61 " --> pdb=" O TYR E 121 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL E 123 " --> pdb=" O VAL E 61 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'E' and resid 393 through 395 506 hydrogen bonds defined for protein. 1449 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: 3.79 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3038 1.33 - 1.45: 3250 1.45 - 1.58: 7591 1.58 - 1.70: 15 1.70 - 1.82: 94 Bond restraints: 13988 Sorted by residual: bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.79e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.79e+01 bond pdb=" C5 ATP E 901 " pdb=" N7 ATP E 901 " ideal model delta sigma weight residual 1.387 1.328 0.059 1.00e-02 1.00e+04 3.51e+01 bond pdb=" CG1 ILE E 190 " pdb=" CD1 ILE E 190 " ideal model delta sigma weight residual 1.513 1.294 0.219 3.90e-02 6.57e+02 3.16e+01 ... (remaining 13983 not shown) Histogram of bond angle deviations from ideal: 93.88 - 102.39: 83 102.39 - 110.90: 4682 110.90 - 119.41: 7339 119.41 - 127.92: 6668 127.92 - 136.43: 164 Bond angle restraints: 18936 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 118.40 21.47 1.00e+00 1.00e+00 4.61e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 118.51 18.32 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 120.57 16.26 1.00e+00 1.00e+00 2.64e+02 angle pdb=" C5 ATP E 901 " pdb=" C4 ATP E 901 " pdb=" N3 ATP E 901 " ideal model delta sigma weight residual 126.80 116.63 10.17 1.00e+00 1.00e+00 1.03e+02 ... (remaining 18931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7013 17.85 - 35.71: 1123 35.71 - 53.56: 290 53.56 - 71.41: 52 71.41 - 89.27: 16 Dihedral angle restraints: 8494 sinusoidal: 3527 harmonic: 4967 Sorted by residual: dihedral pdb=" CA PRO C 628 " pdb=" C PRO C 628 " pdb=" N ASP C 629 " pdb=" CA ASP C 629 " ideal model delta harmonic sigma weight residual 180.00 135.48 44.52 0 5.00e+00 4.00e-02 7.93e+01 dihedral pdb=" CA ASP E 400 " pdb=" C ASP E 400 " pdb=" N GLN E 401 " pdb=" CA GLN E 401 " ideal model delta harmonic sigma weight residual 180.00 135.82 44.18 0 5.00e+00 4.00e-02 7.81e+01 dihedral pdb=" CA SER C 280 " pdb=" C SER C 280 " pdb=" N CYS C 281 " pdb=" CA CYS C 281 " ideal model delta harmonic sigma weight residual -180.00 -136.32 -43.68 0 5.00e+00 4.00e-02 7.63e+01 ... (remaining 8491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1886 0.112 - 0.224: 242 0.224 - 0.335: 27 0.335 - 0.447: 8 0.447 - 0.559: 2 Chirality restraints: 2165 Sorted by residual: chirality pdb=" CG LEU C 414 " pdb=" CB LEU C 414 " pdb=" CD1 LEU C 414 " pdb=" CD2 LEU C 414 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" CG LEU B 570 " pdb=" CB LEU B 570 " pdb=" CD1 LEU B 570 " pdb=" CD2 LEU B 570 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CB ILE C 447 " pdb=" CA ILE C 447 " pdb=" CG1 ILE C 447 " pdb=" CG2 ILE C 447 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 2162 not shown) Planarity restraints: 2384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 609 " 0.062 2.00e-02 2.50e+03 3.51e-02 2.47e+01 pdb=" CG TYR C 609 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR C 609 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR C 609 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR C 609 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 609 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 609 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 609 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 627 " -0.068 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO C 628 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 628 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 628 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 28 " -0.042 2.00e-02 2.50e+03 2.95e-02 1.53e+01 pdb=" CG PHE D 28 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE D 28 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 28 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE D 28 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE D 28 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 28 " -0.031 2.00e-02 2.50e+03 ... (remaining 2381 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3015 2.78 - 3.31: 12583 3.31 - 3.84: 22633 3.84 - 4.37: 24784 4.37 - 4.90: 41975 Nonbonded interactions: 104990 Sorted by model distance: nonbonded pdb=" O ALA C 654 " pdb=" OG1 THR C 658 " model vdw 2.246 2.440 nonbonded pdb=" O TRP B 433 " pdb=" OG SER E 382 " model vdw 2.274 2.440 nonbonded pdb=" O SER B 385 " pdb=" OG SER B 385 " model vdw 2.288 2.440 nonbonded pdb=" O SER D 91 " pdb=" OG SER D 91 " model vdw 2.296 2.440 nonbonded pdb=" O LYS C 202 " pdb=" OG1 THR C 206 " model vdw 2.317 2.440 ... (remaining 104985 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.420 Check model and map are aligned: 0.190 Set scattering table: 0.140 Process input model: 36.650 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.012 0.219 13988 Z= 0.789 Angle : 1.692 21.469 18936 Z= 0.944 Chirality : 0.080 0.559 2165 Planarity : 0.011 0.100 2384 Dihedral : 18.732 89.267 5238 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.80 % Favored : 93.02 % Rotamer: Outliers : 2.93 % Allowed : 19.32 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.94 % 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: -4.71 (0.16), residues: 1633 helix: -3.09 (0.12), residues: 878 sheet: -2.98 (0.38), residues: 139 loop : -2.92 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.006 TRP E 162 HIS 0.024 0.004 HIS C 486 PHE 0.055 0.007 PHE D 28 TYR 0.073 0.007 TYR C 609 ARG 0.022 0.002 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 262 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 VAL cc_start: 0.8948 (t) cc_final: 0.8746 (t) REVERT: C 52 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8298 (tm-30) REVERT: C 139 LYS cc_start: 0.8128 (pttp) cc_final: 0.7854 (pttm) REVERT: C 222 MET cc_start: 0.7180 (tmm) cc_final: 0.6806 (tmm) REVERT: C 252 ILE cc_start: 0.9070 (mt) cc_final: 0.8689 (tt) REVERT: C 410 MET cc_start: 0.7804 (mtt) cc_final: 0.7561 (ttt) REVERT: C 426 LEU cc_start: 0.6801 (mt) cc_final: 0.6504 (mt) REVERT: C 428 LYS cc_start: 0.7166 (tmtt) cc_final: 0.5961 (mptt) REVERT: C 477 LYS cc_start: 0.8000 (mttt) cc_final: 0.7491 (pttt) REVERT: C 683 ARG cc_start: 0.8191 (ttp-170) cc_final: 0.7444 (ttp80) REVERT: C 685 VAL cc_start: 0.7828 (p) cc_final: 0.7620 (p) REVERT: D 81 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8821 (mm) REVERT: D 108 LYS cc_start: 0.8351 (tttt) cc_final: 0.7850 (mmtt) REVERT: D 257 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8572 (p) REVERT: D 335 LEU cc_start: 0.8512 (tt) cc_final: 0.8304 (tt) REVERT: D 367 PHE cc_start: 0.7957 (m-80) cc_final: 0.7446 (m-80) REVERT: D 381 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8523 (mp10) REVERT: E 101 ASP cc_start: 0.8463 (m-30) cc_final: 0.7793 (m-30) REVERT: E 145 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7719 (tp-100) REVERT: E 152 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.7779 (t) REVERT: E 171 CYS cc_start: 0.8694 (t) cc_final: 0.8458 (t) outliers start: 45 outliers final: 7 residues processed: 295 average time/residue: 0.2455 time to fit residues: 107.6847 Evaluate side-chains 204 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 194 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 402 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 96 optimal weight: 0.0670 chunk 150 optimal weight: 1.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 GLN B 292 GLN B 306 HIS B 336 HIS B 340 ASN B 372 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 347 ASN ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 678 HIS D 98 HIS D 119 ASN D 233 GLN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN E 27 HIS ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS E 100 ASN E 168 ASN E 299 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13988 Z= 0.195 Angle : 0.753 10.194 18936 Z= 0.388 Chirality : 0.042 0.182 2165 Planarity : 0.005 0.077 2384 Dihedral : 10.316 86.780 1866 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.51 % Allowed : 23.68 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.13 % 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: -3.19 (0.18), residues: 1633 helix: -1.62 (0.15), residues: 887 sheet: -2.74 (0.39), residues: 141 loop : -2.50 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 249 HIS 0.008 0.001 HIS E 227 PHE 0.037 0.002 PHE D 28 TYR 0.024 0.002 TYR C 453 ARG 0.005 0.001 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 242 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 VAL cc_start: 0.8917 (t) cc_final: 0.8693 (t) REVERT: B 404 LYS cc_start: 0.7689 (tttt) cc_final: 0.7427 (tmmt) REVERT: B 453 PRO cc_start: 0.7843 (Cg_endo) cc_final: 0.7055 (Cg_exo) REVERT: B 544 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.6041 (mm) REVERT: C 13 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: C 52 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8162 (tm-30) REVERT: C 118 PHE cc_start: 0.8153 (m-80) cc_final: 0.7943 (m-10) REVERT: C 222 MET cc_start: 0.6921 (tmm) cc_final: 0.6492 (tmm) REVERT: C 223 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7792 (mm-30) REVERT: C 318 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8523 (t0) REVERT: C 334 GLU cc_start: 0.8288 (tp30) cc_final: 0.8015 (tp30) REVERT: C 346 CYS cc_start: 0.8660 (m) cc_final: 0.8132 (m) REVERT: C 363 CYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7735 (t) REVERT: C 388 LEU cc_start: 0.7949 (tp) cc_final: 0.7583 (tp) REVERT: C 410 MET cc_start: 0.7887 (mtt) cc_final: 0.7452 (ttp) REVERT: C 426 LEU cc_start: 0.6671 (mt) cc_final: 0.6443 (mt) REVERT: C 428 LYS cc_start: 0.7324 (tmtt) cc_final: 0.6358 (mptt) REVERT: C 476 PHE cc_start: 0.6551 (t80) cc_final: 0.6168 (t80) REVERT: D 24 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8406 (tt) REVERT: D 86 GLU cc_start: 0.8399 (tt0) cc_final: 0.8165 (tt0) REVERT: D 108 LYS cc_start: 0.8323 (tttt) cc_final: 0.7836 (mmtt) REVERT: D 381 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8812 (mp10) REVERT: D 420 ASN cc_start: 0.6384 (m110) cc_final: 0.5464 (p0) REVERT: E 55 GLU cc_start: 0.8065 (tp30) cc_final: 0.7785 (pm20) REVERT: E 101 ASP cc_start: 0.8478 (m-30) cc_final: 0.7929 (m-30) REVERT: E 171 CYS cc_start: 0.8143 (t) cc_final: 0.7416 (m) REVERT: E 236 TYR cc_start: 0.7409 (t80) cc_final: 0.7079 (t80) outliers start: 54 outliers final: 23 residues processed: 280 average time/residue: 0.2257 time to fit residues: 96.1900 Evaluate side-chains 233 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 151 optimal weight: 0.0980 chunk 163 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 0.0670 chunk 121 optimal weight: 4.9990 overall best weight: 1.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN B 362 HIS B 416 HIS ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 316 ASN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13988 Z= 0.218 Angle : 0.707 9.383 18936 Z= 0.360 Chirality : 0.042 0.188 2165 Planarity : 0.005 0.071 2384 Dihedral : 9.374 86.853 1856 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.42 % Allowed : 24.92 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -2.42 (0.19), residues: 1633 helix: -0.86 (0.16), residues: 891 sheet: -2.44 (0.42), residues: 140 loop : -2.40 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 428 HIS 0.010 0.001 HIS B 416 PHE 0.042 0.002 PHE B 492 TYR 0.015 0.002 TYR E 304 ARG 0.011 0.000 ARG C 683 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 208 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 VAL cc_start: 0.8873 (t) cc_final: 0.8627 (t) REVERT: B 453 PRO cc_start: 0.7380 (Cg_endo) cc_final: 0.6727 (Cg_exo) REVERT: B 544 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6109 (mm) REVERT: C 13 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: C 118 PHE cc_start: 0.8132 (m-80) cc_final: 0.7895 (m-10) REVERT: C 222 MET cc_start: 0.6488 (tmm) cc_final: 0.6108 (tmm) REVERT: C 318 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8525 (t0) REVERT: C 334 GLU cc_start: 0.8322 (tp30) cc_final: 0.8098 (tp30) REVERT: C 410 MET cc_start: 0.7904 (mtt) cc_final: 0.7539 (ttp) REVERT: C 428 LYS cc_start: 0.7346 (tmtt) cc_final: 0.6406 (mptt) REVERT: D 81 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8524 (tt) REVERT: D 108 LYS cc_start: 0.8329 (tttt) cc_final: 0.7842 (mmtt) REVERT: D 367 PHE cc_start: 0.8043 (m-80) cc_final: 0.7666 (m-10) REVERT: E 10 CYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6265 (t) REVERT: E 55 GLU cc_start: 0.8023 (tp30) cc_final: 0.7760 (pm20) REVERT: E 101 ASP cc_start: 0.8618 (m-30) cc_final: 0.7923 (m-30) REVERT: E 171 CYS cc_start: 0.8206 (t) cc_final: 0.7414 (m) REVERT: E 236 TYR cc_start: 0.7505 (t80) cc_final: 0.7040 (t80) outliers start: 68 outliers final: 32 residues processed: 262 average time/residue: 0.2180 time to fit residues: 88.2777 Evaluate side-chains 224 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 187 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 413 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 HIS C 486 HIS C 577 HIS ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13988 Z= 0.246 Angle : 0.690 8.265 18936 Z= 0.351 Chirality : 0.043 0.264 2165 Planarity : 0.005 0.066 2384 Dihedral : 8.840 78.786 1856 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.47 % Allowed : 25.89 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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 (0.20), residues: 1633 helix: -0.52 (0.17), residues: 894 sheet: -2.52 (0.43), residues: 135 loop : -2.31 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 649 HIS 0.012 0.001 HIS B 416 PHE 0.030 0.002 PHE C 479 TYR 0.017 0.002 TYR C 453 ARG 0.013 0.001 ARG C 683 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 195 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8672 (m-40) cc_final: 0.7989 (m-40) REVERT: B 357 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: B 443 TRP cc_start: 0.8990 (OUTLIER) cc_final: 0.8663 (m100) REVERT: B 544 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6213 (mm) REVERT: C 13 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: C 118 PHE cc_start: 0.8142 (m-80) cc_final: 0.7903 (m-10) REVERT: C 144 MET cc_start: 0.8616 (tpt) cc_final: 0.8275 (tpt) REVERT: C 222 MET cc_start: 0.6684 (tmm) cc_final: 0.6407 (tmm) REVERT: C 281 CYS cc_start: 0.8129 (m) cc_final: 0.7847 (m) REVERT: C 301 LYS cc_start: 0.8664 (mmmm) cc_final: 0.8334 (mmmt) REVERT: C 318 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8474 (t0) REVERT: C 410 MET cc_start: 0.7913 (mtt) cc_final: 0.7585 (ttp) REVERT: C 428 LYS cc_start: 0.7385 (tmtt) cc_final: 0.6353 (mptt) REVERT: C 476 PHE cc_start: 0.6676 (t80) cc_final: 0.6342 (t80) REVERT: C 486 HIS cc_start: 0.4704 (OUTLIER) cc_final: 0.4398 (t-170) REVERT: C 685 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7550 (t) REVERT: D 81 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8545 (tt) REVERT: D 108 LYS cc_start: 0.8325 (tttt) cc_final: 0.7841 (mmtt) REVERT: D 367 PHE cc_start: 0.8032 (m-80) cc_final: 0.7782 (m-10) REVERT: E 10 CYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6227 (t) REVERT: E 55 GLU cc_start: 0.7905 (tp30) cc_final: 0.7684 (pm20) REVERT: E 101 ASP cc_start: 0.8629 (m-30) cc_final: 0.7916 (m-30) REVERT: E 171 CYS cc_start: 0.8251 (t) cc_final: 0.7405 (m) REVERT: E 236 TYR cc_start: 0.7441 (t80) cc_final: 0.7101 (t80) outliers start: 84 outliers final: 48 residues processed: 259 average time/residue: 0.2126 time to fit residues: 85.3013 Evaluate side-chains 238 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 181 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 428 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN C 242 HIS C 486 HIS ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13988 Z= 0.264 Angle : 0.700 10.288 18936 Z= 0.354 Chirality : 0.045 0.455 2165 Planarity : 0.004 0.062 2384 Dihedral : 8.595 72.315 1855 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 6.25 % Allowed : 26.35 % Favored : 67.40 % 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: -1.84 (0.20), residues: 1633 helix: -0.35 (0.17), residues: 892 sheet: -2.60 (0.43), residues: 130 loop : -2.12 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 649 HIS 0.024 0.001 HIS C 486 PHE 0.053 0.002 PHE B 492 TYR 0.015 0.002 TYR E 304 ARG 0.006 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 194 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8733 (m-40) cc_final: 0.8035 (m110) REVERT: B 357 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: B 443 TRP cc_start: 0.9012 (OUTLIER) cc_final: 0.8679 (m100) REVERT: B 544 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6146 (mm) REVERT: B 562 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7221 (p0) REVERT: C 13 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: C 118 PHE cc_start: 0.8154 (m-80) cc_final: 0.7943 (m-10) REVERT: C 144 MET cc_start: 0.8622 (tpt) cc_final: 0.8233 (tpt) REVERT: C 281 CYS cc_start: 0.8079 (m) cc_final: 0.7819 (m) REVERT: C 318 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8609 (t0) REVERT: C 410 MET cc_start: 0.7894 (mtt) cc_final: 0.7502 (ttp) REVERT: C 428 LYS cc_start: 0.7422 (tmtt) cc_final: 0.6306 (mptt) REVERT: C 476 PHE cc_start: 0.6532 (t80) cc_final: 0.6205 (t80) REVERT: C 486 HIS cc_start: 0.3937 (OUTLIER) cc_final: 0.3717 (t-170) REVERT: C 487 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6209 (mt) REVERT: D 26 GLU cc_start: 0.7840 (pp20) cc_final: 0.7341 (pp20) REVERT: D 81 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8648 (mm) REVERT: D 108 LYS cc_start: 0.8336 (tttt) cc_final: 0.7854 (mmtt) REVERT: D 367 PHE cc_start: 0.8076 (m-80) cc_final: 0.7564 (m-10) REVERT: E 10 CYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6372 (t) REVERT: E 55 GLU cc_start: 0.7894 (tp30) cc_final: 0.7687 (pm20) REVERT: E 101 ASP cc_start: 0.8611 (m-30) cc_final: 0.7953 (m-30) REVERT: E 171 CYS cc_start: 0.8338 (t) cc_final: 0.7438 (m) REVERT: E 236 TYR cc_start: 0.7465 (t80) cc_final: 0.7077 (t80) outliers start: 96 outliers final: 60 residues processed: 271 average time/residue: 0.2267 time to fit residues: 94.1335 Evaluate side-chains 252 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 182 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 428 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 13 optimal weight: 0.0020 chunk 84 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 ASN D 410 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13988 Z= 0.192 Angle : 0.654 10.462 18936 Z= 0.330 Chirality : 0.042 0.331 2165 Planarity : 0.004 0.061 2384 Dihedral : 8.220 76.544 1855 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.07 % Allowed : 28.24 % Favored : 66.69 % 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: -1.54 (0.21), residues: 1633 helix: -0.09 (0.18), residues: 886 sheet: -2.51 (0.42), residues: 135 loop : -1.97 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 649 HIS 0.006 0.001 HIS C 486 PHE 0.024 0.002 PHE C 479 TYR 0.013 0.001 TYR C 47 ARG 0.007 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 202 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8716 (m-40) cc_final: 0.8030 (m110) REVERT: B 454 TYR cc_start: 0.7272 (m-80) cc_final: 0.6895 (m-10) REVERT: B 544 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6133 (mm) REVERT: B 562 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7139 (p0) REVERT: C 13 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: C 65 LEU cc_start: 0.8737 (mt) cc_final: 0.8348 (tp) REVERT: C 118 PHE cc_start: 0.8059 (m-80) cc_final: 0.7810 (m-10) REVERT: C 222 MET cc_start: 0.6578 (tmm) cc_final: 0.5969 (tmm) REVERT: C 223 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8114 (mm-30) REVERT: C 262 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8515 (tt) REVERT: C 281 CYS cc_start: 0.7944 (m) cc_final: 0.7650 (m) REVERT: C 318 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8602 (t0) REVERT: C 396 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7823 (tm-30) REVERT: C 410 MET cc_start: 0.7846 (mtt) cc_final: 0.7612 (ttt) REVERT: C 428 LYS cc_start: 0.7457 (tmtt) cc_final: 0.6331 (mptt) REVERT: C 476 PHE cc_start: 0.6442 (t80) cc_final: 0.6084 (t80) REVERT: C 487 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6216 (mt) REVERT: D 26 GLU cc_start: 0.7883 (pp20) cc_final: 0.7464 (pp20) REVERT: D 81 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8508 (tt) REVERT: D 108 LYS cc_start: 0.8312 (tttt) cc_final: 0.7901 (mmtt) REVERT: D 167 HIS cc_start: 0.6896 (OUTLIER) cc_final: 0.6661 (m90) REVERT: D 218 MET cc_start: 0.7222 (tpp) cc_final: 0.6992 (mmt) REVERT: D 282 LEU cc_start: 0.8816 (tp) cc_final: 0.8592 (mp) REVERT: D 428 TRP cc_start: 0.5386 (t-100) cc_final: 0.5037 (t-100) REVERT: E 10 CYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6287 (t) REVERT: E 101 ASP cc_start: 0.8641 (m-30) cc_final: 0.7977 (m-30) REVERT: E 171 CYS cc_start: 0.8186 (t) cc_final: 0.7311 (m) REVERT: E 236 TYR cc_start: 0.7468 (t80) cc_final: 0.7175 (t80) outliers start: 78 outliers final: 53 residues processed: 260 average time/residue: 0.2238 time to fit residues: 89.6372 Evaluate side-chains 246 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 184 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 167 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 428 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 97 optimal weight: 0.0970 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 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 399 GLN ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 HIS ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13988 Z= 0.180 Angle : 0.645 10.876 18936 Z= 0.323 Chirality : 0.042 0.267 2165 Planarity : 0.004 0.059 2384 Dihedral : 7.891 76.222 1853 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.01 % Allowed : 28.69 % Favored : 66.30 % 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: -1.38 (0.21), residues: 1633 helix: 0.07 (0.18), residues: 884 sheet: -2.40 (0.41), residues: 138 loop : -1.94 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 649 HIS 0.008 0.001 HIS C 486 PHE 0.044 0.002 PHE B 492 TYR 0.020 0.001 TYR D 255 ARG 0.006 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 200 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8707 (m-40) cc_final: 0.8056 (m110) REVERT: B 454 TYR cc_start: 0.7271 (m-80) cc_final: 0.6928 (m-10) REVERT: B 544 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6092 (mm) REVERT: B 562 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.7144 (p0) REVERT: C 13 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: C 65 LEU cc_start: 0.8757 (mt) cc_final: 0.8400 (tp) REVERT: C 262 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8537 (tt) REVERT: C 281 CYS cc_start: 0.7892 (m) cc_final: 0.7588 (m) REVERT: C 318 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8476 (t0) REVERT: C 410 MET cc_start: 0.7843 (mtt) cc_final: 0.7556 (ttp) REVERT: C 428 LYS cc_start: 0.7402 (tmtt) cc_final: 0.6261 (mptt) REVERT: C 476 PHE cc_start: 0.6483 (t80) cc_final: 0.6088 (t80) REVERT: C 569 LEU cc_start: 0.8242 (mm) cc_final: 0.7779 (pp) REVERT: D 26 GLU cc_start: 0.7877 (pp20) cc_final: 0.7603 (pp20) REVERT: D 81 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8551 (tt) REVERT: D 108 LYS cc_start: 0.8303 (tttt) cc_final: 0.7889 (mmtt) REVERT: D 167 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6613 (m90) REVERT: D 218 MET cc_start: 0.7189 (tpp) cc_final: 0.6979 (mmt) REVERT: D 367 PHE cc_start: 0.7967 (m-80) cc_final: 0.7687 (m-10) REVERT: D 428 TRP cc_start: 0.5354 (t-100) cc_final: 0.5021 (t-100) REVERT: E 10 CYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6164 (t) REVERT: E 101 ASP cc_start: 0.8605 (m-30) cc_final: 0.7944 (m-30) REVERT: E 171 CYS cc_start: 0.8213 (t) cc_final: 0.7284 (m) REVERT: E 236 TYR cc_start: 0.7555 (t80) cc_final: 0.7231 (t80) outliers start: 77 outliers final: 53 residues processed: 258 average time/residue: 0.2200 time to fit residues: 87.7665 Evaluate side-chains 250 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 189 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 167 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 193 HIS Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 428 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 48 optimal weight: 0.0030 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 145 optimal weight: 0.0670 overall best weight: 1.1932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 ASN ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13988 Z= 0.182 Angle : 0.648 12.947 18936 Z= 0.323 Chirality : 0.041 0.176 2165 Planarity : 0.004 0.057 2384 Dihedral : 7.689 74.897 1853 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.75 % Allowed : 28.69 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.21), residues: 1633 helix: 0.20 (0.18), residues: 883 sheet: -2.23 (0.40), residues: 148 loop : -1.87 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 649 HIS 0.007 0.001 HIS C 486 PHE 0.022 0.001 PHE C 479 TYR 0.016 0.001 TYR D 350 ARG 0.005 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 196 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8701 (m-40) cc_final: 0.8046 (m110) REVERT: B 454 TYR cc_start: 0.7262 (m-80) cc_final: 0.6998 (m-10) REVERT: B 544 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5984 (mm) REVERT: B 562 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.7089 (p0) REVERT: C 13 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: C 65 LEU cc_start: 0.8757 (mt) cc_final: 0.8427 (tp) REVERT: C 262 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8571 (tt) REVERT: C 281 CYS cc_start: 0.7847 (m) cc_final: 0.7531 (m) REVERT: C 318 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8482 (t0) REVERT: C 410 MET cc_start: 0.7860 (mtt) cc_final: 0.7499 (ttp) REVERT: C 428 LYS cc_start: 0.7404 (tmtt) cc_final: 0.6311 (mptt) REVERT: C 476 PHE cc_start: 0.6478 (t80) cc_final: 0.6083 (t80) REVERT: C 487 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.5910 (mm) REVERT: D 81 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8530 (tt) REVERT: D 108 LYS cc_start: 0.8304 (tttt) cc_final: 0.7845 (mmtt) REVERT: D 135 ASN cc_start: 0.8057 (m-40) cc_final: 0.7738 (m-40) REVERT: D 167 HIS cc_start: 0.6852 (OUTLIER) cc_final: 0.6604 (m90) REVERT: D 218 MET cc_start: 0.7199 (tpp) cc_final: 0.6996 (mmt) REVERT: D 367 PHE cc_start: 0.7980 (m-80) cc_final: 0.7678 (m-10) REVERT: E 10 CYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6404 (t) REVERT: E 101 ASP cc_start: 0.8605 (m-30) cc_final: 0.7931 (m-30) REVERT: E 171 CYS cc_start: 0.8201 (t) cc_final: 0.7279 (m) REVERT: E 233 PHE cc_start: 0.7546 (t80) cc_final: 0.7344 (t80) REVERT: E 236 TYR cc_start: 0.7553 (t80) cc_final: 0.7253 (t80) REVERT: E 320 PRO cc_start: 0.8000 (Cg_endo) cc_final: 0.7487 (Cg_exo) outliers start: 73 outliers final: 55 residues processed: 251 average time/residue: 0.2258 time to fit residues: 86.5474 Evaluate side-chains 250 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 186 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 167 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 339 TYR Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 193 HIS Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 428 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 149 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13988 Z= 0.164 Angle : 0.638 12.536 18936 Z= 0.316 Chirality : 0.040 0.154 2165 Planarity : 0.004 0.055 2384 Dihedral : 7.348 75.924 1853 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.90 % Allowed : 29.67 % Favored : 66.43 % 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: -1.05 (0.21), residues: 1633 helix: 0.34 (0.18), residues: 883 sheet: -2.24 (0.42), residues: 139 loop : -1.79 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 375 HIS 0.009 0.001 HIS E 227 PHE 0.048 0.002 PHE C 244 TYR 0.012 0.001 TYR E 430 ARG 0.010 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 202 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8693 (m-40) cc_final: 0.8068 (m110) REVERT: B 394 ASN cc_start: 0.8668 (m110) cc_final: 0.8054 (t0) REVERT: B 544 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5888 (mm) REVERT: C 13 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: C 52 GLN cc_start: 0.8608 (tt0) cc_final: 0.8302 (pt0) REVERT: C 65 LEU cc_start: 0.8748 (mt) cc_final: 0.8452 (tp) REVERT: C 207 SER cc_start: 0.8765 (t) cc_final: 0.8504 (p) REVERT: C 262 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8570 (tt) REVERT: C 318 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8491 (t0) REVERT: C 410 MET cc_start: 0.7839 (mtt) cc_final: 0.7503 (ttp) REVERT: C 428 LYS cc_start: 0.7434 (tmtt) cc_final: 0.6311 (mptt) REVERT: C 476 PHE cc_start: 0.6472 (t80) cc_final: 0.6081 (t80) REVERT: C 487 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.5811 (mm) REVERT: D 81 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8601 (tt) REVERT: D 108 LYS cc_start: 0.8290 (tttt) cc_final: 0.7862 (mmtt) REVERT: D 135 ASN cc_start: 0.8081 (m-40) cc_final: 0.7722 (m-40) REVERT: D 236 LEU cc_start: 0.7316 (mt) cc_final: 0.6989 (tt) REVERT: D 367 PHE cc_start: 0.7926 (m-80) cc_final: 0.7621 (m-10) REVERT: E 10 CYS cc_start: 0.6690 (OUTLIER) cc_final: 0.6305 (t) REVERT: E 101 ASP cc_start: 0.8624 (m-30) cc_final: 0.7948 (m-30) REVERT: E 171 CYS cc_start: 0.8124 (t) cc_final: 0.7196 (m) REVERT: E 233 PHE cc_start: 0.7625 (t80) cc_final: 0.7362 (t80) REVERT: E 236 TYR cc_start: 0.7536 (t80) cc_final: 0.7241 (t80) outliers start: 60 outliers final: 38 residues processed: 249 average time/residue: 0.2148 time to fit residues: 82.9688 Evaluate side-chains 234 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 189 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 339 TYR Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 193 HIS Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 413 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 109 optimal weight: 0.1980 chunk 165 optimal weight: 0.0070 chunk 152 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13988 Z= 0.157 Angle : 0.645 14.082 18936 Z= 0.315 Chirality : 0.040 0.173 2165 Planarity : 0.004 0.073 2384 Dihedral : 7.102 76.063 1853 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.86 % Allowed : 30.84 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1633 helix: 0.42 (0.18), residues: 880 sheet: -2.09 (0.42), residues: 141 loop : -1.75 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 375 HIS 0.010 0.001 HIS E 227 PHE 0.046 0.002 PHE C 244 TYR 0.011 0.001 TYR D 226 ARG 0.009 0.000 ARG C 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 207 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8675 (m-40) cc_final: 0.8026 (m110) REVERT: B 299 HIS cc_start: 0.7238 (m-70) cc_final: 0.6898 (t70) REVERT: B 394 ASN cc_start: 0.8643 (m110) cc_final: 0.7920 (t0) REVERT: C 13 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: C 52 GLN cc_start: 0.8624 (tt0) cc_final: 0.8275 (pt0) REVERT: C 65 LEU cc_start: 0.8721 (mt) cc_final: 0.8429 (tp) REVERT: C 207 SER cc_start: 0.8687 (t) cc_final: 0.8442 (p) REVERT: C 318 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8476 (t0) REVERT: C 410 MET cc_start: 0.7815 (mtt) cc_final: 0.7427 (mtp) REVERT: C 428 LYS cc_start: 0.7405 (tmtt) cc_final: 0.6287 (mptt) REVERT: C 437 GLU cc_start: 0.7528 (mp0) cc_final: 0.7221 (mp0) REVERT: C 476 PHE cc_start: 0.6536 (t80) cc_final: 0.6122 (t80) REVERT: C 487 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.5848 (mm) REVERT: D 81 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8630 (tt) REVERT: D 108 LYS cc_start: 0.8282 (tttt) cc_final: 0.7853 (mmtt) REVERT: D 236 LEU cc_start: 0.7300 (mt) cc_final: 0.6978 (tt) REVERT: D 367 PHE cc_start: 0.7921 (m-80) cc_final: 0.7624 (m-10) REVERT: E 10 CYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6364 (t) REVERT: E 101 ASP cc_start: 0.8629 (m-30) cc_final: 0.7969 (m-30) REVERT: E 171 CYS cc_start: 0.8064 (t) cc_final: 0.7200 (m) REVERT: E 233 PHE cc_start: 0.7614 (t80) cc_final: 0.7286 (t80) REVERT: E 236 TYR cc_start: 0.7533 (t80) cc_final: 0.7287 (t80) outliers start: 44 outliers final: 35 residues processed: 241 average time/residue: 0.2267 time to fit residues: 83.8065 Evaluate side-chains 231 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 339 TYR Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 193 HIS Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 413 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 121 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.132944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.112072 restraints weight = 34731.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.113963 restraints weight = 19414.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.114905 restraints weight = 13283.049| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13988 Z= 0.160 Angle : 0.655 13.687 18936 Z= 0.317 Chirality : 0.040 0.164 2165 Planarity : 0.004 0.052 2384 Dihedral : 6.809 76.611 1853 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.86 % Allowed : 31.10 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.21), residues: 1633 helix: 0.59 (0.18), residues: 868 sheet: -1.98 (0.43), residues: 141 loop : -1.71 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 375 HIS 0.010 0.001 HIS E 227 PHE 0.048 0.002 PHE C 244 TYR 0.014 0.001 TYR E 430 ARG 0.007 0.000 ARG C 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2874.20 seconds wall clock time: 53 minutes 13.74 seconds (3193.74 seconds total)