Starting phenix.real_space_refine on Sat Mar 16 11:00:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctf_30463/03_2024/7ctf_30463_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctf_30463/03_2024/7ctf_30463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctf_30463/03_2024/7ctf_30463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctf_30463/03_2024/7ctf_30463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctf_30463/03_2024/7ctf_30463_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctf_30463/03_2024/7ctf_30463_updated.pdb" } resolution = 4.8 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= 0.010 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 70 5.16 5 C 9314 2.51 5 N 2447 2.21 5 O 2667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A TYR 813": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 489": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 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 TYR 429": "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 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 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 TYR 226": "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 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 TYR 350": "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 ARG 373": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14504 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 805 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} 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: 7.88, per 1000 atoms: 0.54 Number of scatterers: 14504 At special positions: 0 Unit cell: (119.318, 122.633, 150.805, 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 70 16.00 P 6 15.00 O 2667 8.00 N 2447 7.00 C 9314 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: 5.62 Conformation dependent library (CDL) restraints added in 2.8 seconds 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3454 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 7 sheets defined 53.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 762 through 768 Processing helix chain 'A' and resid 772 through 788 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'A' and resid 816 through 828 Processing helix chain 'A' and resid 851 through 859 Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.870A pdb=" N PHE B 298 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS B 299 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 348 through 357 Processing helix chain 'B' and resid 369 through 382 removed outlier: 4.093A pdb=" N PHE B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 413 removed outlier: 3.830A pdb=" N GLN B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 3.621A 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: 3.856A 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 539 Processing helix chain 'B' and resid 567 through 574 removed outlier: 4.333A pdb=" N GLU B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 65 removed outlier: 3.964A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.914A pdb=" N ASN C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 144 through 162 removed outlier: 3.961A 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 258 through 262 Processing helix chain 'C' and resid 265 through 270 Processing helix chain 'C' and resid 282 through 292 removed outlier: 4.376A pdb=" N THR C 287 " --> pdb=" O GLU C 283 " (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 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 348 through 354 removed outlier: 4.484A 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: 4.635A pdb=" N ALA C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 424 removed outlier: 3.993A pdb=" N GLU C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C 414 " --> pdb=" O MET C 410 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL C 415 " --> pdb=" O ASN C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 441 removed outlier: 4.007A pdb=" N TYR C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 3.705A 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 550 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: 4.207A pdb=" N GLU C 590 " --> pdb=" O HIS C 586 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 605 removed outlier: 3.626A 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: 3.779A pdb=" N GLU C 687 " --> pdb=" O ARG C 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 29 removed outlier: 3.839A pdb=" N GLU D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 56 removed outlier: 4.140A pdb=" N GLU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 4.103A 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 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: 4.251A pdb=" N HIS D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 removed outlier: 4.491A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.580A 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 207 No H-bonds generated for 'chain 'D' and resid 204 through 207' Processing helix chain 'D' and resid 223 through 234 removed outlier: 3.834A 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: 3.517A pdb=" N ILE D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 289 removed outlier: 3.807A 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 313 through 319 removed outlier: 3.823A pdb=" N ILE D 317 " --> pdb=" O SER D 313 " (cutoff:3.500A) 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: 3.521A pdb=" N MET D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D 374 " --> pdb=" O PRO D 370 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 375 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 376 " --> pdb=" O VAL D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 removed outlier: 3.896A pdb=" N GLN D 416 " --> pdb=" O MET D 412 " (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: 3.731A pdb=" N THR E 53 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 82 removed outlier: 3.604A pdb=" N ILE E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 109 removed outlier: 3.764A pdb=" N LYS E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN E 108 " --> pdb=" O ARG E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 136 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: 3.676A pdb=" N GLY E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.995A 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: 4.353A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.858A 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 432 removed outlier: 3.675A pdb=" N TYR E 432 " --> pdb=" O ILE E 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 428 through 432' Processing sheet with id= A, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.059A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 313 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 424 " --> pdb=" O LEU B 313 " (cutoff:3.500A) 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: 6.381A pdb=" N VAL C 216 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU C 136 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 6.053A 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 64 through 66 removed outlier: 7.191A pdb=" N ILE D 65 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLY D 191 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ILE D 190 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE D 156 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU D 192 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 158 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 155 " --> pdb=" O LEU D 95 " (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 175 through 178 removed outlier: 8.358A pdb=" N ILE E 33 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL E 154 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE E 35 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE E 156 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 393 through 395 564 hydrogen bonds defined for protein. 1659 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: 3.84 Time building geometry restraints manager: 6.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4527 1.34 - 1.46: 3121 1.46 - 1.58: 7040 1.58 - 1.70: 12 1.70 - 1.81: 104 Bond restraints: 14804 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 6.01e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.30e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.27e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.87e+01 bond pdb=" C PRO C 570 " pdb=" N PRO C 571 " ideal model delta sigma weight residual 1.335 1.409 -0.074 1.30e-02 5.92e+03 3.22e+01 ... (remaining 14799 not shown) Histogram of bond angle deviations from ideal: 95.45 - 103.84: 200 103.84 - 112.24: 7324 112.24 - 120.63: 7728 120.63 - 129.02: 4652 129.02 - 137.41: 134 Bond angle restraints: 20038 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 139.87 116.10 23.77 1.00e+00 1.00e+00 5.65e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 119.95 19.92 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 117.13 19.70 1.00e+00 1.00e+00 3.88e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 120.20 16.63 1.00e+00 1.00e+00 2.76e+02 angle pdb=" C5 ATP E 901 " pdb=" C4 ATP E 901 " pdb=" N3 ATP E 901 " ideal model delta sigma weight residual 126.80 117.28 9.52 1.00e+00 1.00e+00 9.06e+01 ... (remaining 20033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7477 17.71 - 35.42: 1088 35.42 - 53.13: 333 53.13 - 70.83: 86 70.83 - 88.54: 17 Dihedral angle restraints: 9001 sinusoidal: 3731 harmonic: 5270 Sorted by residual: 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 180.00 132.64 47.36 0 5.00e+00 4.00e-02 8.97e+01 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 180.00 136.83 43.17 0 5.00e+00 4.00e-02 7.45e+01 dihedral pdb=" CA GLN D 400 " pdb=" C GLN D 400 " pdb=" N LEU D 401 " pdb=" CA LEU D 401 " ideal model delta harmonic sigma weight residual 180.00 137.65 42.35 0 5.00e+00 4.00e-02 7.17e+01 ... (remaining 8998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1733 0.068 - 0.137: 474 0.137 - 0.205: 76 0.205 - 0.273: 10 0.273 - 0.342: 2 Chirality restraints: 2295 Sorted by residual: 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 -2.25 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA HIS E 195 " pdb=" N HIS E 195 " pdb=" C HIS E 195 " pdb=" CB HIS E 195 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+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 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2292 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 400 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ASP E 400 " 0.063 2.00e-02 2.50e+03 pdb=" O ASP E 400 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN E 401 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 609 " 0.039 2.00e-02 2.50e+03 2.51e-02 1.26e+01 pdb=" CG TYR C 609 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR C 609 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 609 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 609 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 609 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 609 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 609 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 258 " 0.058 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO E 259 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO E 259 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 259 " 0.048 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3808 2.79 - 3.32: 13217 3.32 - 3.85: 24606 3.85 - 4.37: 26737 4.37 - 4.90: 45002 Nonbonded interactions: 113370 Sorted by model distance: nonbonded pdb=" O ALA C 654 " pdb=" OG1 THR C 658 " model vdw 2.264 2.440 nonbonded pdb=" O LYS C 202 " pdb=" OG1 THR C 206 " model vdw 2.287 2.440 nonbonded pdb=" O GLN C 339 " pdb=" OG SER C 342 " model vdw 2.299 2.440 nonbonded pdb=" O HIS C 284 " pdb=" OG1 THR C 287 " model vdw 2.301 2.440 nonbonded pdb=" O PHE C 118 " pdb=" OG1 THR C 122 " model vdw 2.307 2.440 ... (remaining 113365 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: 0.270 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: 1.580 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 39.520 Find NCS groups from input model: 0.380 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: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.009 0.090 14804 Z= 0.561 Angle : 1.363 23.770 20038 Z= 0.788 Chirality : 0.063 0.342 2295 Planarity : 0.009 0.086 2525 Dihedral : 18.999 88.542 5547 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.87 % Favored : 93.08 % Rotamer: Outliers : 8.84 % Allowed : 17.50 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.62 % Twisted General : 0.95 % 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: -4.50 (0.15), residues: 1733 helix: -2.98 (0.11), residues: 945 sheet: -2.85 (0.35), residues: 155 loop : -2.69 (0.21), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP E 162 HIS 0.010 0.002 HIS D 269 PHE 0.055 0.005 PHE C 559 TYR 0.058 0.004 TYR C 609 ARG 0.008 0.001 ARG C 706 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 684 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 THR cc_start: 0.8841 (p) cc_final: 0.8087 (t) REVERT: A 797 GLN cc_start: 0.9455 (mt0) cc_final: 0.9038 (mt0) REVERT: A 798 ILE cc_start: 0.9663 (pt) cc_final: 0.9362 (mp) REVERT: A 799 TYR cc_start: 0.9331 (t80) cc_final: 0.8868 (t80) REVERT: A 801 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8901 (mm110) REVERT: A 802 HIS cc_start: 0.8945 (t-90) cc_final: 0.8609 (t70) REVERT: A 809 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8005 (mm-30) REVERT: A 816 MET cc_start: 0.9129 (ptt) cc_final: 0.8578 (pmm) REVERT: A 819 THR cc_start: 0.8959 (m) cc_final: 0.8168 (p) REVERT: A 834 VAL cc_start: 0.7992 (m) cc_final: 0.7595 (p) REVERT: A 838 ARG cc_start: 0.6516 (ttm-80) cc_final: 0.6282 (mtp-110) REVERT: A 847 LEU cc_start: 0.8727 (tp) cc_final: 0.8315 (tp) REVERT: B 302 MET cc_start: 0.9180 (tmm) cc_final: 0.8315 (tmm) REVERT: B 303 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8331 (tp) REVERT: B 305 LEU cc_start: 0.9194 (tp) cc_final: 0.8877 (pp) REVERT: B 327 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8749 (ttp80) REVERT: B 330 MET cc_start: 0.7848 (mtm) cc_final: 0.7531 (mmm) REVERT: B 331 LEU cc_start: 0.8867 (mp) cc_final: 0.8468 (mp) REVERT: B 335 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8664 (tp) REVERT: B 376 ILE cc_start: 0.9284 (tp) cc_final: 0.9035 (tt) REVERT: B 524 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.5937 (t80) REVERT: B 525 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7398 (mt) REVERT: B 536 LEU cc_start: 0.8858 (mt) cc_final: 0.8546 (tp) REVERT: C 47 TYR cc_start: 0.9124 (t80) cc_final: 0.8777 (t80) REVERT: C 66 ASN cc_start: 0.9344 (m-40) cc_final: 0.7812 (p0) REVERT: C 70 PHE cc_start: 0.9217 (p90) cc_final: 0.8927 (p90) REVERT: C 80 SER cc_start: 0.9468 (OUTLIER) cc_final: 0.8995 (p) REVERT: C 107 LEU cc_start: 0.9341 (mt) cc_final: 0.8905 (mt) REVERT: C 136 LEU cc_start: 0.9446 (mt) cc_final: 0.9158 (mm) REVERT: C 148 LEU cc_start: 0.9230 (tp) cc_final: 0.8770 (tt) REVERT: C 157 ASP cc_start: 0.8868 (m-30) cc_final: 0.8614 (p0) REVERT: C 162 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8195 (tp) REVERT: C 211 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: C 219 LEU cc_start: 0.9334 (mt) cc_final: 0.9133 (mt) REVERT: C 229 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8671 (p) REVERT: C 248 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8868 (pp) REVERT: C 285 LEU cc_start: 0.9413 (tp) cc_final: 0.8834 (tt) REVERT: C 314 PHE cc_start: 0.8789 (t80) cc_final: 0.8425 (t80) REVERT: C 315 LEU cc_start: 0.9584 (tp) cc_final: 0.9373 (tt) REVERT: C 317 HIS cc_start: 0.7928 (m90) cc_final: 0.6975 (m170) REVERT: C 318 ASP cc_start: 0.8769 (t70) cc_final: 0.7990 (t70) REVERT: C 326 LYS cc_start: 0.9269 (ttpt) cc_final: 0.8958 (ttmt) REVERT: C 334 GLU cc_start: 0.8463 (tp30) cc_final: 0.7793 (tp30) REVERT: C 341 LEU cc_start: 0.7912 (mt) cc_final: 0.7513 (mt) REVERT: C 363 CYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8513 (t) REVERT: C 369 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7429 (tt) REVERT: C 409 HIS cc_start: 0.9405 (m-70) cc_final: 0.9125 (m-70) REVERT: C 469 MET cc_start: 0.6965 (ttm) cc_final: 0.6683 (mtt) REVERT: C 604 LEU cc_start: 0.9672 (mt) cc_final: 0.9212 (mm) REVERT: C 634 TYR cc_start: 0.9041 (t80) cc_final: 0.8541 (t80) REVERT: C 635 LYS cc_start: 0.7832 (tttt) cc_final: 0.7453 (tptt) REVERT: C 657 VAL cc_start: 0.9617 (OUTLIER) cc_final: 0.9302 (m) REVERT: C 671 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: C 674 ASN cc_start: 0.8985 (t0) cc_final: 0.8190 (m-40) REVERT: C 693 PHE cc_start: 0.8643 (m-80) cc_final: 0.8375 (m-80) REVERT: D 24 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.7153 (tt) REVERT: D 28 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.6490 (m-10) REVERT: D 64 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7659 (mt) REVERT: D 81 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.8855 (mt) REVERT: D 84 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9366 (pp) REVERT: D 85 MET cc_start: 0.8545 (mmm) cc_final: 0.8271 (mmm) REVERT: D 97 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8473 (p) REVERT: D 107 ASP cc_start: 0.8215 (t0) cc_final: 0.7945 (t0) REVERT: D 164 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7598 (t80) REVERT: D 179 ILE cc_start: 0.9366 (mt) cc_final: 0.9132 (tt) REVERT: D 185 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8727 (m) REVERT: D 187 ILE cc_start: 0.8961 (mt) cc_final: 0.8688 (mt) REVERT: D 201 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8558 (tt) REVERT: D 226 TYR cc_start: 0.8798 (t80) cc_final: 0.8305 (t80) REVERT: D 284 MET cc_start: 0.9123 (tpt) cc_final: 0.8857 (tpp) REVERT: D 297 MET cc_start: 0.8415 (ptm) cc_final: 0.7191 (ptm) REVERT: D 326 ILE cc_start: 0.9477 (mt) cc_final: 0.9134 (mt) REVERT: D 348 MET cc_start: 0.8701 (tpt) cc_final: 0.8134 (tpt) REVERT: D 352 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8763 (mm-30) REVERT: D 377 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: D 380 GLN cc_start: 0.9023 (tt0) cc_final: 0.8607 (tm-30) REVERT: E 10 CYS cc_start: 0.7540 (m) cc_final: 0.6918 (m) REVERT: E 19 GLN cc_start: 0.9271 (tt0) cc_final: 0.8955 (tm-30) REVERT: E 21 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9068 (mt) REVERT: E 27 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.7050 (p90) REVERT: E 34 PHE cc_start: 0.9455 (t80) cc_final: 0.8996 (t80) REVERT: E 35 ILE cc_start: 0.9326 (mt) cc_final: 0.8898 (mm) REVERT: E 49 THR cc_start: 0.8772 (p) cc_final: 0.8489 (p) REVERT: E 76 ILE cc_start: 0.9667 (mt) cc_final: 0.9417 (mt) REVERT: E 105 LEU cc_start: 0.8748 (mt) cc_final: 0.7820 (mt) REVERT: E 126 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8069 (tttm) REVERT: E 129 TYR cc_start: 0.8829 (m-10) cc_final: 0.7880 (m-10) REVERT: E 144 LEU cc_start: 0.9296 (tp) cc_final: 0.9007 (tt) REVERT: E 155 LEU cc_start: 0.9168 (tp) cc_final: 0.8941 (tp) REVERT: E 160 ILE cc_start: 0.9335 (tp) cc_final: 0.8624 (tt) REVERT: E 171 CYS cc_start: 0.7077 (t) cc_final: 0.6747 (t) REVERT: E 172 PHE cc_start: 0.8098 (t80) cc_final: 0.7877 (t80) REVERT: E 212 LEU cc_start: 0.9470 (tp) cc_final: 0.9247 (tp) REVERT: E 227 HIS cc_start: 0.9013 (t70) cc_final: 0.8648 (t-90) REVERT: E 253 LEU cc_start: 0.8725 (tp) cc_final: 0.8364 (mp) REVERT: E 257 ILE cc_start: 0.8418 (tp) cc_final: 0.8003 (tp) REVERT: E 307 LYS cc_start: 0.9537 (mttp) cc_final: 0.9261 (mttm) REVERT: E 314 TYR cc_start: 0.8082 (t80) cc_final: 0.7759 (t80) REVERT: E 380 ILE cc_start: 0.9065 (tp) cc_final: 0.8608 (tp) REVERT: E 401 GLN cc_start: 0.5416 (mm-40) cc_final: 0.4821 (mm-40) REVERT: E 409 CYS cc_start: 0.6693 (t) cc_final: 0.6435 (t) REVERT: E 431 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8364 (pp) outliers start: 144 outliers final: 24 residues processed: 763 average time/residue: 0.2796 time to fit residues: 305.3296 Evaluate side-chains 455 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 404 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN B 304 GLN B 372 GLN C 85 GLN C 146 HIS C 242 HIS ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN C 399 GLN C 409 HIS C 555 ASN C 613 ASN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 HIS D 170 GLN D 252 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS D 288 ASN D 307 GLN D 319 HIS ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN E 227 HIS E 266 GLN E 299 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14804 Z= 0.289 Angle : 0.798 12.077 20038 Z= 0.417 Chirality : 0.045 0.216 2295 Planarity : 0.006 0.068 2525 Dihedral : 9.547 85.906 1964 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.31 % Allowed : 5.59 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.12 % 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: -2.39 (0.18), residues: 1733 helix: -1.04 (0.15), residues: 957 sheet: -2.13 (0.38), residues: 151 loop : -2.11 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 649 HIS 0.012 0.001 HIS C 678 PHE 0.036 0.003 PHE C 559 TYR 0.022 0.002 TYR C 47 ARG 0.007 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 475 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 GLU cc_start: 0.8836 (tp30) cc_final: 0.8595 (mm-30) REVERT: A 798 ILE cc_start: 0.9691 (pt) cc_final: 0.9205 (pt) REVERT: A 799 TYR cc_start: 0.9172 (t80) cc_final: 0.8569 (t80) REVERT: A 801 GLN cc_start: 0.9299 (mm-40) cc_final: 0.8405 (mm-40) REVERT: A 809 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8192 (tm-30) REVERT: A 816 MET cc_start: 0.9239 (ptt) cc_final: 0.8896 (pmm) REVERT: A 819 THR cc_start: 0.9051 (m) cc_final: 0.8275 (p) REVERT: A 826 LEU cc_start: 0.9244 (mt) cc_final: 0.8975 (mt) REVERT: B 303 LEU cc_start: 0.8920 (tt) cc_final: 0.8617 (tp) REVERT: B 319 LYS cc_start: 0.8787 (ptpp) cc_final: 0.8200 (mmtm) REVERT: B 330 MET cc_start: 0.7918 (mtm) cc_final: 0.7659 (mmm) REVERT: B 426 HIS cc_start: 0.8751 (t-90) cc_final: 0.8460 (t70) REVERT: B 432 MET cc_start: 0.7634 (ptm) cc_final: 0.7278 (ptm) REVERT: B 532 LEU cc_start: 0.8951 (tp) cc_final: 0.8590 (tp) REVERT: B 536 LEU cc_start: 0.9002 (mt) cc_final: 0.8565 (pp) REVERT: B 537 THR cc_start: 0.8362 (t) cc_final: 0.7575 (p) REVERT: C 50 ILE cc_start: 0.9513 (mt) cc_final: 0.9261 (tp) REVERT: C 66 ASN cc_start: 0.9344 (m-40) cc_final: 0.8556 (p0) REVERT: C 77 LEU cc_start: 0.9530 (mm) cc_final: 0.9223 (pp) REVERT: C 147 PHE cc_start: 0.8864 (t80) cc_final: 0.8575 (t80) REVERT: C 148 LEU cc_start: 0.9171 (tp) cc_final: 0.8898 (tt) REVERT: C 222 MET cc_start: 0.8658 (tmm) cc_final: 0.8443 (tmm) REVERT: C 223 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8528 (mm-30) REVERT: C 232 ASP cc_start: 0.8824 (m-30) cc_final: 0.8584 (m-30) REVERT: C 301 LYS cc_start: 0.8098 (mmpt) cc_final: 0.7758 (mmmt) REVERT: C 326 LYS cc_start: 0.9371 (ttpt) cc_final: 0.8933 (ttmt) REVERT: C 330 LEU cc_start: 0.9362 (tp) cc_final: 0.8668 (tp) REVERT: C 363 CYS cc_start: 0.9019 (t) cc_final: 0.8796 (m) REVERT: C 410 MET cc_start: 0.9443 (mtm) cc_final: 0.9231 (mtt) REVERT: C 581 TYR cc_start: 0.7978 (m-10) cc_final: 0.7703 (m-10) REVERT: C 582 PHE cc_start: 0.6373 (t80) cc_final: 0.5904 (t80) REVERT: C 634 TYR cc_start: 0.9135 (t80) cc_final: 0.8714 (t80) REVERT: D 24 LEU cc_start: 0.9218 (tt) cc_final: 0.8330 (pp) REVERT: D 38 PHE cc_start: 0.6690 (t80) cc_final: 0.6454 (t80) REVERT: D 64 LEU cc_start: 0.8936 (tt) cc_final: 0.8642 (mm) REVERT: D 107 ASP cc_start: 0.8477 (t0) cc_final: 0.8025 (t0) REVERT: D 111 LEU cc_start: 0.9364 (mt) cc_final: 0.9151 (mt) REVERT: D 164 PHE cc_start: 0.9422 (m-80) cc_final: 0.9173 (m-80) REVERT: D 177 PHE cc_start: 0.8462 (m-10) cc_final: 0.8177 (m-10) REVERT: D 192 LEU cc_start: 0.9145 (mm) cc_final: 0.8930 (mm) REVERT: D 297 MET cc_start: 0.8534 (ptm) cc_final: 0.7489 (ptm) REVERT: D 321 LEU cc_start: 0.8765 (mt) cc_final: 0.8307 (mt) REVERT: D 339 TYR cc_start: 0.7445 (t80) cc_final: 0.6758 (t80) REVERT: D 379 LEU cc_start: 0.9462 (tp) cc_final: 0.8974 (mt) REVERT: D 388 MET cc_start: 0.8845 (mpp) cc_final: 0.8632 (mpp) REVERT: D 401 LEU cc_start: 0.8940 (tp) cc_final: 0.8631 (tp) REVERT: D 406 LEU cc_start: 0.8816 (mt) cc_final: 0.8474 (mt) REVERT: E 19 GLN cc_start: 0.9468 (tt0) cc_final: 0.8708 (tm-30) REVERT: E 64 VAL cc_start: 0.8878 (t) cc_final: 0.8380 (t) REVERT: E 126 LYS cc_start: 0.8388 (mtpp) cc_final: 0.8036 (tttt) REVERT: E 160 ILE cc_start: 0.9388 (tp) cc_final: 0.9116 (mt) REVERT: E 236 TYR cc_start: 0.7247 (t80) cc_final: 0.6891 (t80) REVERT: E 307 LYS cc_start: 0.9473 (mttp) cc_final: 0.9207 (mttm) REVERT: E 409 CYS cc_start: 0.7028 (t) cc_final: 0.6739 (t) outliers start: 5 outliers final: 1 residues processed: 479 average time/residue: 0.2448 time to fit residues: 172.4755 Evaluate side-chains 341 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 340 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 133 optimal weight: 0.0000 chunk 108 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 158 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 HIS B 353 ASN B 362 HIS C 52 GLN C 322 GLN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN C 399 GLN ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14804 Z= 0.198 Angle : 0.715 15.804 20038 Z= 0.359 Chirality : 0.043 0.190 2295 Planarity : 0.004 0.068 2525 Dihedral : 8.383 87.900 1964 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.18 % Allowed : 3.87 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.06 % 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: -1.73 (0.19), residues: 1733 helix: -0.35 (0.16), residues: 945 sheet: -2.02 (0.40), residues: 147 loop : -2.03 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 51 HIS 0.005 0.001 HIS B 362 PHE 0.030 0.002 PHE C 559 TYR 0.018 0.002 TYR C 567 ARG 0.006 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 428 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 GLN cc_start: 0.9078 (pt0) cc_final: 0.8833 (pt0) REVERT: A 799 TYR cc_start: 0.9281 (t80) cc_final: 0.8936 (t80) REVERT: A 801 GLN cc_start: 0.9290 (mm-40) cc_final: 0.8985 (mm110) REVERT: A 813 TYR cc_start: 0.6417 (t80) cc_final: 0.6208 (t80) REVERT: A 816 MET cc_start: 0.9175 (ptt) cc_final: 0.8566 (pmm) REVERT: A 819 THR cc_start: 0.8834 (m) cc_final: 0.8608 (p) REVERT: A 820 MET cc_start: 0.8932 (mmp) cc_final: 0.7627 (mmp) REVERT: A 826 LEU cc_start: 0.9282 (mt) cc_final: 0.9068 (mt) REVERT: B 330 MET cc_start: 0.7934 (mtm) cc_final: 0.7663 (mmm) REVERT: B 426 HIS cc_start: 0.8458 (t-90) cc_final: 0.8232 (t70) REVERT: B 432 MET cc_start: 0.7543 (ptt) cc_final: 0.7182 (ptm) REVERT: B 532 LEU cc_start: 0.8959 (tp) cc_final: 0.8519 (tp) REVERT: B 536 LEU cc_start: 0.8986 (mt) cc_final: 0.8616 (pp) REVERT: C 50 ILE cc_start: 0.9622 (mt) cc_final: 0.9367 (tp) REVERT: C 66 ASN cc_start: 0.9400 (m-40) cc_final: 0.8409 (p0) REVERT: C 105 LEU cc_start: 0.9064 (tp) cc_final: 0.8787 (pt) REVERT: C 147 PHE cc_start: 0.8882 (t80) cc_final: 0.8488 (t80) REVERT: C 148 LEU cc_start: 0.8954 (tp) cc_final: 0.8649 (tt) REVERT: C 219 LEU cc_start: 0.9293 (mt) cc_final: 0.8959 (mt) REVERT: C 221 ASP cc_start: 0.8356 (t0) cc_final: 0.8144 (t0) REVERT: C 285 LEU cc_start: 0.9279 (tt) cc_final: 0.8877 (tt) REVERT: C 324 PHE cc_start: 0.8408 (t80) cc_final: 0.8106 (t80) REVERT: C 326 LYS cc_start: 0.9427 (ttpt) cc_final: 0.8790 (tttp) REVERT: C 330 LEU cc_start: 0.9360 (tp) cc_final: 0.8963 (tp) REVERT: C 334 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8369 (mt-10) REVERT: C 581 TYR cc_start: 0.7777 (m-10) cc_final: 0.7573 (m-10) REVERT: C 582 PHE cc_start: 0.6181 (t80) cc_final: 0.5882 (t80) REVERT: C 592 LEU cc_start: 0.8966 (tp) cc_final: 0.8700 (tp) REVERT: C 693 PHE cc_start: 0.8876 (m-10) cc_final: 0.8544 (m-80) REVERT: D 38 PHE cc_start: 0.6858 (t80) cc_final: 0.6466 (t80) REVERT: D 47 LEU cc_start: 0.9404 (tt) cc_final: 0.9044 (pp) REVERT: D 107 ASP cc_start: 0.8458 (t0) cc_final: 0.8019 (t0) REVERT: D 111 LEU cc_start: 0.9309 (mt) cc_final: 0.9097 (mt) REVERT: D 232 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8717 (mp0) REVERT: D 249 TRP cc_start: 0.8000 (t-100) cc_final: 0.7733 (t-100) REVERT: D 255 TYR cc_start: 0.8507 (t80) cc_final: 0.8234 (t80) REVERT: D 281 MET cc_start: 0.9161 (ppp) cc_final: 0.8938 (ppp) REVERT: D 297 MET cc_start: 0.8331 (ptm) cc_final: 0.7312 (ptm) REVERT: D 312 ASP cc_start: 0.7831 (p0) cc_final: 0.7543 (p0) REVERT: D 321 LEU cc_start: 0.8737 (mt) cc_final: 0.8371 (mt) REVERT: D 329 ILE cc_start: 0.9588 (tp) cc_final: 0.9340 (tp) REVERT: D 339 TYR cc_start: 0.7328 (t80) cc_final: 0.6685 (t80) REVERT: D 346 PHE cc_start: 0.9140 (t80) cc_final: 0.8340 (t80) REVERT: D 348 MET cc_start: 0.8985 (mmm) cc_final: 0.7855 (mmm) REVERT: D 376 PHE cc_start: 0.8662 (t80) cc_final: 0.8460 (t80) REVERT: D 388 MET cc_start: 0.7817 (mpp) cc_final: 0.7564 (mpp) REVERT: D 401 LEU cc_start: 0.8887 (tp) cc_final: 0.8594 (tp) REVERT: D 406 LEU cc_start: 0.8862 (mt) cc_final: 0.8628 (mt) REVERT: E 19 GLN cc_start: 0.9424 (tt0) cc_final: 0.8900 (tm-30) REVERT: E 21 LEU cc_start: 0.9286 (tt) cc_final: 0.8990 (mt) REVERT: E 155 LEU cc_start: 0.9202 (tp) cc_final: 0.8958 (tp) REVERT: E 172 PHE cc_start: 0.8363 (t80) cc_final: 0.7845 (t80) REVERT: E 192 SER cc_start: 0.6820 (p) cc_final: 0.6026 (t) REVERT: E 208 ILE cc_start: 0.9455 (pt) cc_final: 0.9157 (pt) REVERT: E 307 LYS cc_start: 0.9408 (mttp) cc_final: 0.9177 (mttm) REVERT: E 314 TYR cc_start: 0.7941 (t80) cc_final: 0.7391 (t80) REVERT: E 351 LEU cc_start: 0.8910 (mt) cc_final: 0.8310 (pp) outliers start: 3 outliers final: 1 residues processed: 431 average time/residue: 0.2553 time to fit residues: 162.6953 Evaluate side-chains 327 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 325 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 83 optimal weight: 0.0980 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 ASN D 79 HIS ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14804 Z= 0.222 Angle : 0.717 16.813 20038 Z= 0.359 Chirality : 0.044 0.203 2295 Planarity : 0.004 0.059 2525 Dihedral : 8.313 79.200 1964 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.12 % Allowed : 5.22 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.06 % 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: -1.46 (0.20), residues: 1733 helix: -0.13 (0.16), residues: 952 sheet: -1.89 (0.41), residues: 142 loop : -1.93 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 301 HIS 0.005 0.001 HIS B 542 PHE 0.028 0.002 PHE C 559 TYR 0.019 0.002 TYR C 132 ARG 0.009 0.001 ARG B 540 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 391 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 GLN cc_start: 0.8809 (pt0) cc_final: 0.8515 (pt0) REVERT: A 801 GLN cc_start: 0.9482 (mm-40) cc_final: 0.9083 (mm110) REVERT: A 809 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8786 (tm-30) REVERT: A 816 MET cc_start: 0.9295 (ptt) cc_final: 0.8804 (pmm) REVERT: A 820 MET cc_start: 0.8331 (mmp) cc_final: 0.8018 (mmm) REVERT: A 826 LEU cc_start: 0.9260 (mt) cc_final: 0.9041 (mt) REVERT: B 324 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8344 (mp0) REVERT: B 330 MET cc_start: 0.8040 (mtm) cc_final: 0.7731 (mmm) REVERT: B 426 HIS cc_start: 0.8473 (t-90) cc_final: 0.8266 (t70) REVERT: B 432 MET cc_start: 0.7802 (ptt) cc_final: 0.7297 (ptm) REVERT: B 517 TYR cc_start: 0.8083 (t80) cc_final: 0.7877 (t80) REVERT: B 532 LEU cc_start: 0.9083 (tp) cc_final: 0.8880 (tp) REVERT: B 536 LEU cc_start: 0.9002 (mt) cc_final: 0.8714 (tt) REVERT: B 537 THR cc_start: 0.8401 (t) cc_final: 0.7622 (p) REVERT: C 77 LEU cc_start: 0.9407 (mt) cc_final: 0.9003 (pp) REVERT: C 144 MET cc_start: 0.8085 (mmp) cc_final: 0.6642 (mmp) REVERT: C 148 LEU cc_start: 0.8963 (tp) cc_final: 0.8569 (tt) REVERT: C 219 LEU cc_start: 0.9308 (mt) cc_final: 0.8980 (mt) REVERT: C 285 LEU cc_start: 0.9123 (tt) cc_final: 0.8868 (tt) REVERT: C 313 ILE cc_start: 0.9099 (pt) cc_final: 0.8775 (pt) REVERT: C 326 LYS cc_start: 0.9536 (ttpt) cc_final: 0.9299 (ttmt) REVERT: C 410 MET cc_start: 0.9450 (mtm) cc_final: 0.9152 (ptm) REVERT: C 472 LEU cc_start: 0.9247 (mt) cc_final: 0.8980 (mt) REVERT: C 582 PHE cc_start: 0.6477 (t80) cc_final: 0.6262 (t80) REVERT: C 592 LEU cc_start: 0.9035 (tp) cc_final: 0.8819 (tp) REVERT: C 688 LEU cc_start: 0.9269 (mm) cc_final: 0.9065 (mm) REVERT: D 28 PHE cc_start: 0.8529 (m-10) cc_final: 0.8267 (m-80) REVERT: D 38 PHE cc_start: 0.6902 (t80) cc_final: 0.6675 (t80) REVERT: D 75 MET cc_start: 0.9285 (ptt) cc_final: 0.9039 (ptm) REVERT: D 84 LEU cc_start: 0.9751 (pp) cc_final: 0.9393 (pp) REVERT: D 107 ASP cc_start: 0.8425 (t0) cc_final: 0.7980 (t0) REVERT: D 111 LEU cc_start: 0.9315 (mt) cc_final: 0.9087 (mt) REVERT: D 177 PHE cc_start: 0.8244 (m-80) cc_final: 0.8009 (m-10) REVERT: D 297 MET cc_start: 0.7985 (ptm) cc_final: 0.7380 (ttp) REVERT: D 321 LEU cc_start: 0.8858 (mt) cc_final: 0.8515 (mt) REVERT: D 329 ILE cc_start: 0.9558 (tp) cc_final: 0.9340 (tp) REVERT: D 333 LYS cc_start: 0.9329 (tmmt) cc_final: 0.9025 (mtpt) REVERT: D 348 MET cc_start: 0.9115 (mmm) cc_final: 0.8266 (mmm) REVERT: D 376 PHE cc_start: 0.8876 (t80) cc_final: 0.8572 (t80) REVERT: E 19 GLN cc_start: 0.9455 (tt0) cc_final: 0.8761 (tm-30) REVERT: E 105 LEU cc_start: 0.8099 (mt) cc_final: 0.7839 (mt) REVERT: E 129 TYR cc_start: 0.8443 (m-10) cc_final: 0.8174 (m-10) REVERT: E 132 ASP cc_start: 0.9407 (m-30) cc_final: 0.9150 (p0) REVERT: E 160 ILE cc_start: 0.9401 (tt) cc_final: 0.8927 (mt) REVERT: E 168 ASN cc_start: 0.7039 (m-40) cc_final: 0.6819 (m110) REVERT: E 172 PHE cc_start: 0.8703 (t80) cc_final: 0.8161 (t80) REVERT: E 191 LEU cc_start: 0.9008 (tp) cc_final: 0.8592 (tp) REVERT: E 314 TYR cc_start: 0.7952 (t80) cc_final: 0.7344 (t80) REVERT: E 351 LEU cc_start: 0.8957 (mt) cc_final: 0.8560 (pp) outliers start: 2 outliers final: 1 residues processed: 393 average time/residue: 0.2401 time to fit residues: 140.3393 Evaluate side-chains 316 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 HIS B 362 HIS B 372 GLN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 356 ASN C 399 GLN C 406 HIS ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.7283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14804 Z= 0.277 Angle : 0.748 16.426 20038 Z= 0.377 Chirality : 0.044 0.170 2295 Planarity : 0.005 0.063 2525 Dihedral : 8.294 74.006 1964 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.12 % Allowed : 3.99 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.06 % 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: -1.32 (0.20), residues: 1733 helix: -0.07 (0.16), residues: 961 sheet: -1.67 (0.43), residues: 136 loop : -1.82 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 301 HIS 0.006 0.001 HIS D 57 PHE 0.027 0.002 PHE C 559 TYR 0.020 0.002 TYR C 47 ARG 0.013 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 368 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 PHE cc_start: 0.9598 (t80) cc_final: 0.9393 (t80) REVERT: A 801 GLN cc_start: 0.9485 (mm-40) cc_final: 0.9059 (mt0) REVERT: A 816 MET cc_start: 0.9354 (ptt) cc_final: 0.9056 (pmm) REVERT: A 826 LEU cc_start: 0.9258 (mt) cc_final: 0.9040 (mt) REVERT: B 298 PHE cc_start: 0.8327 (m-10) cc_final: 0.8001 (m-80) REVERT: B 324 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8509 (mt-10) REVERT: B 330 MET cc_start: 0.8066 (mtm) cc_final: 0.7788 (mmm) REVERT: B 426 HIS cc_start: 0.8513 (t-90) cc_final: 0.8151 (t70) REVERT: B 432 MET cc_start: 0.7849 (ptt) cc_final: 0.7342 (ptm) REVERT: B 532 LEU cc_start: 0.9121 (tp) cc_final: 0.8907 (tt) REVERT: B 536 LEU cc_start: 0.9020 (mt) cc_final: 0.8736 (tt) REVERT: C 77 LEU cc_start: 0.9425 (mt) cc_final: 0.9007 (pp) REVERT: C 148 LEU cc_start: 0.9089 (tp) cc_final: 0.8666 (tt) REVERT: C 285 LEU cc_start: 0.9122 (tt) cc_final: 0.8902 (tt) REVERT: C 293 LEU cc_start: 0.9048 (pt) cc_final: 0.8116 (mm) REVERT: C 313 ILE cc_start: 0.9033 (pt) cc_final: 0.8790 (pt) REVERT: C 326 LYS cc_start: 0.9505 (ttpt) cc_final: 0.8924 (tttp) REVERT: C 333 LEU cc_start: 0.9690 (mt) cc_final: 0.9475 (mt) REVERT: C 410 MET cc_start: 0.9473 (mtm) cc_final: 0.9177 (ptm) REVERT: C 412 TYR cc_start: 0.8547 (t80) cc_final: 0.8325 (t80) REVERT: C 663 MET cc_start: 0.7648 (mtt) cc_final: 0.6254 (ppp) REVERT: C 688 LEU cc_start: 0.9286 (mm) cc_final: 0.9010 (mm) REVERT: D 38 PHE cc_start: 0.7053 (t80) cc_final: 0.6668 (t80) REVERT: D 75 MET cc_start: 0.9247 (ptt) cc_final: 0.8968 (ptt) REVERT: D 107 ASP cc_start: 0.8525 (t0) cc_final: 0.8115 (t0) REVERT: D 177 PHE cc_start: 0.8309 (m-80) cc_final: 0.8074 (m-10) REVERT: D 297 MET cc_start: 0.7951 (ptm) cc_final: 0.7246 (ttp) REVERT: D 312 ASP cc_start: 0.8152 (p0) cc_final: 0.7890 (p0) REVERT: D 321 LEU cc_start: 0.8895 (mt) cc_final: 0.8470 (mt) REVERT: D 339 TYR cc_start: 0.7606 (t80) cc_final: 0.7291 (t80) REVERT: D 348 MET cc_start: 0.9174 (mmm) cc_final: 0.8578 (mpp) REVERT: D 350 TYR cc_start: 0.8952 (t80) cc_final: 0.8747 (t80) REVERT: E 105 LEU cc_start: 0.7947 (mt) cc_final: 0.7666 (mt) REVERT: E 129 TYR cc_start: 0.8351 (m-10) cc_final: 0.7922 (m-10) REVERT: E 130 LEU cc_start: 0.9407 (tt) cc_final: 0.9176 (tt) REVERT: E 132 ASP cc_start: 0.9463 (m-30) cc_final: 0.9150 (p0) REVERT: E 133 MET cc_start: 0.8387 (mmm) cc_final: 0.8157 (mmm) REVERT: E 141 PHE cc_start: 0.8086 (m-80) cc_final: 0.7830 (m-80) REVERT: E 160 ILE cc_start: 0.9386 (tt) cc_final: 0.8834 (mt) REVERT: E 309 ILE cc_start: 0.9537 (mm) cc_final: 0.9290 (mm) REVERT: E 314 TYR cc_start: 0.8420 (t80) cc_final: 0.7669 (t80) outliers start: 2 outliers final: 1 residues processed: 370 average time/residue: 0.2671 time to fit residues: 148.4708 Evaluate side-chains 305 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 78 optimal weight: 0.0770 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN B 438 GLN C 52 GLN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS D 21 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN E 227 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.7553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14804 Z= 0.180 Angle : 0.691 13.795 20038 Z= 0.339 Chirality : 0.043 0.196 2295 Planarity : 0.004 0.062 2525 Dihedral : 7.798 77.679 1964 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.12 % Allowed : 2.64 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.89 (0.20), residues: 1733 helix: 0.32 (0.17), residues: 947 sheet: -1.10 (0.45), residues: 124 loop : -1.78 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 301 HIS 0.009 0.001 HIS C 335 PHE 0.028 0.002 PHE C 559 TYR 0.027 0.001 TYR E 304 ARG 0.012 0.001 ARG D 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 401 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 801 GLN cc_start: 0.9444 (mm-40) cc_final: 0.9001 (mt0) REVERT: A 809 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8780 (tm-30) REVERT: A 826 LEU cc_start: 0.9245 (mt) cc_final: 0.8995 (mt) REVERT: B 393 HIS cc_start: 0.7991 (m-70) cc_final: 0.7755 (m-70) REVERT: B 432 MET cc_start: 0.8221 (ptt) cc_final: 0.7676 (ptm) REVERT: B 536 LEU cc_start: 0.9018 (mt) cc_final: 0.8674 (tt) REVERT: B 537 THR cc_start: 0.8475 (t) cc_final: 0.7689 (p) REVERT: C 77 LEU cc_start: 0.9277 (mt) cc_final: 0.8888 (pp) REVERT: C 148 LEU cc_start: 0.9055 (tp) cc_final: 0.8592 (tt) REVERT: C 219 LEU cc_start: 0.9218 (mt) cc_final: 0.9004 (mt) REVERT: C 293 LEU cc_start: 0.8794 (pt) cc_final: 0.8096 (mm) REVERT: C 312 ASN cc_start: 0.8846 (t0) cc_final: 0.7323 (t0) REVERT: C 313 ILE cc_start: 0.9057 (pt) cc_final: 0.8827 (pt) REVERT: C 334 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8348 (tp30) REVERT: C 410 MET cc_start: 0.9437 (mtm) cc_final: 0.9199 (ptp) REVERT: D 28 PHE cc_start: 0.8358 (m-10) cc_final: 0.8153 (m-80) REVERT: D 38 PHE cc_start: 0.6719 (t80) cc_final: 0.6437 (t80) REVERT: D 75 MET cc_start: 0.9119 (ptt) cc_final: 0.8879 (ptt) REVERT: D 81 LEU cc_start: 0.9373 (mt) cc_final: 0.9114 (mt) REVERT: D 107 ASP cc_start: 0.8533 (t0) cc_final: 0.8212 (t0) REVERT: D 169 ASN cc_start: 0.8533 (t0) cc_final: 0.8286 (t0) REVERT: D 311 MET cc_start: 0.6059 (mpp) cc_final: 0.4657 (mpp) REVERT: D 312 ASP cc_start: 0.8005 (p0) cc_final: 0.7706 (p0) REVERT: D 321 LEU cc_start: 0.8642 (mt) cc_final: 0.8301 (mt) REVERT: D 350 TYR cc_start: 0.8873 (t80) cc_final: 0.8549 (t80) REVERT: D 378 HIS cc_start: 0.9143 (t70) cc_final: 0.8759 (t70) REVERT: D 406 LEU cc_start: 0.8797 (mt) cc_final: 0.8475 (mt) REVERT: E 34 PHE cc_start: 0.8974 (t80) cc_final: 0.8609 (t80) REVERT: E 105 LEU cc_start: 0.7834 (mt) cc_final: 0.7447 (mt) REVERT: E 132 ASP cc_start: 0.9444 (m-30) cc_final: 0.9100 (p0) REVERT: E 141 PHE cc_start: 0.8034 (m-80) cc_final: 0.7805 (m-80) REVERT: E 160 ILE cc_start: 0.9456 (tt) cc_final: 0.8924 (mt) REVERT: E 163 GLU cc_start: 0.9040 (mp0) cc_final: 0.8823 (mp0) REVERT: E 208 ILE cc_start: 0.9402 (pt) cc_final: 0.9154 (pt) REVERT: E 309 ILE cc_start: 0.9511 (mm) cc_final: 0.9298 (mm) REVERT: E 314 TYR cc_start: 0.7941 (t80) cc_final: 0.7122 (t80) REVERT: E 416 ILE cc_start: 0.9050 (mm) cc_final: 0.8833 (mm) outliers start: 2 outliers final: 1 residues processed: 403 average time/residue: 0.2414 time to fit residues: 145.0063 Evaluate side-chains 312 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 311 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 143 optimal weight: 7.9990 chunk 95 optimal weight: 0.0470 chunk 169 optimal weight: 1.9990 chunk 106 optimal weight: 0.0570 chunk 103 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.7852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14804 Z= 0.174 Angle : 0.686 10.573 20038 Z= 0.339 Chirality : 0.043 0.215 2295 Planarity : 0.004 0.058 2525 Dihedral : 7.597 81.122 1964 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.06 % Allowed : 2.09 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -1.03 (0.20), residues: 1733 helix: 0.12 (0.17), residues: 970 sheet: -0.81 (0.45), residues: 126 loop : -1.84 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP B 301 HIS 0.009 0.001 HIS C 486 PHE 0.027 0.002 PHE B 492 TYR 0.020 0.001 TYR E 304 ARG 0.009 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 389 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 809 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8832 (tm-30) REVERT: A 816 MET cc_start: 0.9477 (pmm) cc_final: 0.9219 (pmm) REVERT: A 826 LEU cc_start: 0.9272 (mt) cc_final: 0.8965 (mt) REVERT: B 324 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8431 (mt-10) REVERT: B 432 MET cc_start: 0.8173 (ptt) cc_final: 0.7639 (ptm) REVERT: B 536 LEU cc_start: 0.8978 (mt) cc_final: 0.8658 (tt) REVERT: B 537 THR cc_start: 0.8475 (t) cc_final: 0.7725 (p) REVERT: C 54 MET cc_start: 0.9292 (mmp) cc_final: 0.9036 (mmm) REVERT: C 77 LEU cc_start: 0.9296 (mt) cc_final: 0.8876 (pp) REVERT: C 139 LYS cc_start: 0.8629 (ptpt) cc_final: 0.8200 (ptpp) REVERT: C 148 LEU cc_start: 0.9101 (tp) cc_final: 0.8537 (tt) REVERT: C 293 LEU cc_start: 0.8796 (pt) cc_final: 0.7814 (mm) REVERT: C 312 ASN cc_start: 0.8921 (t0) cc_final: 0.8068 (t0) REVERT: C 313 ILE cc_start: 0.9027 (pt) cc_final: 0.8699 (pt) REVERT: C 333 LEU cc_start: 0.9692 (mt) cc_final: 0.9485 (mt) REVERT: C 334 GLU cc_start: 0.9153 (mt-10) cc_final: 0.7901 (tp30) REVERT: C 410 MET cc_start: 0.9496 (mtm) cc_final: 0.9129 (ptp) REVERT: C 582 PHE cc_start: 0.6844 (t80) cc_final: 0.5754 (t80) REVERT: C 588 LEU cc_start: 0.9069 (mm) cc_final: 0.8743 (mm) REVERT: C 693 PHE cc_start: 0.8554 (m-80) cc_final: 0.8227 (m-80) REVERT: D 38 PHE cc_start: 0.6764 (t80) cc_final: 0.6455 (t80) REVERT: D 75 MET cc_start: 0.9005 (ptt) cc_final: 0.8565 (ptt) REVERT: D 81 LEU cc_start: 0.9352 (mt) cc_final: 0.9105 (mt) REVERT: D 107 ASP cc_start: 0.8651 (t0) cc_final: 0.8199 (t0) REVERT: D 169 ASN cc_start: 0.8521 (t0) cc_final: 0.8268 (t0) REVERT: D 255 TYR cc_start: 0.8537 (t80) cc_final: 0.8279 (t80) REVERT: D 269 HIS cc_start: 0.8933 (m-70) cc_final: 0.8515 (m-70) REVERT: D 281 MET cc_start: 0.9063 (ppp) cc_final: 0.8829 (ppp) REVERT: D 285 LEU cc_start: 0.9258 (mp) cc_final: 0.8839 (mp) REVERT: D 312 ASP cc_start: 0.8015 (p0) cc_final: 0.7719 (p0) REVERT: D 321 LEU cc_start: 0.8637 (mt) cc_final: 0.8320 (mt) REVERT: D 348 MET cc_start: 0.9292 (mtm) cc_final: 0.9062 (mtm) REVERT: D 350 TYR cc_start: 0.8891 (t80) cc_final: 0.8581 (t80) REVERT: D 351 ASN cc_start: 0.9441 (t0) cc_final: 0.9060 (t0) REVERT: D 352 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8813 (mm-30) REVERT: D 378 HIS cc_start: 0.9167 (t70) cc_final: 0.8823 (t70) REVERT: D 399 TYR cc_start: 0.8303 (p90) cc_final: 0.7974 (p90) REVERT: D 428 TRP cc_start: 0.6998 (t-100) cc_final: 0.5594 (t-100) REVERT: E 105 LEU cc_start: 0.7891 (mt) cc_final: 0.7545 (mt) REVERT: E 132 ASP cc_start: 0.9375 (m-30) cc_final: 0.9107 (p0) REVERT: E 133 MET cc_start: 0.8456 (mmm) cc_final: 0.7825 (mmm) REVERT: E 141 PHE cc_start: 0.8341 (m-80) cc_final: 0.8047 (m-80) REVERT: E 160 ILE cc_start: 0.9400 (tt) cc_final: 0.8887 (mt) REVERT: E 168 ASN cc_start: 0.7779 (m110) cc_final: 0.7426 (t0) REVERT: E 208 ILE cc_start: 0.9299 (pt) cc_final: 0.9068 (pt) REVERT: E 314 TYR cc_start: 0.7816 (t80) cc_final: 0.7028 (t80) REVERT: E 383 GLN cc_start: 0.8897 (pp30) cc_final: 0.8679 (pp30) REVERT: E 416 ILE cc_start: 0.9009 (mm) cc_final: 0.8738 (mm) outliers start: 1 outliers final: 1 residues processed: 390 average time/residue: 0.2327 time to fit residues: 137.0776 Evaluate side-chains 312 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 311 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 32 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 HIS B 426 HIS ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** 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 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.8139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14804 Z= 0.219 Angle : 0.716 11.863 20038 Z= 0.358 Chirality : 0.044 0.224 2295 Planarity : 0.004 0.053 2525 Dihedral : 7.676 82.819 1964 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.06 % Allowed : 1.23 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.92 (0.20), residues: 1733 helix: 0.24 (0.17), residues: 948 sheet: -0.83 (0.46), residues: 125 loop : -1.78 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP B 301 HIS 0.008 0.001 HIS C 486 PHE 0.028 0.002 PHE B 539 TYR 0.022 0.002 TYR E 304 ARG 0.008 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 371 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 809 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8911 (tm-30) REVERT: A 826 LEU cc_start: 0.9306 (mt) cc_final: 0.8954 (mt) REVERT: B 324 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8483 (mt-10) REVERT: B 432 MET cc_start: 0.8060 (ptt) cc_final: 0.7704 (ptm) REVERT: B 536 LEU cc_start: 0.8986 (mt) cc_final: 0.8673 (tt) REVERT: B 537 THR cc_start: 0.8549 (t) cc_final: 0.7785 (p) REVERT: C 54 MET cc_start: 0.9292 (mmp) cc_final: 0.9017 (mmm) REVERT: C 77 LEU cc_start: 0.9316 (mt) cc_final: 0.8889 (pp) REVERT: C 148 LEU cc_start: 0.8953 (tp) cc_final: 0.8525 (tt) REVERT: C 293 LEU cc_start: 0.8861 (pt) cc_final: 0.7896 (mm) REVERT: C 312 ASN cc_start: 0.8950 (t0) cc_final: 0.7631 (t0) REVERT: C 313 ILE cc_start: 0.9057 (pt) cc_final: 0.8556 (pt) REVERT: C 334 GLU cc_start: 0.9164 (mt-10) cc_final: 0.7854 (tp30) REVERT: C 410 MET cc_start: 0.9511 (mtm) cc_final: 0.9195 (ptp) REVERT: C 582 PHE cc_start: 0.6777 (t80) cc_final: 0.6001 (t80) REVERT: C 588 LEU cc_start: 0.9189 (mm) cc_final: 0.8857 (mm) REVERT: C 688 LEU cc_start: 0.9429 (mm) cc_final: 0.9224 (mm) REVERT: D 38 PHE cc_start: 0.6895 (t80) cc_final: 0.6586 (t80) REVERT: D 75 MET cc_start: 0.9034 (ptt) cc_final: 0.8650 (ptt) REVERT: D 81 LEU cc_start: 0.9419 (mt) cc_final: 0.9069 (mt) REVERT: D 104 GLN cc_start: 0.8687 (mp10) cc_final: 0.8465 (mp10) REVERT: D 107 ASP cc_start: 0.8504 (t0) cc_final: 0.8000 (t0) REVERT: D 169 ASN cc_start: 0.8559 (t0) cc_final: 0.8316 (t0) REVERT: D 255 TYR cc_start: 0.8524 (t80) cc_final: 0.8308 (t80) REVERT: D 269 HIS cc_start: 0.8863 (m-70) cc_final: 0.8498 (m-70) REVERT: D 297 MET cc_start: 0.7705 (ptm) cc_final: 0.7024 (ppp) REVERT: D 312 ASP cc_start: 0.8115 (p0) cc_final: 0.7819 (p0) REVERT: D 321 LEU cc_start: 0.8885 (mt) cc_final: 0.8501 (mt) REVERT: D 348 MET cc_start: 0.9333 (mtm) cc_final: 0.9114 (mtm) REVERT: D 351 ASN cc_start: 0.9434 (t0) cc_final: 0.9114 (t0) REVERT: D 352 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8708 (mm-30) REVERT: D 378 HIS cc_start: 0.9263 (t70) cc_final: 0.8924 (t70) REVERT: D 399 TYR cc_start: 0.8472 (p90) cc_final: 0.7975 (p90) REVERT: D 402 MET cc_start: 0.7695 (mpp) cc_final: 0.7418 (mmt) REVERT: D 412 MET cc_start: 0.9040 (mmt) cc_final: 0.8835 (mmm) REVERT: D 428 TRP cc_start: 0.7192 (t-100) cc_final: 0.5680 (t-100) REVERT: E 34 PHE cc_start: 0.8995 (t80) cc_final: 0.8676 (t80) REVERT: E 105 LEU cc_start: 0.7922 (mt) cc_final: 0.7704 (mt) REVERT: E 132 ASP cc_start: 0.9468 (m-30) cc_final: 0.9217 (p0) REVERT: E 141 PHE cc_start: 0.8324 (m-80) cc_final: 0.8065 (m-80) REVERT: E 160 ILE cc_start: 0.9331 (tt) cc_final: 0.8883 (mt) REVERT: E 314 TYR cc_start: 0.8020 (t80) cc_final: 0.7207 (t80) REVERT: E 383 GLN cc_start: 0.9015 (pp30) cc_final: 0.8667 (pp30) REVERT: E 416 ILE cc_start: 0.9074 (mm) cc_final: 0.8831 (mm) outliers start: 1 outliers final: 1 residues processed: 372 average time/residue: 0.2325 time to fit residues: 131.2399 Evaluate side-chains 300 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 68 optimal weight: 0.0670 chunk 124 optimal weight: 0.0870 chunk 48 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 HIS B 435 HIS ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 HIS ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 HIS ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** E 27 HIS ** 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 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.8335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14804 Z= 0.176 Angle : 0.727 13.171 20038 Z= 0.355 Chirality : 0.044 0.197 2295 Planarity : 0.004 0.058 2525 Dihedral : 7.334 86.215 1964 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.12 % Allowed : 0.86 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1733 helix: 0.15 (0.17), residues: 963 sheet: -0.74 (0.47), residues: 121 loop : -1.84 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP B 301 HIS 0.008 0.001 HIS C 486 PHE 0.026 0.002 PHE C 479 TYR 0.018 0.001 TYR E 304 ARG 0.012 0.001 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 390 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 801 GLN cc_start: 0.9363 (mm-40) cc_final: 0.8843 (mt0) REVERT: A 809 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8833 (tm-30) REVERT: A 826 LEU cc_start: 0.9247 (mt) cc_final: 0.8979 (mt) REVERT: B 324 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8405 (mt-10) REVERT: B 403 GLU cc_start: 0.8759 (mp0) cc_final: 0.8440 (mp0) REVERT: B 426 HIS cc_start: 0.7841 (t-90) cc_final: 0.7640 (t70) REVERT: B 432 MET cc_start: 0.8037 (ptt) cc_final: 0.7682 (ptm) REVERT: B 440 LEU cc_start: 0.9282 (mm) cc_final: 0.8659 (tp) REVERT: B 536 LEU cc_start: 0.8995 (mt) cc_final: 0.8692 (tt) REVERT: B 537 THR cc_start: 0.8532 (t) cc_final: 0.7773 (p) REVERT: C 77 LEU cc_start: 0.9242 (mt) cc_final: 0.8775 (pp) REVERT: C 148 LEU cc_start: 0.8977 (tp) cc_final: 0.8491 (tt) REVERT: C 293 LEU cc_start: 0.8725 (pt) cc_final: 0.7944 (mm) REVERT: C 312 ASN cc_start: 0.8967 (t0) cc_final: 0.7915 (t0) REVERT: C 313 ILE cc_start: 0.8955 (pt) cc_final: 0.8701 (pt) REVERT: C 334 GLU cc_start: 0.9119 (mt-10) cc_final: 0.7886 (tp30) REVERT: C 410 MET cc_start: 0.9513 (mtm) cc_final: 0.9118 (ptp) REVERT: C 582 PHE cc_start: 0.6825 (t80) cc_final: 0.5794 (t80) REVERT: C 588 LEU cc_start: 0.9185 (mm) cc_final: 0.8822 (mm) REVERT: C 688 LEU cc_start: 0.9401 (mm) cc_final: 0.9157 (mm) REVERT: D 38 PHE cc_start: 0.6740 (t80) cc_final: 0.6472 (t80) REVERT: D 75 MET cc_start: 0.8907 (ptt) cc_final: 0.8473 (ptt) REVERT: D 81 LEU cc_start: 0.9358 (mt) cc_final: 0.8960 (mt) REVERT: D 104 GLN cc_start: 0.8618 (mp10) cc_final: 0.8318 (mp10) REVERT: D 107 ASP cc_start: 0.8539 (t0) cc_final: 0.8050 (t0) REVERT: D 169 ASN cc_start: 0.8468 (t0) cc_final: 0.8189 (t0) REVERT: D 232 GLU cc_start: 0.9182 (mp0) cc_final: 0.8949 (pm20) REVERT: D 269 HIS cc_start: 0.8873 (m-70) cc_final: 0.8427 (m-70) REVERT: D 297 MET cc_start: 0.7251 (ptm) cc_final: 0.6591 (ttp) REVERT: D 312 ASP cc_start: 0.7936 (p0) cc_final: 0.7664 (p0) REVERT: D 321 LEU cc_start: 0.8691 (mt) cc_final: 0.8414 (mt) REVERT: D 332 MET cc_start: 0.9522 (pmm) cc_final: 0.9260 (pmm) REVERT: D 339 TYR cc_start: 0.7662 (t80) cc_final: 0.7254 (t80) REVERT: D 348 MET cc_start: 0.9328 (mtm) cc_final: 0.9058 (mtm) REVERT: D 351 ASN cc_start: 0.9437 (t0) cc_final: 0.9193 (t0) REVERT: D 352 GLU cc_start: 0.9370 (mm-30) cc_final: 0.8799 (mm-30) REVERT: D 378 HIS cc_start: 0.9264 (t70) cc_final: 0.8914 (t70) REVERT: D 399 TYR cc_start: 0.8426 (p90) cc_final: 0.7956 (p90) REVERT: D 428 TRP cc_start: 0.7348 (t-100) cc_final: 0.5999 (t-100) REVERT: E 34 PHE cc_start: 0.8839 (t80) cc_final: 0.8586 (t80) REVERT: E 105 LEU cc_start: 0.7985 (mt) cc_final: 0.7745 (mt) REVERT: E 132 ASP cc_start: 0.9447 (m-30) cc_final: 0.9153 (p0) REVERT: E 141 PHE cc_start: 0.8276 (m-80) cc_final: 0.8018 (m-80) REVERT: E 208 ILE cc_start: 0.9222 (pt) cc_final: 0.9010 (pt) REVERT: E 314 TYR cc_start: 0.7820 (t80) cc_final: 0.7103 (t80) REVERT: E 383 GLN cc_start: 0.8837 (pp30) cc_final: 0.8549 (pp30) REVERT: E 415 PHE cc_start: 0.8754 (t80) cc_final: 0.8465 (t80) REVERT: E 416 ILE cc_start: 0.8987 (mm) cc_final: 0.8688 (mm) outliers start: 2 outliers final: 1 residues processed: 391 average time/residue: 0.2336 time to fit residues: 137.5504 Evaluate side-chains 319 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 318 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 175 optimal weight: 0.0980 chunk 161 optimal weight: 10.0000 chunk 139 optimal weight: 0.2980 chunk 14 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** 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 168 ASN E 227 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.8573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14804 Z= 0.178 Angle : 0.719 13.948 20038 Z= 0.349 Chirality : 0.044 0.175 2295 Planarity : 0.004 0.051 2525 Dihedral : 7.119 89.968 1964 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.12 % Allowed : 0.43 % Favored : 99.45 % 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: -0.87 (0.20), residues: 1733 helix: 0.29 (0.17), residues: 956 sheet: -0.59 (0.45), residues: 130 loop : -1.84 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP B 301 HIS 0.004 0.001 HIS D 269 PHE 0.028 0.002 PHE B 539 TYR 0.018 0.001 TYR C 47 ARG 0.006 0.000 ARG D 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 385 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 801 GLN cc_start: 0.9380 (mm-40) cc_final: 0.8859 (mt0) REVERT: A 809 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8850 (tm-30) REVERT: A 826 LEU cc_start: 0.9240 (mt) cc_final: 0.8985 (mt) REVERT: B 324 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8383 (mt-10) REVERT: B 440 LEU cc_start: 0.9212 (mm) cc_final: 0.8538 (tp) REVERT: B 536 LEU cc_start: 0.9000 (mt) cc_final: 0.8687 (tt) REVERT: B 537 THR cc_start: 0.8537 (t) cc_final: 0.7766 (p) REVERT: C 51 TRP cc_start: 0.8151 (t60) cc_final: 0.7872 (t60) REVERT: C 54 MET cc_start: 0.9256 (mmp) cc_final: 0.8975 (mmm) REVERT: C 77 LEU cc_start: 0.9258 (mt) cc_final: 0.8800 (pp) REVERT: C 148 LEU cc_start: 0.8959 (tp) cc_final: 0.8416 (tt) REVERT: C 293 LEU cc_start: 0.8750 (pt) cc_final: 0.7620 (mm) REVERT: C 312 ASN cc_start: 0.8964 (t0) cc_final: 0.7940 (t0) REVERT: C 313 ILE cc_start: 0.9004 (pt) cc_final: 0.8751 (pt) REVERT: C 318 ASP cc_start: 0.8364 (t70) cc_final: 0.8149 (t70) REVERT: C 334 GLU cc_start: 0.9137 (mt-10) cc_final: 0.7792 (tp30) REVERT: C 410 MET cc_start: 0.9488 (mtm) cc_final: 0.9143 (ptp) REVERT: C 582 PHE cc_start: 0.6815 (t80) cc_final: 0.5800 (t80) REVERT: C 588 LEU cc_start: 0.9119 (mm) cc_final: 0.8805 (mm) REVERT: C 688 LEU cc_start: 0.9405 (mm) cc_final: 0.9176 (mm) REVERT: D 38 PHE cc_start: 0.6696 (t80) cc_final: 0.6360 (t80) REVERT: D 104 GLN cc_start: 0.8726 (mp10) cc_final: 0.8478 (mp10) REVERT: D 107 ASP cc_start: 0.8713 (t0) cc_final: 0.8275 (t0) REVERT: D 169 ASN cc_start: 0.8473 (t0) cc_final: 0.8204 (t0) REVERT: D 232 GLU cc_start: 0.9184 (mp0) cc_final: 0.8890 (pm20) REVERT: D 256 LEU cc_start: 0.9131 (mp) cc_final: 0.8733 (mp) REVERT: D 259 ASP cc_start: 0.8189 (m-30) cc_final: 0.7766 (m-30) REVERT: D 269 HIS cc_start: 0.8909 (m-70) cc_final: 0.8302 (m-70) REVERT: D 275 ASN cc_start: 0.9319 (p0) cc_final: 0.8905 (p0) REVERT: D 297 MET cc_start: 0.7348 (ptm) cc_final: 0.6316 (ttm) REVERT: D 312 ASP cc_start: 0.7953 (p0) cc_final: 0.7600 (p0) REVERT: D 321 LEU cc_start: 0.8669 (mt) cc_final: 0.8375 (mt) REVERT: D 332 MET cc_start: 0.9517 (pmm) cc_final: 0.9273 (pmm) REVERT: D 339 TYR cc_start: 0.7688 (t80) cc_final: 0.7212 (t80) REVERT: D 348 MET cc_start: 0.9334 (mtm) cc_final: 0.9063 (mtm) REVERT: D 351 ASN cc_start: 0.9414 (t0) cc_final: 0.9122 (t0) REVERT: D 352 GLU cc_start: 0.9405 (mm-30) cc_final: 0.8847 (mm-30) REVERT: D 378 HIS cc_start: 0.9223 (t70) cc_final: 0.9011 (t70) REVERT: D 399 TYR cc_start: 0.8082 (p90) cc_final: 0.7753 (p90) REVERT: D 428 TRP cc_start: 0.7381 (t-100) cc_final: 0.6084 (t-100) REVERT: E 105 LEU cc_start: 0.7926 (mt) cc_final: 0.7666 (mt) REVERT: E 129 TYR cc_start: 0.8530 (m-10) cc_final: 0.7531 (m-10) REVERT: E 132 ASP cc_start: 0.9386 (m-30) cc_final: 0.9121 (p0) REVERT: E 133 MET cc_start: 0.8479 (mmm) cc_final: 0.7547 (mmm) REVERT: E 141 PHE cc_start: 0.8324 (m-80) cc_final: 0.7984 (m-80) REVERT: E 314 TYR cc_start: 0.7856 (t80) cc_final: 0.7141 (t80) REVERT: E 383 GLN cc_start: 0.8902 (pp30) cc_final: 0.8546 (pp30) REVERT: E 416 ILE cc_start: 0.8980 (mm) cc_final: 0.8688 (mm) outliers start: 2 outliers final: 1 residues processed: 386 average time/residue: 0.2312 time to fit residues: 134.9545 Evaluate side-chains 320 residues out of total 1642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 319 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 GLN B 426 HIS ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 HIS ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** 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 227 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.070049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.053676 restraints weight = 72480.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055300 restraints weight = 52160.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.056507 restraints weight = 40241.316| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.8756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14804 Z= 0.178 Angle : 0.707 13.758 20038 Z= 0.344 Chirality : 0.044 0.203 2295 Planarity : 0.004 0.052 2525 Dihedral : 7.024 86.978 1964 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.12 % Allowed : 0.55 % Favored : 99.32 % 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: -0.82 (0.21), residues: 1733 helix: 0.32 (0.17), residues: 953 sheet: -0.71 (0.44), residues: 138 loop : -1.78 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 301 HIS 0.011 0.001 HIS C 678 PHE 0.026 0.002 PHE C 479 TYR 0.018 0.001 TYR C 47 ARG 0.007 0.001 ARG E 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3442.40 seconds wall clock time: 62 minutes 46.46 seconds (3766.46 seconds total)