Starting phenix.real_space_refine on Fri Feb 16 08:39:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpp_22418/02_2024/7jpp_22418_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpp_22418/02_2024/7jpp_22418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpp_22418/02_2024/7jpp_22418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpp_22418/02_2024/7jpp_22418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpp_22418/02_2024/7jpp_22418_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpp_22418/02_2024/7jpp_22418_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 9547 2.51 5 N 2516 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 792": "OE1" <-> "OE2" Residue "A TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 860": "OD1" <-> "OD2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B GLU 574": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ASP 232": "OD1" <-> "OD2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 451": "OE1" <-> "OE2" Residue "C TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 675": "OE1" <-> "OE2" Residue "C ARG 680": "NH1" <-> "NH2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 159": "OD1" <-> "OD2" Residue "D TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D ASP 424": "OD1" <-> "OD2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 221": "OD1" <-> "OD2" Residue "E GLU 247": "OE1" <-> "OE2" Residue "E ARG 248": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 271": "NH1" <-> "NH2" Residue "E GLU 272": "OE1" <-> "OE2" Residue "E ASP 284": "OD1" <-> "OD2" Residue "E ASP 360": "OD1" <-> "OD2" Residue "E ASP 371": "OD1" <-> "OD2" Residue "E PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14872 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 790 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "B" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2515 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 8, 'TRANS': 298} Chain: "C" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4886 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 24, 'TRANS': 572} Chain breaks: 7 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: 1 Chain: "E" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3312 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 19, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.39, per 1000 atoms: 0.56 Number of scatterers: 14872 At special positions: 0 Unit cell: (93.09, 119.84, 154.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 6 15.00 Mg 2 11.99 O 2732 8.00 N 2516 7.00 C 9547 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: 5.82 Conformation dependent library (CDL) restraints added in 2.9 seconds 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 5 sheets defined 54.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 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 809 removed outlier: 3.664A pdb=" N ALA A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 828 removed outlier: 3.602A pdb=" N ALA A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 859 Processing helix chain 'B' and resid 270 through 275 Processing helix chain 'B' and resid 284 through 306 removed outlier: 3.937A pdb=" N GLN B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N HIS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'B' and resid 348 through 357 Processing helix chain 'B' and resid 369 through 381 Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 403 through 413 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 440 removed outlier: 3.717A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 486 through 502 removed outlier: 3.713A pdb=" N LEU B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 529 through 541 Processing helix chain 'B' and resid 563 through 572 Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 37 through 86 removed outlier: 4.034A pdb=" N PHE C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 70 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER C 82 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 128 removed outlier: 4.417A pdb=" N PHE C 118 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 158 Processing helix chain 'C' and resid 181 through 191 Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.732A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.961A pdb=" N LEU C 262 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.521A pdb=" N SER C 269 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 270' Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.563A pdb=" N PHE C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 338 Processing helix chain 'C' and resid 340 through 344 removed outlier: 3.714A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 356 Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 370 through 377 removed outlier: 3.712A pdb=" N GLU C 377 " --> pdb=" O ARG C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 389 removed outlier: 3.816A pdb=" N VAL C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 425 removed outlier: 3.513A pdb=" N GLU C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 Processing helix chain 'C' and resid 452 through 461 removed outlier: 3.616A pdb=" N VAL C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 481 Processing helix chain 'C' and resid 488 through 500 Processing helix chain 'C' and resid 550 through 567 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 585 through 592 Processing helix chain 'C' and resid 596 through 605 removed outlier: 3.859A pdb=" N LEU C 600 " --> pdb=" O PRO C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 637 Processing helix chain 'C' and resid 646 through 660 Processing helix chain 'C' and resid 676 through 689 Processing helix chain 'D' and resid 18 through 28 Processing helix chain 'D' and resid 41 through 56 Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 107 through 117 Processing helix chain 'D' and resid 121 through 124 No H-bonds generated for 'chain 'D' and resid 121 through 124' Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 198 through 201 No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.842A pdb=" N LYS D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.813A pdb=" N ILE D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 289 Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'D' and resid 313 through 320 removed outlier: 3.567A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'D' and resid 369 through 381 Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 423 through 430 Processing helix chain 'E' and resid 12 through 22 Processing helix chain 'E' and resid 44 through 53 Processing helix chain 'E' and resid 69 through 84 Processing helix chain 'E' and resid 99 through 110 Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 127 through 130 Processing helix chain 'E' and resid 135 through 142 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 184 through 193 removed outlier: 4.401A pdb=" N HIS E 193 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 233 through 242 Proline residue: E 239 - end of helix Processing helix chain 'E' and resid 250 through 266 Proline residue: E 259 - end of helix removed outlier: 4.010A pdb=" N LYS E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS E 263 " --> pdb=" O PRO E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 304 through 317 removed outlier: 3.811A pdb=" N LEU E 315 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 328 Processing helix chain 'E' and resid 359 through 369 Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.979A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.915A 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 427 through 431 Processing sheet with id= A, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.558A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 311 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 388 " --> pdb=" O TYR B 419 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE B 421 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 390 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N SER B 423 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE B 392 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE B 335 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU B 391 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 337 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 271 through 277 removed outlier: 6.402A pdb=" N ILE C 100 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLU C 274 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C 102 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE C 276 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA C 104 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL C 215 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE C 249 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 214 through 216 removed outlier: 8.103A pdb=" N ILE D 215 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU D 64 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL D 154 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE D 190 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE D 156 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU D 192 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU D 158 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 385 through 387 Processing sheet with id= E, first strand: chain 'E' and resid 175 through 179 removed outlier: 3.708A pdb=" N PHE E 175 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ILE E 33 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL E 154 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE E 35 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE E 156 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLY E 37 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER E 158 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1803 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: 4.05 Time building geometry restraints manager: 6.26 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: 4256 1.34 - 1.46: 2834 1.46 - 1.58: 7980 1.58 - 1.70: 10 1.70 - 1.82: 104 Bond restraints: 15184 Sorted by residual: bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.42e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.33e+01 bond pdb=" C5 ATP E 501 " pdb=" C6 ATP E 501 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.93e+01 bond pdb=" C5 ATP E 501 " pdb=" N7 ATP E 501 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 15179 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.64: 259 105.64 - 113.15: 8133 113.15 - 120.66: 7163 120.66 - 128.17: 4872 128.17 - 135.68: 125 Bond angle restraints: 20552 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 139.87 117.99 21.88 1.00e+00 1.00e+00 4.79e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 118.19 18.64 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 123.89 15.98 1.00e+00 1.00e+00 2.55e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 123.79 13.04 1.00e+00 1.00e+00 1.70e+02 angle pdb=" C5 ATP E 501 " pdb=" C4 ATP E 501 " pdb=" N3 ATP E 501 " ideal model delta sigma weight residual 126.80 118.19 8.61 1.00e+00 1.00e+00 7.41e+01 ... (remaining 20547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 8197 17.63 - 35.26: 814 35.26 - 52.88: 151 52.88 - 70.51: 45 70.51 - 88.14: 28 Dihedral angle restraints: 9235 sinusoidal: 3841 harmonic: 5394 Sorted by residual: dihedral pdb=" CA THR C 130 " pdb=" C THR C 130 " pdb=" N PRO C 131 " pdb=" CA PRO C 131 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA HIS D 34 " pdb=" C HIS D 34 " pdb=" N SER D 35 " pdb=" CA SER D 35 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLN D 358 " pdb=" C GLN D 358 " pdb=" N ARG D 359 " pdb=" CA ARG D 359 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2009 0.088 - 0.176: 303 0.176 - 0.264: 28 0.264 - 0.352: 2 0.352 - 0.441: 2 Chirality restraints: 2344 Sorted by residual: chirality pdb=" CB ILE C 435 " pdb=" CA ILE C 435 " pdb=" CG1 ILE C 435 " pdb=" CG2 ILE C 435 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA LEU A 832 " pdb=" N LEU A 832 " pdb=" C LEU A 832 " pdb=" CB LEU A 832 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 2341 not shown) Planarity restraints: 2591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 238 " 0.063 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO E 239 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO E 239 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 239 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 44 " -0.007 2.00e-02 2.50e+03 2.23e-02 9.93e+00 pdb=" CG TYR D 44 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D 44 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR D 44 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR D 44 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 44 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 44 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 44 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 122 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C THR C 122 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 122 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU C 123 " -0.018 2.00e-02 2.50e+03 ... (remaining 2588 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 84 2.63 - 3.20: 12674 3.20 - 3.76: 22799 3.76 - 4.33: 30546 4.33 - 4.90: 49643 Nonbonded interactions: 115746 Sorted by model distance: nonbonded pdb=" O1B ATP E 501 " pdb="MG MG E 502 " model vdw 2.061 2.170 nonbonded pdb=" O1G ATP D 901 " pdb="MG MG D 902 " model vdw 2.148 2.170 nonbonded pdb=" OH TYR D 44 " pdb=" OE1 GLU D 83 " model vdw 2.235 2.440 nonbonded pdb=" O1A ATP E 501 " pdb="MG MG E 502 " model vdw 2.280 2.170 nonbonded pdb=" O LEU C 419 " pdb=" OG1 THR C 423 " model vdw 2.297 2.440 ... (remaining 115741 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 7.950 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 41.770 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 : 0.007 0.080 15184 Z= 0.459 Angle : 1.181 21.883 20552 Z= 0.700 Chirality : 0.064 0.441 2344 Planarity : 0.007 0.094 2591 Dihedral : 15.662 88.139 5707 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 1786 helix: -0.84 (0.14), residues: 1054 sheet: -0.61 (0.41), residues: 131 loop : -1.96 (0.22), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP E 162 HIS 0.013 0.002 HIS C 81 PHE 0.043 0.004 PHE B 539 TYR 0.050 0.003 TYR D 44 ARG 0.019 0.002 ARG B 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 815 THR cc_start: 0.7774 (p) cc_final: 0.7103 (p) REVERT: A 820 MET cc_start: 0.8113 (tpp) cc_final: 0.7855 (tpp) REVERT: B 288 LYS cc_start: 0.8007 (tppt) cc_final: 0.7687 (tptt) REVERT: B 557 LEU cc_start: 0.7192 (tp) cc_final: 0.6861 (tp) REVERT: C 29 TYR cc_start: 0.8132 (m-80) cc_final: 0.7926 (m-80) REVERT: C 148 LEU cc_start: 0.8794 (mp) cc_final: 0.8580 (mm) REVERT: C 369 LEU cc_start: 0.8532 (tp) cc_final: 0.8216 (mt) REVERT: C 372 PHE cc_start: 0.7773 (t80) cc_final: 0.7531 (t80) REVERT: C 467 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7922 (mp0) REVERT: C 673 MET cc_start: 0.4573 (tmm) cc_final: 0.4256 (tmm) REVERT: D 50 LEU cc_start: 0.8803 (tt) cc_final: 0.8171 (mp) REVERT: D 138 PHE cc_start: 0.6761 (t80) cc_final: 0.6541 (t80) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.2868 time to fit residues: 125.4524 Evaluate side-chains 177 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN B 411 GLN ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 GLN B 563 ASN C 35 ASN C 87 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 149 GLN E 48 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15184 Z= 0.172 Angle : 0.552 10.334 20552 Z= 0.286 Chirality : 0.039 0.143 2344 Planarity : 0.004 0.068 2591 Dihedral : 8.161 87.608 2017 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.61 % Allowed : 7.33 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1786 helix: 0.26 (0.15), residues: 1072 sheet: -0.21 (0.42), residues: 136 loop : -1.76 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 448 HIS 0.007 0.001 HIS C 637 PHE 0.037 0.002 PHE C 497 TYR 0.015 0.001 TYR C 482 ARG 0.006 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 GLU cc_start: 0.8219 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 815 THR cc_start: 0.7852 (p) cc_final: 0.7649 (p) REVERT: B 273 ARG cc_start: 0.6804 (tpm170) cc_final: 0.5644 (tpm170) REVERT: B 288 LYS cc_start: 0.8115 (tppt) cc_final: 0.7662 (tptt) REVERT: B 411 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7698 (mm110) REVERT: B 557 LEU cc_start: 0.6954 (tp) cc_final: 0.6699 (tp) REVERT: C 369 LEU cc_start: 0.8370 (tp) cc_final: 0.8127 (mt) REVERT: C 372 PHE cc_start: 0.7638 (t80) cc_final: 0.7386 (t80) REVERT: C 467 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7903 (mp0) REVERT: D 50 LEU cc_start: 0.9000 (tt) cc_final: 0.8314 (mp) outliers start: 27 outliers final: 15 residues processed: 212 average time/residue: 0.2945 time to fit residues: 92.1392 Evaluate side-chains 172 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 157 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 384 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 161 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 HIS C 339 GLN C 379 GLN D 216 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15184 Z= 0.368 Angle : 0.654 10.177 20552 Z= 0.342 Chirality : 0.044 0.159 2344 Planarity : 0.004 0.056 2591 Dihedral : 8.227 89.196 2017 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.86 % Allowed : 9.60 % Favored : 87.54 % 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: -0.56 (0.19), residues: 1786 helix: 0.45 (0.16), residues: 1065 sheet: 0.05 (0.46), residues: 114 loop : -1.89 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 51 HIS 0.008 0.001 HIS C 406 PHE 0.034 0.002 PHE E 203 TYR 0.028 0.002 TYR E 204 ARG 0.004 0.001 ARG D 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 163 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8047 (tm-30) REVERT: B 288 LYS cc_start: 0.8180 (tppt) cc_final: 0.7800 (mtmm) REVERT: B 557 LEU cc_start: 0.6920 (tp) cc_final: 0.6686 (tp) REVERT: C 369 LEU cc_start: 0.8376 (tp) cc_final: 0.8173 (mt) REVERT: C 372 PHE cc_start: 0.7801 (t80) cc_final: 0.7517 (t80) REVERT: D 50 LEU cc_start: 0.8963 (tt) cc_final: 0.8233 (mp) outliers start: 48 outliers final: 26 residues processed: 199 average time/residue: 0.2693 time to fit residues: 80.2497 Evaluate side-chains 171 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 384 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 154 optimal weight: 0.0070 chunk 46 optimal weight: 2.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN D 347 GLN D 410 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15184 Z= 0.178 Angle : 0.505 8.578 20552 Z= 0.262 Chirality : 0.038 0.139 2344 Planarity : 0.003 0.052 2591 Dihedral : 7.860 89.018 2017 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.91 % Allowed : 12.10 % Favored : 85.99 % 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: -0.06 (0.20), residues: 1786 helix: 0.93 (0.16), residues: 1064 sheet: 0.32 (0.47), residues: 114 loop : -1.85 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 428 HIS 0.007 0.001 HIS C 637 PHE 0.018 0.001 PHE E 203 TYR 0.016 0.001 TYR D 339 ARG 0.004 0.000 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 MET cc_start: 0.8068 (mmm) cc_final: 0.7494 (mmm) REVERT: B 288 LYS cc_start: 0.8126 (tppt) cc_final: 0.7670 (tptt) REVERT: C 32 LYS cc_start: 0.5789 (ptmt) cc_final: 0.5197 (tptm) REVERT: C 372 PHE cc_start: 0.7705 (t80) cc_final: 0.7343 (t80) REVERT: C 612 LYS cc_start: 0.5692 (mmtp) cc_final: 0.5445 (ptpp) REVERT: D 50 LEU cc_start: 0.9001 (tt) cc_final: 0.8286 (mp) outliers start: 32 outliers final: 15 residues processed: 199 average time/residue: 0.2902 time to fit residues: 85.3547 Evaluate side-chains 163 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 839 ASN Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 324 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15184 Z= 0.198 Angle : 0.526 11.714 20552 Z= 0.270 Chirality : 0.039 0.184 2344 Planarity : 0.003 0.051 2591 Dihedral : 7.482 89.053 2017 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.79 % Allowed : 14.25 % Favored : 83.96 % 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: 0.12 (0.20), residues: 1786 helix: 1.06 (0.16), residues: 1060 sheet: 0.46 (0.48), residues: 114 loop : -1.77 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 51 HIS 0.006 0.001 HIS C 637 PHE 0.020 0.001 PHE E 203 TYR 0.016 0.001 TYR B 508 ARG 0.005 0.000 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 MET cc_start: 0.8079 (mmm) cc_final: 0.7524 (mmm) REVERT: B 288 LYS cc_start: 0.8143 (tppt) cc_final: 0.7683 (tptt) REVERT: C 30 PHE cc_start: 0.4912 (t80) cc_final: 0.4616 (t80) REVERT: C 32 LYS cc_start: 0.5931 (ptmt) cc_final: 0.5403 (tptm) REVERT: C 372 PHE cc_start: 0.7647 (t80) cc_final: 0.7333 (t80) REVERT: D 50 LEU cc_start: 0.9019 (tt) cc_final: 0.8331 (mp) outliers start: 30 outliers final: 23 residues processed: 184 average time/residue: 0.2671 time to fit residues: 74.3449 Evaluate side-chains 175 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 384 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 101 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15184 Z= 0.169 Angle : 0.496 10.336 20552 Z= 0.255 Chirality : 0.038 0.139 2344 Planarity : 0.003 0.049 2591 Dihedral : 6.925 87.881 2017 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.85 % Allowed : 14.55 % Favored : 83.60 % 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: 0.31 (0.20), residues: 1786 helix: 1.23 (0.16), residues: 1061 sheet: 0.45 (0.47), residues: 117 loop : -1.70 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 51 HIS 0.006 0.001 HIS C 637 PHE 0.017 0.001 PHE E 203 TYR 0.017 0.001 TYR B 508 ARG 0.005 0.000 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 MET cc_start: 0.8080 (mmm) cc_final: 0.7531 (mmm) REVERT: B 288 LYS cc_start: 0.8134 (tppt) cc_final: 0.7687 (tptt) REVERT: C 30 PHE cc_start: 0.4909 (t80) cc_final: 0.4602 (t80) REVERT: C 32 LYS cc_start: 0.5992 (ptmt) cc_final: 0.5428 (tptm) REVERT: C 144 MET cc_start: 0.7993 (tpt) cc_final: 0.7581 (tpt) REVERT: C 372 PHE cc_start: 0.7654 (t80) cc_final: 0.7256 (t80) REVERT: D 44 TYR cc_start: 0.8721 (t80) cc_final: 0.8293 (t80) REVERT: D 50 LEU cc_start: 0.9003 (tt) cc_final: 0.8291 (mp) REVERT: D 175 ASN cc_start: 0.7876 (m-40) cc_final: 0.7338 (m110) REVERT: E 211 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8265 (tt) outliers start: 31 outliers final: 22 residues processed: 187 average time/residue: 0.2548 time to fit residues: 72.1473 Evaluate side-chains 178 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 839 ASN Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 324 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 0.1980 chunk 19 optimal weight: 8.9990 chunk 98 optimal weight: 0.0170 chunk 126 optimal weight: 0.0470 chunk 97 optimal weight: 0.6980 chunk 145 optimal weight: 0.0570 chunk 96 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN D 358 GLN E 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15184 Z= 0.122 Angle : 0.482 12.274 20552 Z= 0.245 Chirality : 0.037 0.137 2344 Planarity : 0.003 0.046 2591 Dihedral : 6.471 87.781 2017 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.61 % Allowed : 15.56 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1786 helix: 1.47 (0.16), residues: 1060 sheet: 0.45 (0.47), residues: 131 loop : -1.52 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 443 HIS 0.006 0.000 HIS C 637 PHE 0.020 0.001 PHE B 492 TYR 0.018 0.001 TYR B 508 ARG 0.006 0.000 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 MET cc_start: 0.8063 (mmm) cc_final: 0.7524 (mmm) REVERT: B 288 LYS cc_start: 0.8180 (tppt) cc_final: 0.7716 (tptt) REVERT: B 363 MET cc_start: 0.6042 (ppp) cc_final: 0.5525 (mtm) REVERT: B 572 LYS cc_start: 0.7720 (mttp) cc_final: 0.7437 (tttt) REVERT: C 32 LYS cc_start: 0.5923 (ptmt) cc_final: 0.5326 (tptm) REVERT: D 44 TYR cc_start: 0.8512 (t80) cc_final: 0.8259 (t80) REVERT: D 50 LEU cc_start: 0.8996 (tt) cc_final: 0.8261 (mp) REVERT: D 175 ASN cc_start: 0.7840 (m-40) cc_final: 0.7294 (m-40) outliers start: 27 outliers final: 18 residues processed: 187 average time/residue: 0.2695 time to fit residues: 75.1053 Evaluate side-chains 172 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 244 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 0.0030 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15184 Z= 0.145 Angle : 0.505 13.182 20552 Z= 0.251 Chirality : 0.038 0.171 2344 Planarity : 0.003 0.046 2591 Dihedral : 6.441 88.138 2017 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.61 % Allowed : 15.62 % Favored : 82.77 % 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: 0.74 (0.20), residues: 1786 helix: 1.52 (0.16), residues: 1063 sheet: 0.89 (0.49), residues: 117 loop : -1.50 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 443 HIS 0.006 0.001 HIS C 637 PHE 0.036 0.001 PHE C 653 TYR 0.018 0.001 TYR B 508 ARG 0.007 0.000 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 MET cc_start: 0.8077 (mmm) cc_final: 0.7528 (mmm) REVERT: B 288 LYS cc_start: 0.8174 (tppt) cc_final: 0.7707 (tptt) REVERT: B 363 MET cc_start: 0.5627 (ppp) cc_final: 0.4766 (mtm) REVERT: C 32 LYS cc_start: 0.5916 (ptmt) cc_final: 0.5477 (tptm) REVERT: C 372 PHE cc_start: 0.7465 (t80) cc_final: 0.7209 (t80) REVERT: D 44 TYR cc_start: 0.8715 (t80) cc_final: 0.8389 (t80) REVERT: D 50 LEU cc_start: 0.8980 (tt) cc_final: 0.8257 (mp) REVERT: D 175 ASN cc_start: 0.7869 (m-40) cc_final: 0.7318 (m-40) REVERT: E 211 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8230 (tt) outliers start: 27 outliers final: 19 residues processed: 179 average time/residue: 0.2576 time to fit residues: 69.8601 Evaluate side-chains 174 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 244 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15184 Z= 0.164 Angle : 0.518 13.747 20552 Z= 0.258 Chirality : 0.038 0.186 2344 Planarity : 0.003 0.046 2591 Dihedral : 6.475 89.200 2017 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.49 % Allowed : 16.04 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1786 helix: 1.54 (0.16), residues: 1065 sheet: 0.70 (0.47), residues: 124 loop : -1.45 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 51 HIS 0.006 0.001 HIS C 637 PHE 0.028 0.001 PHE C 653 TYR 0.017 0.001 TYR B 508 ARG 0.007 0.000 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 MET cc_start: 0.8105 (mmm) cc_final: 0.7580 (mmm) REVERT: B 288 LYS cc_start: 0.8158 (tppt) cc_final: 0.7713 (tptt) REVERT: C 32 LYS cc_start: 0.5900 (ptmt) cc_final: 0.5551 (tptm) REVERT: C 372 PHE cc_start: 0.7311 (t80) cc_final: 0.7049 (t80) REVERT: D 44 TYR cc_start: 0.8733 (t80) cc_final: 0.8405 (t80) REVERT: D 50 LEU cc_start: 0.8985 (tt) cc_final: 0.8283 (mp) REVERT: D 175 ASN cc_start: 0.7871 (m-40) cc_final: 0.7314 (m-40) REVERT: E 211 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8289 (tt) outliers start: 25 outliers final: 23 residues processed: 181 average time/residue: 0.2554 time to fit residues: 70.8222 Evaluate side-chains 179 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 839 ASN Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 244 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15184 Z= 0.166 Angle : 0.527 14.595 20552 Z= 0.261 Chirality : 0.038 0.164 2344 Planarity : 0.003 0.046 2591 Dihedral : 6.460 89.930 2017 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.61 % Allowed : 15.80 % Favored : 82.59 % 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: 0.73 (0.20), residues: 1786 helix: 1.55 (0.16), residues: 1064 sheet: 0.67 (0.49), residues: 112 loop : -1.50 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 51 HIS 0.006 0.001 HIS C 637 PHE 0.027 0.001 PHE C 653 TYR 0.017 0.001 TYR B 508 ARG 0.007 0.000 ARG A 786 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 816 MET cc_start: 0.8095 (mmm) cc_final: 0.7526 (mmm) REVERT: B 273 ARG cc_start: 0.6929 (tpm170) cc_final: 0.6384 (tpt90) REVERT: B 288 LYS cc_start: 0.8116 (tppt) cc_final: 0.7682 (tptt) REVERT: C 32 LYS cc_start: 0.5978 (ptmt) cc_final: 0.5596 (tptm) REVERT: C 372 PHE cc_start: 0.7300 (t80) cc_final: 0.7026 (t80) REVERT: D 44 TYR cc_start: 0.8602 (t80) cc_final: 0.8367 (t80) REVERT: D 50 LEU cc_start: 0.9006 (tt) cc_final: 0.8308 (mp) REVERT: D 175 ASN cc_start: 0.7902 (m-40) cc_final: 0.7299 (m-40) REVERT: E 211 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8293 (tt) outliers start: 27 outliers final: 22 residues processed: 182 average time/residue: 0.2547 time to fit residues: 70.4368 Evaluate side-chains 179 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 244 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 0.7980 chunk 130 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104479 restraints weight = 24466.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107280 restraints weight = 15001.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109218 restraints weight = 10804.755| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15184 Z= 0.151 Angle : 0.513 15.144 20552 Z= 0.254 Chirality : 0.037 0.153 2344 Planarity : 0.003 0.046 2591 Dihedral : 6.349 89.910 2017 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.61 % Allowed : 15.62 % Favored : 82.77 % 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 (0.20), residues: 1786 helix: 1.59 (0.16), residues: 1065 sheet: 0.94 (0.49), residues: 117 loop : -1.49 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 443 HIS 0.006 0.001 HIS C 637 PHE 0.026 0.001 PHE B 492 TYR 0.017 0.001 TYR B 508 ARG 0.007 0.000 ARG A 786 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2809.72 seconds wall clock time: 52 minutes 22.18 seconds (3142.18 seconds total)