Starting phenix.real_space_refine on Wed Feb 21 02:02:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vai_31842/02_2024/7vai_31842.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vai_31842/02_2024/7vai_31842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vai_31842/02_2024/7vai_31842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vai_31842/02_2024/7vai_31842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vai_31842/02_2024/7vai_31842.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vai_31842/02_2024/7vai_31842.pdb" } resolution = 3.1 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= 0.004 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: 4 Type Number sf(0) Gaussians S 103 5.16 5 C 18705 2.51 5 N 5116 2.21 5 O 5538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A ASP 436": "OD1" <-> "OD2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 43": "OD1" <-> "OD2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B ASP 390": "OD1" <-> "OD2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C ASP 325": "OD1" <-> "OD2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C ASP 410": "OD1" <-> "OD2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C ASP 493": "OD1" <-> "OD2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D ASP 176": "OD1" <-> "OD2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 401": "OE1" <-> "OE2" Residue "D ASP 416": "OD1" <-> "OD2" Residue "D TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 468": "OE1" <-> "OE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 290": "OD1" <-> "OD2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E ASP 319": "OD1" <-> "OD2" Residue "E ASP 457": "OD1" <-> "OD2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 26": "OD1" <-> "OD2" Residue "F ASP 34": "OD1" <-> "OD2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F ASP 380": "OD1" <-> "OD2" Residue "F ASP 416": "OD1" <-> "OD2" Residue "G ASP 54": "OD1" <-> "OD2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ASP 110": "OD1" <-> "OD2" Residue "G GLU 152": "OE1" <-> "OE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I GLU 93": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ASP 108": "OD1" <-> "OD2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J GLU 113": "OE1" <-> "OE2" Residue "J ASP 127": "OD1" <-> "OD2" Residue "J ASP 176": "OD1" <-> "OD2" Residue "K GLU 101": "OE1" <-> "OE2" Residue "K ASP 108": "OD1" <-> "OD2" Residue "K GLU 117": "OE1" <-> "OE2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L ASP 176": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29462 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Time building chain proxies: 15.33, per 1000 atoms: 0.52 Number of scatterers: 29462 At special positions: 0 Unit cell: (147.84, 143.44, 176.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 103 16.00 O 5538 8.00 N 5116 7.00 C 18705 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: 11.73 Conformation dependent library (CDL) restraints added in 5.8 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 28 sheets defined 46.1% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.560A pdb=" N THR A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.158A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.355A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.991A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.519A pdb=" N TYR A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.662A pdb=" N ALA A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.994A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 removed outlier: 3.901A pdb=" N VAL A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 531 removed outlier: 3.569A pdb=" N ALA A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 541 removed outlier: 3.629A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 4.119A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.667A pdb=" N TYR A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.600A pdb=" N SER B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 268 through 273 removed outlier: 4.024A pdb=" N THR B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 5.004A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.578A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 removed outlier: 3.524A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.784A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'B' and resid 464 through 472 Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 533 removed outlier: 3.648A pdb=" N ALA B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.638A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 550 through 554 removed outlier: 3.508A pdb=" N TYR B 553 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 554 " --> pdb=" O ALA B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 550 through 554' Processing helix chain 'B' and resid 558 through 576 removed outlier: 3.523A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.505A pdb=" N GLY C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.640A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.256A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 298 through 316 Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 410 through 415 removed outlier: 3.734A pdb=" N ALA C 414 " --> pdb=" O ASP C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 removed outlier: 3.636A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.006A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 Processing helix chain 'C' and resid 543 through 550 Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 576 removed outlier: 3.690A pdb=" N TYR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.661A pdb=" N MET D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.726A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.135A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 removed outlier: 3.501A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.980A pdb=" N VAL D 366 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 396 Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.581A pdb=" N SER D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 468 through 473 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.632A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.638A pdb=" N ARG E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.679A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 Processing helix chain 'E' and resid 197 through 211 removed outlier: 4.193A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 removed outlier: 3.680A pdb=" N SER E 215 " --> pdb=" O GLY E 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 212 through 215' Processing helix chain 'E' and resid 227 through 231 Processing helix chain 'E' and resid 233 through 250 Processing helix chain 'E' and resid 259 through 272 removed outlier: 3.670A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 275 No H-bonds generated for 'chain 'E' and resid 273 through 275' Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.658A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.650A pdb=" N HIS E 344 " --> pdb=" O SER E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.886A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 366 " --> pdb=" O MET E 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 361 through 366' Processing helix chain 'E' and resid 374 through 399 removed outlier: 3.501A pdb=" N GLY E 389 " --> pdb=" O ALA E 385 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.897A pdb=" N ARG E 409 " --> pdb=" O THR E 405 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.653A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.550A pdb=" N ILE F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.799A pdb=" N SER F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.824A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.747A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 359 through 365 removed outlier: 3.513A pdb=" N MET F 362 " --> pdb=" O SER F 359 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASN F 363 " --> pdb=" O ARG F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 4.113A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 removed outlier: 3.581A pdb=" N ARG F 409 " --> pdb=" O THR F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.786A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 removed outlier: 3.740A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 70 removed outlier: 3.896A pdb=" N LEU G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS G 58 " --> pdb=" O ASP G 54 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU G 59 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 83 Processing helix chain 'G' and resid 122 through 207 removed outlier: 4.040A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE G 130 " --> pdb=" O ALA G 126 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 6 through 16 removed outlier: 3.909A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.535A pdb=" N GLU H 34 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'H' and resid 85 through 98 removed outlier: 3.541A pdb=" N TYR H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 105 Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 94 removed outlier: 3.925A pdb=" N LEU J 66 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 100 through 115 Processing helix chain 'J' and resid 131 through 139 removed outlier: 3.956A pdb=" N ARG J 138 " --> pdb=" O LEU J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 186 removed outlier: 5.164A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 119 removed outlier: 4.335A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA K 112 " --> pdb=" O ASP K 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 Processing helix chain 'L' and resid 93 through 97 removed outlier: 3.707A pdb=" N GLN L 96 " --> pdb=" O ALA L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 124 through 132 Proline residue: L 129 - end of helix removed outlier: 3.724A pdb=" N GLU L 132 " --> pdb=" O PRO L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 187 removed outlier: 4.986A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.642A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 6.578A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 35 through 43 removed outlier: 5.928A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.796A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.708A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 5.805A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 42 through 51 removed outlier: 5.971A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 54 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 143 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 143 through 144 current: chain 'L' and resid 161 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 290 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 148 removed outlier: 6.625A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 164 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 384 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AA9, first strand: chain 'B' and resid 134 through 140 removed outlier: 3.715A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 147 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 204 through 205 removed outlier: 4.748A pdb=" N VAL B 218 " --> pdb=" O PHE B 205 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB3, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB4, first strand: chain 'C' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AB6, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.882A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.763A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.715A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.195A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE D 311 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL D 255 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE D 313 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU D 257 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N SER D 315 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.565A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.721A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.589A pdb=" N ALA E 188 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE E 256 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL E 190 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N GLN E 336 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N LEU E 355 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLN E 338 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.726A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.672A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 92 through 94 Processing sheet with id=AC7, first strand: chain 'F' and resid 124 through 125 removed outlier: 4.717A pdb=" N VAL F 300 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.667A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 91 through 95 Processing sheet with id=AD1, first strand: chain 'H' and resid 19 through 21 removed outlier: 6.228A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA H 2 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU H 72 " --> pdb=" O VAL H 45 " (cutoff:3.500A) 1247 hydrogen bonds defined for protein. 3570 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: 10.45 Time building geometry restraints manager: 12.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9622 1.33 - 1.45: 3526 1.45 - 1.57: 16673 1.57 - 1.69: 0 1.69 - 1.80: 194 Bond restraints: 30015 Sorted by residual: bond pdb=" C ILE E 106 " pdb=" N THR E 107 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.44e-02 4.82e+03 5.81e+00 bond pdb=" C GLY B 349 " pdb=" N TYR B 350 " ideal model delta sigma weight residual 1.329 1.296 0.033 1.60e-02 3.91e+03 4.14e+00 bond pdb=" CB GLN B 316 " pdb=" CG GLN B 316 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.08e+00 bond pdb=" CB THR B 285 " pdb=" CG2 THR B 285 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.05e+00 bond pdb=" CB GLN C 316 " pdb=" CG GLN C 316 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.94e+00 ... (remaining 30010 not shown) Histogram of bond angle deviations from ideal: 97.01 - 104.41: 640 104.41 - 111.82: 14284 111.82 - 119.23: 10391 119.23 - 126.63: 14968 126.63 - 134.04: 375 Bond angle restraints: 40658 Sorted by residual: angle pdb=" C GLY E 97 " pdb=" N LYS E 98 " pdb=" CA LYS E 98 " ideal model delta sigma weight residual 120.69 107.74 12.95 2.95e+00 1.15e-01 1.93e+01 angle pdb=" N VAL D 76 " pdb=" CA VAL D 76 " pdb=" C VAL D 76 " ideal model delta sigma weight residual 113.53 109.62 3.91 9.80e-01 1.04e+00 1.59e+01 angle pdb=" N VAL E 76 " pdb=" CA VAL E 76 " pdb=" C VAL E 76 " ideal model delta sigma weight residual 111.62 108.59 3.03 7.90e-01 1.60e+00 1.47e+01 angle pdb=" C GLN G 166 " pdb=" N VAL G 167 " pdb=" CA VAL G 167 " ideal model delta sigma weight residual 123.16 119.14 4.02 1.06e+00 8.90e-01 1.44e+01 angle pdb=" C THR D 258 " pdb=" N ASP D 259 " pdb=" CA ASP D 259 " ideal model delta sigma weight residual 122.47 117.36 5.11 1.50e+00 4.44e-01 1.16e+01 ... (remaining 40653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 16481 17.68 - 35.36: 1496 35.36 - 53.04: 251 53.04 - 70.72: 46 70.72 - 88.41: 30 Dihedral angle restraints: 18304 sinusoidal: 7482 harmonic: 10822 Sorted by residual: dihedral pdb=" CA GLU E 22 " pdb=" C GLU E 22 " pdb=" N ASN E 23 " pdb=" CA ASN E 23 " ideal model delta harmonic sigma weight residual -180.00 -138.54 -41.46 0 5.00e+00 4.00e-02 6.88e+01 dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N THR F 258 " pdb=" CA THR F 258 " ideal model delta harmonic sigma weight residual -180.00 -150.03 -29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LEU E 257 " pdb=" C LEU E 257 " pdb=" N THR E 258 " pdb=" CA THR E 258 " ideal model delta harmonic sigma weight residual -180.00 -150.51 -29.49 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2675 0.043 - 0.086: 1367 0.086 - 0.128: 454 0.128 - 0.171: 59 0.171 - 0.214: 5 Chirality restraints: 4560 Sorted by residual: chirality pdb=" CA HIS E 458 " pdb=" N HIS E 458 " pdb=" C HIS E 458 " pdb=" CB HIS E 458 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO C 420 " pdb=" N PRO C 420 " pdb=" C PRO C 420 " pdb=" CB PRO C 420 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 4557 not shown) Planarity restraints: 5330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 185 " -0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO E 186 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 186 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 186 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 316 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.21e+00 pdb=" N PRO F 317 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO F 317 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 317 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B 262 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.56e+00 pdb=" C MET B 262 " -0.037 2.00e-02 2.50e+03 pdb=" O MET B 262 " 0.014 2.00e-02 2.50e+03 pdb=" N THR B 263 " 0.012 2.00e-02 2.50e+03 ... (remaining 5327 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 806 2.68 - 3.24: 28944 3.24 - 3.79: 45315 3.79 - 4.35: 60423 4.35 - 4.90: 102986 Nonbonded interactions: 238474 Sorted by model distance: nonbonded pdb=" O ALA I 103 " pdb=" N LEU I 107 " model vdw 2.128 2.520 nonbonded pdb=" OE2 GLU J 110 " pdb=" ND2 ASN J 165 " model vdw 2.137 2.520 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.140 2.440 nonbonded pdb=" OH TYR E 386 " pdb=" OE2 GLU E 419 " model vdw 2.143 2.440 nonbonded pdb=" O ARG C 547 " pdb=" OH TYR C 562 " model vdw 2.147 2.440 ... (remaining 238469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } 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 individual isotropic 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: 4.430 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: 0.020 Extract box with map and model: 21.290 Check model and map are aligned: 0.480 Set scattering table: 0.310 Process input model: 78.960 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.190 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 : 0.011 0.084 30015 Z= 0.743 Angle : 0.822 12.950 40658 Z= 0.461 Chirality : 0.053 0.214 4560 Planarity : 0.005 0.066 5330 Dihedral : 13.981 88.406 11386 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 0.13 % Allowed : 8.53 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.40 (0.12), residues: 3764 helix: -1.06 (0.12), residues: 1518 sheet: -1.44 (0.21), residues: 571 loop : -2.06 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 175 HIS 0.008 0.001 HIS A 283 PHE 0.029 0.002 PHE D 60 TYR 0.028 0.002 TYR F 54 ARG 0.010 0.001 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 429 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6803 (tm-30) REVERT: A 154 ARG cc_start: 0.6926 (ptp-110) cc_final: 0.6517 (ptp-110) REVERT: A 156 ARG cc_start: 0.7137 (ttm-80) cc_final: 0.6559 (mtm-85) REVERT: A 481 ARG cc_start: 0.6802 (mtp-110) cc_final: 0.6572 (mtp-110) REVERT: A 491 ARG cc_start: 0.6793 (ttt90) cc_final: 0.6464 (mmt180) REVERT: A 541 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6533 (mt0) REVERT: B 124 LYS cc_start: 0.7297 (ptpp) cc_final: 0.6907 (mttm) REVERT: B 323 MET cc_start: 0.8706 (mtt) cc_final: 0.8480 (mtm) REVERT: B 363 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7636 (mm-30) REVERT: B 408 ARG cc_start: 0.7519 (ttt180) cc_final: 0.7295 (ttm-80) REVERT: B 441 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7530 (tt0) REVERT: B 459 GLN cc_start: 0.8041 (tp40) cc_final: 0.7785 (tp40) REVERT: B 461 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7481 (tt0) REVERT: B 532 ARG cc_start: 0.6464 (ttm110) cc_final: 0.5838 (ttp-110) REVERT: B 548 ILE cc_start: 0.8252 (tt) cc_final: 0.7642 (mt) REVERT: C 93 ARG cc_start: 0.7853 (mmt-90) cc_final: 0.7399 (mmt90) REVERT: C 114 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7211 (mt-10) REVERT: C 130 ARG cc_start: 0.7280 (ptp90) cc_final: 0.6748 (ptt90) REVERT: C 154 ARG cc_start: 0.7021 (mtp-110) cc_final: 0.6672 (mtm-85) REVERT: C 344 MET cc_start: 0.8010 (ttm) cc_final: 0.7609 (ttt) REVERT: C 465 GLN cc_start: 0.6609 (tm-30) cc_final: 0.6233 (tt0) REVERT: C 467 ILE cc_start: 0.7148 (mm) cc_final: 0.6892 (tt) REVERT: C 492 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6890 (mt-10) REVERT: C 500 TYR cc_start: 0.8531 (m-80) cc_final: 0.8331 (m-80) REVERT: C 538 GLU cc_start: 0.6974 (pm20) cc_final: 0.6685 (mp0) REVERT: C 546 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6680 (pt0) REVERT: C 547 ARG cc_start: 0.7521 (tpp-160) cc_final: 0.7161 (tpp-160) REVERT: D 98 LYS cc_start: 0.8274 (mttt) cc_final: 0.7898 (mtmt) REVERT: D 129 GLN cc_start: 0.7863 (mt0) cc_final: 0.7454 (mm-40) REVERT: D 280 ARG cc_start: 0.8015 (ttt-90) cc_final: 0.7733 (ttp80) REVERT: E 232 ILE cc_start: 0.8386 (pt) cc_final: 0.8171 (mt) REVERT: E 353 ASP cc_start: 0.7810 (t0) cc_final: 0.6971 (t0) REVERT: E 420 ARG cc_start: 0.7544 (mtp-110) cc_final: 0.7286 (mtp-110) REVERT: E 450 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6773 (mt-10) REVERT: F 206 GLN cc_start: 0.7558 (mt0) cc_final: 0.7221 (mp10) REVERT: F 373 GLU cc_start: 0.7066 (pm20) cc_final: 0.6697 (pm20) REVERT: F 420 ARG cc_start: 0.7539 (mtm110) cc_final: 0.7327 (mtm110) REVERT: G 13 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7693 (tt0) REVERT: G 53 LEU cc_start: 0.6601 (tp) cc_final: 0.6364 (tp) REVERT: G 132 ARG cc_start: 0.4816 (mtm110) cc_final: 0.4541 (mtm110) REVERT: G 139 ARG cc_start: 0.6600 (mtp-110) cc_final: 0.6295 (mtp180) REVERT: G 185 GLN cc_start: 0.7866 (tp40) cc_final: 0.7409 (tt0) REVERT: H 79 GLU cc_start: 0.4506 (mt-10) cc_final: 0.3874 (mt-10) REVERT: J 78 GLU cc_start: 0.2572 (mm-30) cc_final: 0.2030 (mt-10) REVERT: J 88 ARG cc_start: 0.3079 (mtt180) cc_final: 0.2861 (ttm170) REVERT: J 92 GLU cc_start: 0.3713 (mt-10) cc_final: 0.3467 (mt-10) REVERT: J 148 LEU cc_start: 0.2864 (pt) cc_final: 0.2128 (tp) REVERT: K 93 GLU cc_start: 0.5703 (tp30) cc_final: 0.5107 (mp0) REVERT: L 74 GLN cc_start: 0.6034 (pt0) cc_final: 0.5810 (pt0) REVERT: L 85 ARG cc_start: 0.4696 (tmm160) cc_final: 0.4023 (ttp-170) REVERT: L 160 LYS cc_start: 0.7534 (mtmt) cc_final: 0.6944 (mmtm) outliers start: 4 outliers final: 2 residues processed: 432 average time/residue: 0.5341 time to fit residues: 334.6028 Evaluate side-chains 314 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 312 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain J residue 163 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 1.9990 chunk 282 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 292 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 chunk 338 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 283 HIS A 571 GLN B 238 GLN B 316 GLN B 469 GLN C 290 ASN C 418 HIS D 206 GLN D 222 ASN D 424 ASN E 132 GLN E 166 GLN E 170 GLN F 23 ASN F 323 HIS F 413 GLN F 448 GLN H 30 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30015 Z= 0.165 Angle : 0.555 9.950 40658 Z= 0.284 Chirality : 0.044 0.160 4560 Planarity : 0.005 0.048 5330 Dihedral : 4.540 37.379 4182 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.07 % Allowed : 11.87 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.13), residues: 3764 helix: 0.41 (0.13), residues: 1537 sheet: -0.70 (0.23), residues: 506 loop : -1.42 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 119 HIS 0.004 0.001 HIS E 458 PHE 0.015 0.001 PHE D 414 TYR 0.016 0.001 TYR E 13 ARG 0.005 0.000 ARG J 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 375 time to evaluate : 3.182 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6736 (tm-30) REVERT: A 154 ARG cc_start: 0.6962 (ptp-110) cc_final: 0.6546 (ptp-110) REVERT: A 156 ARG cc_start: 0.7194 (ttm-80) cc_final: 0.6654 (mtm-85) REVERT: A 261 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7451 (mp0) REVERT: A 481 ARG cc_start: 0.6659 (mtp-110) cc_final: 0.6381 (mtt-85) REVERT: A 491 ARG cc_start: 0.6784 (ttt90) cc_final: 0.6527 (mmt180) REVERT: A 541 GLN cc_start: 0.7025 (mm-40) cc_final: 0.6309 (mt0) REVERT: B 124 LYS cc_start: 0.7415 (ptpp) cc_final: 0.6783 (mttm) REVERT: B 133 MET cc_start: 0.7808 (mtp) cc_final: 0.7063 (mmm) REVERT: B 154 ARG cc_start: 0.7126 (ttt-90) cc_final: 0.6790 (ttt180) REVERT: B 156 ARG cc_start: 0.6833 (ttm110) cc_final: 0.6375 (ttp-110) REVERT: B 363 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7685 (mm-30) REVERT: B 532 ARG cc_start: 0.6445 (ttm110) cc_final: 0.5891 (ttp80) REVERT: B 547 ARG cc_start: 0.8049 (ttm170) cc_final: 0.7703 (ttm110) REVERT: C 93 ARG cc_start: 0.7863 (mmt-90) cc_final: 0.7517 (mmt90) REVERT: C 114 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7219 (mt-10) REVERT: C 122 MET cc_start: 0.8217 (mtt) cc_final: 0.7993 (mtp) REVERT: C 130 ARG cc_start: 0.7088 (ptp90) cc_final: 0.6533 (ptt90) REVERT: C 154 ARG cc_start: 0.7000 (mtp-110) cc_final: 0.6636 (mtm-85) REVERT: C 344 MET cc_start: 0.7882 (ttm) cc_final: 0.7472 (ttt) REVERT: C 465 GLN cc_start: 0.6496 (tm-30) cc_final: 0.6117 (tt0) REVERT: C 469 GLN cc_start: 0.7660 (tp40) cc_final: 0.7370 (tt0) REVERT: C 546 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6415 (pt0) REVERT: C 547 ARG cc_start: 0.7535 (tpp-160) cc_final: 0.7190 (tpp-160) REVERT: D 22 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7399 (mm-30) REVERT: D 98 LYS cc_start: 0.8148 (mttt) cc_final: 0.7769 (mtmt) REVERT: D 129 GLN cc_start: 0.7674 (mt0) cc_final: 0.7453 (mm-40) REVERT: D 413 GLN cc_start: 0.7024 (mt0) cc_final: 0.6802 (mp10) REVERT: D 420 ARG cc_start: 0.7903 (tpm170) cc_final: 0.7321 (ttp-170) REVERT: E 318 ASP cc_start: 0.8163 (t70) cc_final: 0.7868 (t0) REVERT: E 353 ASP cc_start: 0.7749 (t0) cc_final: 0.6859 (t0) REVERT: E 420 ARG cc_start: 0.7491 (mtp-110) cc_final: 0.7129 (mtm110) REVERT: F 183 LYS cc_start: 0.6995 (mppt) cc_final: 0.6742 (mtpp) REVERT: F 206 GLN cc_start: 0.7627 (mt0) cc_final: 0.7296 (mp10) REVERT: F 420 ARG cc_start: 0.7437 (mtm110) cc_final: 0.7139 (mtm110) REVERT: G 17 GLN cc_start: 0.7825 (mm110) cc_final: 0.7592 (mm-40) REVERT: G 94 GLU cc_start: 0.6316 (tp30) cc_final: 0.6058 (tp30) REVERT: G 132 ARG cc_start: 0.5214 (mtm110) cc_final: 0.4541 (mtm110) REVERT: G 139 ARG cc_start: 0.6522 (mtp-110) cc_final: 0.6215 (mtp180) REVERT: G 175 GLN cc_start: 0.7875 (mt0) cc_final: 0.7660 (mt0) REVERT: G 185 GLN cc_start: 0.7625 (tp40) cc_final: 0.7395 (tt0) REVERT: H 34 GLU cc_start: 0.6807 (mm-30) cc_final: 0.5833 (pt0) REVERT: J 78 GLU cc_start: 0.2474 (mm-30) cc_final: 0.1923 (mt-10) REVERT: J 86 ARG cc_start: 0.3947 (mmm160) cc_final: 0.3644 (mtp85) REVERT: J 148 LEU cc_start: 0.2618 (pt) cc_final: 0.1902 (tt) REVERT: K 93 GLU cc_start: 0.5621 (tp30) cc_final: 0.5034 (mp0) REVERT: L 74 GLN cc_start: 0.5825 (pt0) cc_final: 0.5584 (pt0) REVERT: L 149 ARG cc_start: 0.5839 (ttp80) cc_final: 0.5459 (ttt-90) REVERT: L 160 LYS cc_start: 0.7406 (mtmt) cc_final: 0.6822 (mmtm) outliers start: 33 outliers final: 24 residues processed: 400 average time/residue: 0.4848 time to fit residues: 295.8968 Evaluate side-chains 349 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 325 time to evaluate : 4.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain J residue 163 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 339 optimal weight: 2.9990 chunk 366 optimal weight: 0.0010 chunk 302 optimal weight: 9.9990 chunk 336 optimal weight: 0.0020 chunk 115 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 GLN D 344 HIS E 166 GLN L 130 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30015 Z= 0.166 Angle : 0.516 10.787 40658 Z= 0.262 Chirality : 0.043 0.170 4560 Planarity : 0.004 0.043 5330 Dihedral : 4.207 35.822 4182 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.65 % Allowed : 12.94 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.21 (0.14), residues: 3764 helix: 0.95 (0.14), residues: 1555 sheet: -0.40 (0.23), residues: 509 loop : -1.06 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 119 HIS 0.003 0.001 HIS D 375 PHE 0.015 0.001 PHE D 60 TYR 0.017 0.001 TYR H 42 ARG 0.006 0.000 ARG C 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 342 time to evaluate : 3.511 Fit side-chains REVERT: A 128 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6662 (tm-30) REVERT: A 154 ARG cc_start: 0.7020 (ptp-110) cc_final: 0.6362 (ptm-80) REVERT: A 156 ARG cc_start: 0.7154 (ttm-80) cc_final: 0.6589 (mtm-85) REVERT: A 261 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7421 (mp0) REVERT: A 481 ARG cc_start: 0.6675 (mtp-110) cc_final: 0.6302 (mtp85) REVERT: A 491 ARG cc_start: 0.6773 (ttt90) cc_final: 0.6522 (mmt180) REVERT: A 541 GLN cc_start: 0.7022 (mm-40) cc_final: 0.6296 (mt0) REVERT: A 547 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7349 (ttm-80) REVERT: B 43 ASP cc_start: 0.8353 (t0) cc_final: 0.8102 (t0) REVERT: B 124 LYS cc_start: 0.7413 (ptpp) cc_final: 0.6995 (mttm) REVERT: B 133 MET cc_start: 0.7812 (mtp) cc_final: 0.7142 (mmm) REVERT: B 154 ARG cc_start: 0.7218 (ttt-90) cc_final: 0.6808 (ttt180) REVERT: B 156 ARG cc_start: 0.6895 (ttm110) cc_final: 0.6656 (ttt180) REVERT: B 363 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7734 (mm-30) REVERT: B 532 ARG cc_start: 0.6444 (ttm110) cc_final: 0.5928 (ttp80) REVERT: C 114 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7218 (mt-10) REVERT: C 130 ARG cc_start: 0.7043 (ptp90) cc_final: 0.6444 (ptt90) REVERT: C 344 MET cc_start: 0.7872 (ttm) cc_final: 0.7475 (ttt) REVERT: C 465 GLN cc_start: 0.6333 (tm-30) cc_final: 0.5888 (tt0) REVERT: C 546 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6396 (pt0) REVERT: C 547 ARG cc_start: 0.7484 (tpp-160) cc_final: 0.7139 (tpp-160) REVERT: D 22 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7467 (mm-30) REVERT: D 98 LYS cc_start: 0.8138 (mttt) cc_final: 0.7776 (mtmt) REVERT: D 129 GLN cc_start: 0.7649 (mt0) cc_final: 0.7442 (mm-40) REVERT: D 406 GLU cc_start: 0.6064 (tp30) cc_final: 0.5631 (tp30) REVERT: D 413 GLN cc_start: 0.7044 (mt0) cc_final: 0.6815 (mp10) REVERT: E 187 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: E 318 ASP cc_start: 0.8138 (t70) cc_final: 0.7825 (t0) REVERT: E 353 ASP cc_start: 0.7694 (t0) cc_final: 0.6827 (t70) REVERT: E 420 ARG cc_start: 0.7552 (mtp-110) cc_final: 0.7326 (mtm110) REVERT: F 183 LYS cc_start: 0.7013 (mppt) cc_final: 0.6793 (mtpp) REVERT: F 206 GLN cc_start: 0.7516 (mt0) cc_final: 0.7221 (mp10) REVERT: G 94 GLU cc_start: 0.6441 (tp30) cc_final: 0.6161 (tp30) REVERT: G 132 ARG cc_start: 0.5407 (mtm110) cc_final: 0.4875 (mtm110) REVERT: G 139 ARG cc_start: 0.6556 (mtp-110) cc_final: 0.6238 (mtp180) REVERT: G 185 GLN cc_start: 0.7617 (tp40) cc_final: 0.7283 (tt0) REVERT: H 6 ASP cc_start: 0.4543 (OUTLIER) cc_final: 0.4293 (p0) REVERT: H 34 GLU cc_start: 0.6744 (mm-30) cc_final: 0.5813 (pt0) REVERT: J 78 GLU cc_start: 0.2562 (mm-30) cc_final: 0.1981 (mt-10) REVERT: J 86 ARG cc_start: 0.4058 (mmm160) cc_final: 0.3798 (mtp85) REVERT: J 150 LEU cc_start: 0.3602 (OUTLIER) cc_final: 0.2951 (mt) REVERT: K 93 GLU cc_start: 0.5769 (tp30) cc_final: 0.5139 (mp0) REVERT: L 149 ARG cc_start: 0.5931 (ttp80) cc_final: 0.5704 (ttt-90) REVERT: L 160 LYS cc_start: 0.7381 (mtmt) cc_final: 0.6898 (ptpt) outliers start: 51 outliers final: 32 residues processed: 375 average time/residue: 0.4574 time to fit residues: 261.9491 Evaluate side-chains 343 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 308 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 20.0000 chunk 255 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 340 optimal weight: 9.9990 chunk 360 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 322 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN C 316 GLN D 170 GLN D 377 GLN E 222 ASN E 336 GLN L 74 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 30015 Z= 0.484 Angle : 0.698 9.119 40658 Z= 0.359 Chirality : 0.051 0.199 4560 Planarity : 0.006 0.071 5330 Dihedral : 5.022 40.100 4182 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.66 % Allowed : 14.63 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.63 (0.13), residues: 3764 helix: 0.50 (0.13), residues: 1538 sheet: -0.66 (0.22), residues: 542 loop : -1.14 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 471 HIS 0.005 0.002 HIS F 458 PHE 0.026 0.003 PHE D 60 TYR 0.024 0.002 TYR H 42 ARG 0.005 0.001 ARG E 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 303 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6790 (tm-30) REVERT: A 154 ARG cc_start: 0.7147 (ptp-110) cc_final: 0.6324 (ptm-80) REVERT: A 156 ARG cc_start: 0.7171 (ttm-80) cc_final: 0.6578 (mtm-85) REVERT: A 481 ARG cc_start: 0.6719 (mtp-110) cc_final: 0.6471 (mtt-85) REVERT: A 491 ARG cc_start: 0.6889 (ttt90) cc_final: 0.6611 (mmt180) REVERT: B 124 LYS cc_start: 0.7405 (ptpp) cc_final: 0.6942 (mttm) REVERT: B 133 MET cc_start: 0.7848 (mtp) cc_final: 0.7352 (mmm) REVERT: B 154 ARG cc_start: 0.7252 (ttt-90) cc_final: 0.6777 (ttt180) REVERT: B 156 ARG cc_start: 0.6871 (ttm110) cc_final: 0.6457 (ttt180) REVERT: B 271 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5755 (pm20) REVERT: B 363 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7818 (mm-30) REVERT: B 532 ARG cc_start: 0.6625 (ttm110) cc_final: 0.5961 (ttp80) REVERT: C 93 ARG cc_start: 0.7912 (mmt-90) cc_final: 0.7625 (mmt90) REVERT: C 130 ARG cc_start: 0.7046 (ptp90) cc_final: 0.6403 (ptt90) REVERT: C 344 MET cc_start: 0.7853 (ttm) cc_final: 0.7479 (ttt) REVERT: C 465 GLN cc_start: 0.6633 (tm-30) cc_final: 0.6221 (tt0) REVERT: C 492 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7089 (mt-10) REVERT: C 546 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6991 (tp30) REVERT: D 98 LYS cc_start: 0.8153 (mttt) cc_final: 0.7862 (mtmt) REVERT: D 129 GLN cc_start: 0.7815 (mt0) cc_final: 0.7477 (mm-40) REVERT: D 334 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: D 388 ASN cc_start: 0.7687 (m-40) cc_final: 0.6922 (t0) REVERT: D 406 GLU cc_start: 0.6164 (tp30) cc_final: 0.5868 (tp30) REVERT: E 196 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7147 (pt) REVERT: E 318 ASP cc_start: 0.8217 (t70) cc_final: 0.7920 (t70) REVERT: E 458 HIS cc_start: 0.6644 (OUTLIER) cc_final: 0.5313 (p-80) REVERT: F 68 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8343 (mp) REVERT: F 183 LYS cc_start: 0.7045 (mppt) cc_final: 0.6806 (mtpp) REVERT: F 305 LYS cc_start: 0.8004 (mppt) cc_final: 0.7651 (mmmt) REVERT: F 442 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8257 (mp) REVERT: G 13 GLN cc_start: 0.7851 (tt0) cc_final: 0.7646 (tt0) REVERT: G 132 ARG cc_start: 0.5344 (mtm110) cc_final: 0.4766 (mtm110) REVERT: G 185 GLN cc_start: 0.7767 (tp40) cc_final: 0.7249 (tt0) REVERT: G 190 ASP cc_start: 0.7873 (p0) cc_final: 0.7596 (p0) REVERT: G 207 GLU cc_start: 0.5004 (OUTLIER) cc_final: 0.4500 (tm-30) REVERT: H 6 ASP cc_start: 0.4447 (OUTLIER) cc_final: 0.4196 (p0) REVERT: H 34 GLU cc_start: 0.6612 (mm-30) cc_final: 0.5808 (pt0) REVERT: J 86 ARG cc_start: 0.3933 (mmm160) cc_final: 0.3530 (ttt180) REVERT: J 148 LEU cc_start: 0.2686 (pt) cc_final: 0.2029 (tt) REVERT: J 150 LEU cc_start: 0.3931 (OUTLIER) cc_final: 0.3156 (mt) REVERT: K 93 GLU cc_start: 0.5859 (tp30) cc_final: 0.5259 (mp0) REVERT: L 149 ARG cc_start: 0.6013 (ttp80) cc_final: 0.5639 (ttt-90) REVERT: L 160 LYS cc_start: 0.7553 (mtmt) cc_final: 0.7055 (mmtp) outliers start: 82 outliers final: 57 residues processed: 371 average time/residue: 0.4526 time to fit residues: 259.8744 Evaluate side-chains 353 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 287 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 307 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 323 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 206 GLN L 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30015 Z= 0.241 Angle : 0.558 10.736 40658 Z= 0.285 Chirality : 0.045 0.175 4560 Planarity : 0.005 0.047 5330 Dihedral : 4.593 38.088 4182 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.50 % Allowed : 15.89 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.27 (0.14), residues: 3764 helix: 0.85 (0.14), residues: 1539 sheet: -0.37 (0.23), residues: 520 loop : -1.03 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 119 HIS 0.003 0.001 HIS L 130 PHE 0.017 0.001 PHE D 60 TYR 0.019 0.001 TYR H 42 ARG 0.007 0.000 ARG K 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 306 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: A 128 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6679 (tm-30) REVERT: A 154 ARG cc_start: 0.7158 (ptp-110) cc_final: 0.6744 (ptp-110) REVERT: A 156 ARG cc_start: 0.7148 (ttm-80) cc_final: 0.6553 (mtm-85) REVERT: A 481 ARG cc_start: 0.6705 (mtp-110) cc_final: 0.6379 (mtp85) REVERT: A 491 ARG cc_start: 0.6811 (ttt90) cc_final: 0.6566 (mmt180) REVERT: B 124 LYS cc_start: 0.7434 (ptpp) cc_final: 0.6941 (mttm) REVERT: B 133 MET cc_start: 0.7833 (mtp) cc_final: 0.7359 (mmm) REVERT: B 154 ARG cc_start: 0.7209 (ttt-90) cc_final: 0.6828 (ttt180) REVERT: B 156 ARG cc_start: 0.6863 (ttm110) cc_final: 0.6484 (ttt180) REVERT: B 271 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5793 (pm20) REVERT: B 363 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7775 (mm-30) REVERT: B 532 ARG cc_start: 0.6603 (ttm110) cc_final: 0.6010 (ttp80) REVERT: C 93 ARG cc_start: 0.7900 (mmt-90) cc_final: 0.7606 (mmt90) REVERT: C 130 ARG cc_start: 0.7039 (ptp90) cc_final: 0.6390 (ptt90) REVERT: C 165 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7561 (mm-30) REVERT: C 287 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8723 (mp) REVERT: C 344 MET cc_start: 0.7872 (ttm) cc_final: 0.7488 (ttt) REVERT: C 465 GLN cc_start: 0.6466 (tm-30) cc_final: 0.6007 (tt0) REVERT: C 481 ARG cc_start: 0.6435 (mmm160) cc_final: 0.6166 (mtp-110) REVERT: C 492 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7003 (mt-10) REVERT: C 546 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6450 (pt0) REVERT: D 98 LYS cc_start: 0.8150 (mttt) cc_final: 0.7825 (mtmt) REVERT: D 129 GLN cc_start: 0.7756 (mt0) cc_final: 0.7463 (mm-40) REVERT: D 334 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: D 388 ASN cc_start: 0.7656 (m-40) cc_final: 0.6830 (t0) REVERT: D 406 GLU cc_start: 0.6013 (tp30) cc_final: 0.5634 (tp30) REVERT: D 413 GLN cc_start: 0.7106 (mt0) cc_final: 0.6844 (mp10) REVERT: D 420 ARG cc_start: 0.7835 (tpm170) cc_final: 0.7089 (ttp-170) REVERT: E 318 ASP cc_start: 0.8210 (t70) cc_final: 0.7790 (t0) REVERT: E 458 HIS cc_start: 0.6384 (OUTLIER) cc_final: 0.5205 (p-80) REVERT: F 68 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8203 (mp) REVERT: F 184 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5096 (mt-10) REVERT: F 305 LYS cc_start: 0.8010 (mppt) cc_final: 0.7680 (mmmt) REVERT: G 13 GLN cc_start: 0.7818 (tt0) cc_final: 0.7603 (tt0) REVERT: G 132 ARG cc_start: 0.5305 (mtm110) cc_final: 0.4773 (mtm110) REVERT: G 185 GLN cc_start: 0.7644 (tp40) cc_final: 0.7188 (tt0) REVERT: G 207 GLU cc_start: 0.5085 (OUTLIER) cc_final: 0.4624 (tm-30) REVERT: H 6 ASP cc_start: 0.4374 (OUTLIER) cc_final: 0.4138 (p0) REVERT: H 34 GLU cc_start: 0.6566 (mm-30) cc_final: 0.5756 (pt0) REVERT: J 86 ARG cc_start: 0.3750 (mmm160) cc_final: 0.3413 (ttp-170) REVERT: J 112 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.4980 (mt) REVERT: J 148 LEU cc_start: 0.2571 (OUTLIER) cc_final: 0.1922 (tt) REVERT: J 150 LEU cc_start: 0.3859 (OUTLIER) cc_final: 0.3032 (mt) REVERT: K 93 GLU cc_start: 0.5777 (tp30) cc_final: 0.5202 (mp0) REVERT: L 158 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.5356 (mp0) REVERT: L 160 LYS cc_start: 0.7548 (mtmt) cc_final: 0.7037 (mmtm) outliers start: 77 outliers final: 49 residues processed: 370 average time/residue: 0.4608 time to fit residues: 265.1359 Evaluate side-chains 359 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 297 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 158 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 360 optimal weight: 4.9990 chunk 299 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 418 HIS L 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 30015 Z= 0.424 Angle : 0.662 10.170 40658 Z= 0.339 Chirality : 0.049 0.191 4560 Planarity : 0.006 0.065 5330 Dihedral : 4.953 39.669 4182 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.21 % Allowed : 16.25 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.50 (0.14), residues: 3764 helix: 0.61 (0.13), residues: 1539 sheet: -0.53 (0.22), residues: 545 loop : -1.09 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 119 HIS 0.006 0.001 HIS E 458 PHE 0.026 0.002 PHE D 60 TYR 0.017 0.002 TYR H 42 ARG 0.008 0.001 ARG K 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 292 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: A 128 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6637 (tm-30) REVERT: A 154 ARG cc_start: 0.7217 (ptp-110) cc_final: 0.6884 (ptp-110) REVERT: A 156 ARG cc_start: 0.7183 (ttm-80) cc_final: 0.6587 (mtm-85) REVERT: A 481 ARG cc_start: 0.6703 (mtp-110) cc_final: 0.6413 (mtp85) REVERT: A 525 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6793 (mt-10) REVERT: B 124 LYS cc_start: 0.7361 (ptpp) cc_final: 0.6865 (mttm) REVERT: B 133 MET cc_start: 0.7829 (mtp) cc_final: 0.7415 (mmm) REVERT: B 154 ARG cc_start: 0.7296 (ttt-90) cc_final: 0.6855 (ttt180) REVERT: B 156 ARG cc_start: 0.6833 (ttm110) cc_final: 0.6439 (ttt180) REVERT: B 363 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7851 (mm-30) REVERT: C 93 ARG cc_start: 0.7912 (mmt-90) cc_final: 0.7663 (mmt90) REVERT: C 130 ARG cc_start: 0.7038 (ptp90) cc_final: 0.6390 (ptt90) REVERT: C 165 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7635 (mm-30) REVERT: C 287 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8789 (mp) REVERT: C 344 MET cc_start: 0.7873 (ttm) cc_final: 0.7505 (ttt) REVERT: C 465 GLN cc_start: 0.6589 (tm-30) cc_final: 0.6150 (tt0) REVERT: C 492 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6949 (mt-10) REVERT: C 546 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7005 (tp30) REVERT: D 88 MET cc_start: 0.8698 (mtp) cc_final: 0.8445 (mtt) REVERT: D 98 LYS cc_start: 0.8201 (mttt) cc_final: 0.7861 (mtmt) REVERT: D 129 GLN cc_start: 0.7840 (mt0) cc_final: 0.7483 (mm-40) REVERT: D 334 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: D 388 ASN cc_start: 0.7671 (m-40) cc_final: 0.6968 (t0) REVERT: D 406 GLU cc_start: 0.6056 (tp30) cc_final: 0.5728 (tp30) REVERT: E 130 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7559 (p90) REVERT: E 187 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7586 (m-10) REVERT: E 318 ASP cc_start: 0.8236 (t70) cc_final: 0.7909 (t70) REVERT: E 458 HIS cc_start: 0.6741 (OUTLIER) cc_final: 0.5394 (p-80) REVERT: F 68 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8332 (mp) REVERT: F 184 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5095 (mt-10) REVERT: F 305 LYS cc_start: 0.7995 (mppt) cc_final: 0.7658 (mmmt) REVERT: G 13 GLN cc_start: 0.7865 (tt0) cc_final: 0.7650 (tt0) REVERT: G 207 GLU cc_start: 0.4911 (OUTLIER) cc_final: 0.4535 (tm-30) REVERT: H 6 ASP cc_start: 0.4387 (OUTLIER) cc_final: 0.4150 (p0) REVERT: H 34 GLU cc_start: 0.6526 (mm-30) cc_final: 0.5726 (pt0) REVERT: J 86 ARG cc_start: 0.3757 (mmm160) cc_final: 0.3437 (ttt180) REVERT: J 112 LEU cc_start: 0.5323 (OUTLIER) cc_final: 0.5006 (mt) REVERT: J 148 LEU cc_start: 0.2635 (pt) cc_final: 0.1983 (tt) REVERT: J 150 LEU cc_start: 0.3834 (OUTLIER) cc_final: 0.3188 (mt) REVERT: K 93 GLU cc_start: 0.5807 (tp30) cc_final: 0.5257 (mp0) REVERT: L 158 GLU cc_start: 0.5611 (OUTLIER) cc_final: 0.5004 (mp0) REVERT: L 160 LYS cc_start: 0.7574 (mtmt) cc_final: 0.7076 (mmtm) outliers start: 99 outliers final: 70 residues processed: 376 average time/residue: 0.4411 time to fit residues: 260.9333 Evaluate side-chains 367 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 284 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 158 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 263 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 303 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 359 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 219 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30015 Z= 0.144 Angle : 0.511 11.364 40658 Z= 0.260 Chirality : 0.043 0.178 4560 Planarity : 0.004 0.044 5330 Dihedral : 4.318 35.622 4182 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.47 % Allowed : 16.96 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.04 (0.14), residues: 3764 helix: 1.14 (0.14), residues: 1548 sheet: -0.22 (0.23), residues: 520 loop : -0.90 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 119 HIS 0.003 0.001 HIS B 145 PHE 0.012 0.001 PHE A 230 TYR 0.012 0.001 TYR H 42 ARG 0.007 0.000 ARG C 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 314 time to evaluate : 3.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6654 (tm-30) REVERT: A 154 ARG cc_start: 0.7231 (ptp-110) cc_final: 0.6808 (ptp-110) REVERT: A 156 ARG cc_start: 0.7114 (ttm-80) cc_final: 0.6517 (mtm-85) REVERT: A 393 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6075 (pp20) REVERT: A 481 ARG cc_start: 0.6658 (mtp-110) cc_final: 0.6368 (mtp85) REVERT: A 525 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6781 (mt-10) REVERT: B 124 LYS cc_start: 0.7367 (ptpp) cc_final: 0.6893 (mttm) REVERT: B 133 MET cc_start: 0.7842 (mtp) cc_final: 0.7395 (mmm) REVERT: B 154 ARG cc_start: 0.7222 (ttt-90) cc_final: 0.6762 (ttt180) REVERT: B 156 ARG cc_start: 0.6818 (ttm110) cc_final: 0.6478 (ttt180) REVERT: B 268 GLU cc_start: 0.7412 (mp0) cc_final: 0.6734 (mp0) REVERT: B 363 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7761 (mm-30) REVERT: C 93 ARG cc_start: 0.7821 (mmt-90) cc_final: 0.7581 (mmt90) REVERT: C 130 ARG cc_start: 0.6991 (ptp90) cc_final: 0.6360 (ptt90) REVERT: C 165 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7509 (mm-30) REVERT: C 264 ASP cc_start: 0.7222 (m-30) cc_final: 0.6990 (m-30) REVERT: C 287 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8705 (mp) REVERT: C 342 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7164 (mt-10) REVERT: C 344 MET cc_start: 0.7873 (ttm) cc_final: 0.7488 (ttt) REVERT: C 465 GLN cc_start: 0.6496 (tm-30) cc_final: 0.6018 (tt0) REVERT: C 481 ARG cc_start: 0.6433 (mmm160) cc_final: 0.6162 (mtp-110) REVERT: C 546 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6463 (pt0) REVERT: D 88 MET cc_start: 0.8657 (mtp) cc_final: 0.8446 (mtt) REVERT: D 98 LYS cc_start: 0.8142 (mttt) cc_final: 0.7819 (mtmt) REVERT: D 129 GLN cc_start: 0.7709 (mt0) cc_final: 0.7479 (mm-40) REVERT: D 388 ASN cc_start: 0.7620 (m-40) cc_final: 0.6809 (t0) REVERT: D 413 GLN cc_start: 0.7124 (mt0) cc_final: 0.6860 (mp10) REVERT: D 420 ARG cc_start: 0.7794 (tpm170) cc_final: 0.6969 (ttp-170) REVERT: E 318 ASP cc_start: 0.8205 (t70) cc_final: 0.7770 (t0) REVERT: E 458 HIS cc_start: 0.6212 (OUTLIER) cc_final: 0.5109 (p-80) REVERT: F 184 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5065 (mt-10) REVERT: F 206 GLN cc_start: 0.7476 (mt0) cc_final: 0.7193 (mp10) REVERT: G 132 ARG cc_start: 0.5190 (mtm110) cc_final: 0.4755 (mtm110) REVERT: G 185 GLN cc_start: 0.7533 (tp40) cc_final: 0.7112 (tt0) REVERT: G 207 GLU cc_start: 0.4838 (OUTLIER) cc_final: 0.4460 (tm-30) REVERT: H 6 ASP cc_start: 0.4328 (OUTLIER) cc_final: 0.4118 (p0) REVERT: H 34 GLU cc_start: 0.6501 (mm-30) cc_final: 0.5684 (pt0) REVERT: J 92 GLU cc_start: 0.4257 (mt-10) cc_final: 0.4006 (mt-10) REVERT: J 112 LEU cc_start: 0.5165 (OUTLIER) cc_final: 0.4816 (mt) REVERT: J 148 LEU cc_start: 0.2468 (OUTLIER) cc_final: 0.1817 (tt) REVERT: J 150 LEU cc_start: 0.4016 (OUTLIER) cc_final: 0.3225 (mt) REVERT: K 93 GLU cc_start: 0.5771 (tp30) cc_final: 0.5188 (mp0) REVERT: L 158 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.5253 (mp0) REVERT: L 160 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7086 (mmtm) outliers start: 76 outliers final: 46 residues processed: 376 average time/residue: 0.4776 time to fit residues: 281.5264 Evaluate side-chains 354 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 298 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 158 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 228 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30015 Z= 0.254 Angle : 0.553 11.066 40658 Z= 0.281 Chirality : 0.045 0.180 4560 Planarity : 0.005 0.047 5330 Dihedral : 4.427 35.395 4182 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.53 % Allowed : 17.32 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.04 (0.14), residues: 3764 helix: 1.10 (0.14), residues: 1551 sheet: -0.22 (0.23), residues: 518 loop : -0.87 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 119 HIS 0.003 0.001 HIS L 130 PHE 0.020 0.002 PHE D 60 TYR 0.013 0.001 TYR H 42 ARG 0.006 0.000 ARG E 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 295 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: A 128 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6573 (tm-30) REVERT: A 154 ARG cc_start: 0.7219 (ptp-110) cc_final: 0.6797 (ptp-110) REVERT: A 156 ARG cc_start: 0.7177 (ttm-80) cc_final: 0.6595 (mtm-85) REVERT: A 241 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8131 (mp) REVERT: A 481 ARG cc_start: 0.6710 (mtp-110) cc_final: 0.6423 (mtp85) REVERT: A 525 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6640 (mt-10) REVERT: A 571 GLN cc_start: 0.6708 (mp10) cc_final: 0.6427 (mm-40) REVERT: B 124 LYS cc_start: 0.7376 (ptpp) cc_final: 0.6914 (mttm) REVERT: B 133 MET cc_start: 0.7861 (mtp) cc_final: 0.7422 (mmm) REVERT: B 154 ARG cc_start: 0.7251 (ttt-90) cc_final: 0.6844 (ttt180) REVERT: B 156 ARG cc_start: 0.6897 (ttm110) cc_final: 0.6480 (ttt180) REVERT: B 363 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7805 (mm-30) REVERT: C 93 ARG cc_start: 0.7823 (mmt-90) cc_final: 0.7588 (mmt90) REVERT: C 130 ARG cc_start: 0.7008 (ptp90) cc_final: 0.6380 (ptt90) REVERT: C 287 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8756 (mp) REVERT: C 342 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7255 (mt-10) REVERT: C 344 MET cc_start: 0.7868 (ttm) cc_final: 0.7481 (ttt) REVERT: C 465 GLN cc_start: 0.6620 (tm-30) cc_final: 0.6128 (tt0) REVERT: C 481 ARG cc_start: 0.6461 (mmm160) cc_final: 0.6206 (mtp-110) REVERT: C 492 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6897 (mt-10) REVERT: C 546 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6461 (pt0) REVERT: D 88 MET cc_start: 0.8685 (mtp) cc_final: 0.8440 (mtt) REVERT: D 98 LYS cc_start: 0.8170 (mttt) cc_final: 0.7850 (mtmt) REVERT: D 129 GLN cc_start: 0.7741 (mt0) cc_final: 0.7487 (mm-40) REVERT: D 334 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: D 388 ASN cc_start: 0.7641 (m-40) cc_final: 0.6827 (t0) REVERT: D 413 GLN cc_start: 0.7136 (mt0) cc_final: 0.6861 (mp10) REVERT: D 420 ARG cc_start: 0.7857 (tpm170) cc_final: 0.7012 (ttp-170) REVERT: E 318 ASP cc_start: 0.8234 (t70) cc_final: 0.7785 (t0) REVERT: E 458 HIS cc_start: 0.6652 (OUTLIER) cc_final: 0.5394 (p-80) REVERT: F 68 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8224 (mp) REVERT: F 184 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.5105 (mt-10) REVERT: F 206 GLN cc_start: 0.7510 (mt0) cc_final: 0.7227 (mp10) REVERT: F 305 LYS cc_start: 0.7999 (mppt) cc_final: 0.7688 (mmmt) REVERT: G 13 GLN cc_start: 0.7827 (tt0) cc_final: 0.7617 (tt0) REVERT: G 132 ARG cc_start: 0.5270 (mtm110) cc_final: 0.4794 (mtm110) REVERT: G 185 GLN cc_start: 0.7582 (tp40) cc_final: 0.7155 (tt0) REVERT: G 207 GLU cc_start: 0.4820 (OUTLIER) cc_final: 0.4480 (tm-30) REVERT: H 6 ASP cc_start: 0.4360 (OUTLIER) cc_final: 0.4143 (p0) REVERT: H 34 GLU cc_start: 0.6485 (mm-30) cc_final: 0.5674 (pt0) REVERT: J 92 GLU cc_start: 0.4338 (mt-10) cc_final: 0.4080 (mt-10) REVERT: J 112 LEU cc_start: 0.5206 (OUTLIER) cc_final: 0.4858 (mt) REVERT: J 148 LEU cc_start: 0.2476 (OUTLIER) cc_final: 0.1829 (tt) REVERT: J 150 LEU cc_start: 0.4035 (OUTLIER) cc_final: 0.3223 (mt) REVERT: K 93 GLU cc_start: 0.5817 (tp30) cc_final: 0.5218 (mp0) REVERT: L 158 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.5293 (mp0) REVERT: L 160 LYS cc_start: 0.7554 (mtmt) cc_final: 0.7068 (mmtm) outliers start: 78 outliers final: 57 residues processed: 360 average time/residue: 0.4620 time to fit residues: 261.0219 Evaluate side-chains 361 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 291 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 158 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 6.9990 chunk 344 optimal weight: 0.5980 chunk 314 optimal weight: 8.9990 chunk 335 optimal weight: 20.0000 chunk 201 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 302 optimal weight: 6.9990 chunk 316 optimal weight: 0.0000 chunk 333 optimal weight: 9.9990 overall best weight: 2.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30015 Z= 0.215 Angle : 0.536 11.099 40658 Z= 0.272 Chirality : 0.044 0.189 4560 Planarity : 0.005 0.046 5330 Dihedral : 4.352 33.754 4182 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.56 % Allowed : 17.26 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.14 (0.14), residues: 3764 helix: 1.20 (0.14), residues: 1542 sheet: -0.10 (0.23), residues: 510 loop : -0.83 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 119 HIS 0.003 0.001 HIS C 185 PHE 0.018 0.001 PHE D 60 TYR 0.012 0.001 TYR H 42 ARG 0.009 0.000 ARG K 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 304 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7029 (mt-10) REVERT: A 128 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6605 (tm-30) REVERT: A 154 ARG cc_start: 0.7220 (ptp-110) cc_final: 0.6439 (ptm-80) REVERT: A 156 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.6642 (mtm-85) REVERT: A 481 ARG cc_start: 0.6679 (mtp-110) cc_final: 0.6397 (mtp85) REVERT: A 525 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6552 (mt-10) REVERT: A 571 GLN cc_start: 0.6682 (mp10) cc_final: 0.6361 (mm-40) REVERT: B 124 LYS cc_start: 0.7374 (ptpp) cc_final: 0.6921 (mttm) REVERT: B 133 MET cc_start: 0.7859 (mtp) cc_final: 0.7423 (mmm) REVERT: B 154 ARG cc_start: 0.7247 (ttt-90) cc_final: 0.6823 (ttt180) REVERT: B 156 ARG cc_start: 0.6888 (ttm110) cc_final: 0.6478 (ttt180) REVERT: B 363 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7793 (mm-30) REVERT: C 93 ARG cc_start: 0.7814 (mmt-90) cc_final: 0.7583 (mmt90) REVERT: C 130 ARG cc_start: 0.6987 (ptp90) cc_final: 0.6357 (ptt90) REVERT: C 287 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8736 (mp) REVERT: C 342 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7229 (mt-10) REVERT: C 344 MET cc_start: 0.7866 (ttm) cc_final: 0.7480 (ttt) REVERT: C 465 GLN cc_start: 0.6622 (tm-30) cc_final: 0.6126 (tt0) REVERT: C 481 ARG cc_start: 0.6459 (mmm160) cc_final: 0.6198 (mtp-110) REVERT: C 492 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6894 (mt-10) REVERT: C 546 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6396 (pt0) REVERT: D 88 MET cc_start: 0.8678 (mtp) cc_final: 0.8446 (mtt) REVERT: D 98 LYS cc_start: 0.8164 (mttt) cc_final: 0.7842 (mtmt) REVERT: D 129 GLN cc_start: 0.7718 (mt0) cc_final: 0.7380 (mm-40) REVERT: D 334 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: D 388 ASN cc_start: 0.7628 (m-40) cc_final: 0.6827 (t0) REVERT: D 413 GLN cc_start: 0.7105 (mt0) cc_final: 0.6832 (mp10) REVERT: D 420 ARG cc_start: 0.7844 (tpm170) cc_final: 0.6979 (ttp-170) REVERT: E 318 ASP cc_start: 0.8221 (t70) cc_final: 0.7897 (t70) REVERT: E 458 HIS cc_start: 0.6540 (OUTLIER) cc_final: 0.5309 (p-80) REVERT: F 68 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8209 (mp) REVERT: F 184 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5095 (mt-10) REVERT: F 206 GLN cc_start: 0.7494 (mt0) cc_final: 0.7205 (mp10) REVERT: F 305 LYS cc_start: 0.7994 (mppt) cc_final: 0.7691 (mmmt) REVERT: G 13 GLN cc_start: 0.7815 (tt0) cc_final: 0.7609 (tt0) REVERT: G 132 ARG cc_start: 0.5277 (mtm110) cc_final: 0.4796 (mtm110) REVERT: G 185 GLN cc_start: 0.7563 (tp40) cc_final: 0.7144 (tt0) REVERT: G 207 GLU cc_start: 0.4766 (OUTLIER) cc_final: 0.4464 (tm-30) REVERT: H 6 ASP cc_start: 0.4287 (OUTLIER) cc_final: 0.3971 (p0) REVERT: H 34 GLU cc_start: 0.6414 (mm-30) cc_final: 0.5626 (pt0) REVERT: J 92 GLU cc_start: 0.4321 (mt-10) cc_final: 0.4073 (mt-10) REVERT: J 112 LEU cc_start: 0.5103 (OUTLIER) cc_final: 0.4751 (mt) REVERT: J 148 LEU cc_start: 0.2420 (OUTLIER) cc_final: 0.1762 (tt) REVERT: J 150 LEU cc_start: 0.4035 (OUTLIER) cc_final: 0.3235 (mt) REVERT: K 93 GLU cc_start: 0.5808 (tp30) cc_final: 0.5212 (mp0) REVERT: L 158 GLU cc_start: 0.5673 (OUTLIER) cc_final: 0.5094 (mp0) REVERT: L 160 LYS cc_start: 0.7549 (mtmt) cc_final: 0.7064 (mmtm) outliers start: 79 outliers final: 58 residues processed: 371 average time/residue: 0.4550 time to fit residues: 262.6940 Evaluate side-chains 367 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 297 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 158 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 0.8980 chunk 354 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 371 optimal weight: 6.9990 chunk 342 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 228 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30015 Z= 0.230 Angle : 0.548 11.112 40658 Z= 0.277 Chirality : 0.044 0.184 4560 Planarity : 0.005 0.046 5330 Dihedral : 4.370 33.494 4182 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.53 % Allowed : 17.42 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.15 (0.14), residues: 3764 helix: 1.21 (0.14), residues: 1548 sheet: -0.11 (0.23), residues: 512 loop : -0.83 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 119 HIS 0.003 0.001 HIS B 185 PHE 0.019 0.001 PHE D 60 TYR 0.012 0.001 TYR H 42 ARG 0.009 0.000 ARG K 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 297 time to evaluate : 3.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7042 (mt-10) REVERT: A 128 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6608 (tm-30) REVERT: A 154 ARG cc_start: 0.7223 (ptp-110) cc_final: 0.6482 (ptm-80) REVERT: A 156 ARG cc_start: 0.7260 (ttm-80) cc_final: 0.6649 (mtm-85) REVERT: A 241 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 481 ARG cc_start: 0.6695 (mtp-110) cc_final: 0.6419 (mtp85) REVERT: A 525 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6537 (mt-10) REVERT: A 571 GLN cc_start: 0.6676 (mp10) cc_final: 0.6346 (mm-40) REVERT: B 124 LYS cc_start: 0.7371 (ptpp) cc_final: 0.6912 (mttm) REVERT: B 133 MET cc_start: 0.7863 (mtp) cc_final: 0.7430 (mmm) REVERT: B 154 ARG cc_start: 0.7192 (ttt-90) cc_final: 0.6796 (ttt180) REVERT: B 156 ARG cc_start: 0.6893 (ttm110) cc_final: 0.6483 (ttt180) REVERT: B 363 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7797 (mm-30) REVERT: C 93 ARG cc_start: 0.7815 (mmt-90) cc_final: 0.7586 (mmt90) REVERT: C 130 ARG cc_start: 0.6996 (ptp90) cc_final: 0.6372 (ptt90) REVERT: C 287 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8751 (mp) REVERT: C 342 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7231 (mt-10) REVERT: C 344 MET cc_start: 0.7857 (ttm) cc_final: 0.7485 (ttt) REVERT: C 465 GLN cc_start: 0.6624 (tm-30) cc_final: 0.6128 (tt0) REVERT: C 481 ARG cc_start: 0.6448 (mmm160) cc_final: 0.6191 (mtp-110) REVERT: C 492 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6871 (mt-10) REVERT: C 546 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6409 (pt0) REVERT: D 88 MET cc_start: 0.8680 (mtp) cc_final: 0.8411 (mtt) REVERT: D 98 LYS cc_start: 0.8170 (mttt) cc_final: 0.7848 (mtmt) REVERT: D 129 GLN cc_start: 0.7728 (mt0) cc_final: 0.7392 (mm-40) REVERT: D 334 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: D 388 ASN cc_start: 0.7633 (m-40) cc_final: 0.6835 (t0) REVERT: D 413 GLN cc_start: 0.7100 (mt0) cc_final: 0.6832 (mp10) REVERT: D 420 ARG cc_start: 0.7858 (tpm170) cc_final: 0.6997 (ttp-170) REVERT: E 318 ASP cc_start: 0.8224 (t70) cc_final: 0.7893 (t70) REVERT: E 458 HIS cc_start: 0.6574 (OUTLIER) cc_final: 0.5313 (p-80) REVERT: F 68 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8214 (mp) REVERT: F 184 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.5101 (mt-10) REVERT: F 206 GLN cc_start: 0.7497 (mt0) cc_final: 0.7207 (mp10) REVERT: F 305 LYS cc_start: 0.7984 (mppt) cc_final: 0.7675 (mmmt) REVERT: G 13 GLN cc_start: 0.7821 (tt0) cc_final: 0.7617 (tt0) REVERT: G 207 GLU cc_start: 0.4765 (OUTLIER) cc_final: 0.4464 (tm-30) REVERT: H 1 MET cc_start: 0.5100 (mtt) cc_final: 0.4715 (mtt) REVERT: H 34 GLU cc_start: 0.6383 (mm-30) cc_final: 0.5669 (pt0) REVERT: J 92 GLU cc_start: 0.4451 (mt-10) cc_final: 0.4193 (mt-10) REVERT: J 148 LEU cc_start: 0.2452 (OUTLIER) cc_final: 0.1834 (tt) REVERT: J 150 LEU cc_start: 0.4026 (OUTLIER) cc_final: 0.3271 (mt) REVERT: K 93 GLU cc_start: 0.5795 (tp30) cc_final: 0.5186 (mp0) REVERT: L 158 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.5014 (mp0) REVERT: L 160 LYS cc_start: 0.7549 (mtmt) cc_final: 0.7065 (mmtp) outliers start: 78 outliers final: 61 residues processed: 361 average time/residue: 0.4532 time to fit residues: 255.1065 Evaluate side-chains 365 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 293 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 158 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 7.9990 chunk 315 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 272 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 304 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 407 ASN L 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.089897 restraints weight = 43973.250| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.59 r_work: 0.2865 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 30015 Z= 0.520 Angle : 0.716 10.685 40658 Z= 0.367 Chirality : 0.051 0.207 4560 Planarity : 0.007 0.079 5330 Dihedral : 5.056 36.670 4182 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.72 % Allowed : 17.39 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.41 (0.14), residues: 3764 helix: 0.70 (0.13), residues: 1538 sheet: -0.52 (0.22), residues: 566 loop : -1.05 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 119 HIS 0.006 0.002 HIS E 458 PHE 0.029 0.003 PHE D 60 TYR 0.020 0.002 TYR D 411 ARG 0.010 0.001 ARG K 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6854.82 seconds wall clock time: 124 minutes 46.30 seconds (7486.30 seconds total)