Starting phenix.real_space_refine on Mon Nov 18 18:33:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzj_26913/11_2024/7uzj_26913.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzj_26913/11_2024/7uzj_26913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzj_26913/11_2024/7uzj_26913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzj_26913/11_2024/7uzj_26913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzj_26913/11_2024/7uzj_26913.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzj_26913/11_2024/7uzj_26913.cif" } resolution = 3.3 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= 0.006 sd= 1.169 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 255 5.16 5 C 31415 2.51 5 N 8533 2.21 5 O 9418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 309 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 49624 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4568 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 558} Chain breaks: 2 Chain: "B" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4657 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 570} Chain: "C" Number of atoms: 4648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4648 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3603 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Chain: "E" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3632 Classifications: {'peptide': 464} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 436} Chain breaks: 1 Chain: "F" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3576 Classifications: {'peptide': 457} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 429} Chain breaks: 1 Chain: "G" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 9, 'TRANS': 348} Chain breaks: 1 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1689 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 3, 'TRANS': 203} Chain breaks: 1 Chain: "I" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1774 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 212} Chain: "J" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1808 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "K" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1774 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 212} Chain: "L" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "M" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 914 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain: "N" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 929 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "O" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 929 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "P" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3529 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 8, 'TRANS': 421} Chain breaks: 1 Chain: "Q" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2122 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 9, 'TRANS': 252} Chain: "R" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2126 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain: "S" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2147 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain: "T" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1377 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.83, per 1000 atoms: 0.52 Number of scatterers: 49624 At special positions: 0 Unit cell: (200.34, 186.56, 190.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 255 16.00 P 2 15.00 Mg 1 11.99 O 9418 8.00 N 8533 7.00 C 31415 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 - 3.00 Amino acid : True - 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: 12.30 Conformation dependent library (CDL) restraints added in 6.0 seconds 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11744 Finding SS restraints... Secondary structure from input PDB file: 231 helices and 35 sheets defined 57.4% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.86 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 259 through 266 Processing helix chain 'A' and resid 280 through 291 Processing helix chain 'A' and resid 319 through 340 removed outlier: 4.347A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.642A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.903A pdb=" N GLY A 373 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 Processing helix chain 'A' and resid 419 through 427 removed outlier: 3.775A pdb=" N GLY A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 457 through 469 removed outlier: 4.460A pdb=" N GLU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 497 removed outlier: 3.501A pdb=" N LEU A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 Processing helix chain 'A' and resid 526 through 530 removed outlier: 3.625A pdb=" N ARG A 530 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 558 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 593 through 615 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 251 through 255 removed outlier: 4.101A pdb=" N GLY B 255 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 267 removed outlier: 3.670A pdb=" N SER B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.589A pdb=" N VAL B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 319 through 340 removed outlier: 4.940A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 365 removed outlier: 3.643A pdb=" N TRP B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 387 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 419 through 429 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 457 through 469 removed outlier: 5.313A pdb=" N GLU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 497 removed outlier: 3.552A pdb=" N LEU B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLN B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 519 Processing helix chain 'B' and resid 533 through 559 removed outlier: 3.769A pdb=" N THR B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 584 removed outlier: 6.518A pdb=" N GLU B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 593 through 614 Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 255 through 267 Processing helix chain 'C' and resid 280 through 291 removed outlier: 3.936A pdb=" N VAL C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 340 removed outlier: 4.282A pdb=" N ALA C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 337 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 365 Processing helix chain 'C' and resid 370 through 374 removed outlier: 4.120A pdb=" N GLY C 373 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 412 through 416 removed outlier: 3.879A pdb=" N ASP C 416 " --> pdb=" O PRO C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 427 removed outlier: 3.625A pdb=" N GLY C 427 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 457 through 469 removed outlier: 4.884A pdb=" N GLU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 497 removed outlier: 3.925A pdb=" N LEU C 475 " --> pdb=" O GLU C 471 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 519 Processing helix chain 'C' and resid 533 through 559 Processing helix chain 'C' and resid 566 through 584 removed outlier: 6.749A pdb=" N GLU C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 593 through 614 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 237 through 251 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 268 through 272 Processing helix chain 'D' and resid 273 through 288 Processing helix chain 'D' and resid 299 through 314 Processing helix chain 'D' and resid 319 through 323 removed outlier: 3.523A pdb=" N GLY D 322 " --> pdb=" O GLY D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 336 removed outlier: 3.592A pdb=" N THR D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 363 through 371 removed outlier: 3.689A pdb=" N TYR D 371 " --> pdb=" O ASP D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 385 Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.701A pdb=" N ALA D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 440 removed outlier: 4.210A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 444 Processing helix chain 'D' and resid 445 through 462 removed outlier: 3.567A pdb=" N GLN D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 removed outlier: 3.506A pdb=" N GLN D 482 " --> pdb=" O ASP D 478 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 487 No H-bonds generated for 'chain 'D' and resid 486 through 487' Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 496 through 504 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 237 through 251 removed outlier: 3.500A pdb=" N GLU E 249 " --> pdb=" O LYS E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 255 removed outlier: 4.359A pdb=" N ASP E 255 " --> pdb=" O GLY E 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 255' Processing helix chain 'E' and resid 267 through 288 removed outlier: 3.734A pdb=" N ARG E 271 " --> pdb=" O PRO E 267 " (cutoff:3.500A) Proline residue: E 275 - end of helix Processing helix chain 'E' and resid 299 through 314 removed outlier: 3.588A pdb=" N ALA E 306 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 removed outlier: 3.645A pdb=" N ILE E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 360 Processing helix chain 'E' and resid 363 through 373 removed outlier: 3.557A pdb=" N TYR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 386 Processing helix chain 'E' and resid 401 through 406 removed outlier: 3.590A pdb=" N ALA E 405 " --> pdb=" O LEU E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 440 removed outlier: 3.681A pdb=" N ASN E 420 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA E 437 " --> pdb=" O GLN E 433 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 444 Processing helix chain 'E' and resid 445 through 462 removed outlier: 3.756A pdb=" N GLN E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 486 through 487 No H-bonds generated for 'chain 'E' and resid 486 through 487' Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 496 through 504 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.861A pdb=" N LEU F 128 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 198 through 210 Processing helix chain 'F' and resid 237 through 251 Processing helix chain 'F' and resid 252 through 255 removed outlier: 4.461A pdb=" N ASP F 255 " --> pdb=" O GLY F 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 255' Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.672A pdb=" N TYR F 303 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 314 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 323 Processing helix chain 'F' and resid 326 through 336 removed outlier: 3.685A pdb=" N ILE F 334 " --> pdb=" O ASP F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 360 Processing helix chain 'F' and resid 363 through 373 removed outlier: 3.512A pdb=" N ILE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 386 removed outlier: 3.527A pdb=" N ARG F 386 " --> pdb=" O GLN F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 406 removed outlier: 3.536A pdb=" N ALA F 405 " --> pdb=" O LEU F 401 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE F 406 " --> pdb=" O MET F 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 401 through 406' Processing helix chain 'F' and resid 414 through 440 removed outlier: 3.906A pdb=" N ASN F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 444 Processing helix chain 'F' and resid 445 through 462 removed outlier: 3.527A pdb=" N TYR F 451 " --> pdb=" O ASP F 447 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN F 456 " --> pdb=" O LEU F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 486 through 487 No H-bonds generated for 'chain 'F' and resid 486 through 487' Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 496 through 504 removed outlier: 3.957A pdb=" N GLU F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 27 removed outlier: 3.806A pdb=" N THR G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 81 removed outlier: 3.579A pdb=" N LEU G 51 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY G 53 " --> pdb=" O ASP G 49 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 89 Processing helix chain 'G' and resid 98 through 104 Processing helix chain 'G' and resid 117 through 158 removed outlier: 4.039A pdb=" N LEU G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G 147 " --> pdb=" O TYR G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 Processing helix chain 'G' and resid 193 through 202 removed outlier: 4.474A pdb=" N GLU G 202 " --> pdb=" O ILE G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 254 through 310 removed outlier: 4.164A pdb=" N LYS G 262 " --> pdb=" O MET G 258 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN G 266 " --> pdb=" O LYS G 262 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER G 269 " --> pdb=" O MET G 265 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS G 273 " --> pdb=" O SER G 269 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Proline residue: G 278 - end of helix removed outlier: 3.735A pdb=" N SER G 288 " --> pdb=" O LYS G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 340 Processing helix chain 'G' and resid 341 through 343 No H-bonds generated for 'chain 'G' and resid 341 through 343' Processing helix chain 'H' and resid 12 through 77 removed outlier: 4.670A pdb=" N ARG H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 84 removed outlier: 3.733A pdb=" N ILE H 84 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 175 Processing helix chain 'H' and resid 175 through 221 removed outlier: 3.535A pdb=" N ARG H 179 " --> pdb=" O VAL H 175 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP H 192 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG H 201 " --> pdb=" O GLU H 197 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS H 204 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE H 205 " --> pdb=" O ARG H 201 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU H 207 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 108 removed outlier: 4.375A pdb=" N LYS I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE I 38 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN I 39 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS I 107 " --> pdb=" O SER I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 128 removed outlier: 3.794A pdb=" N GLY I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU I 121 " --> pdb=" O ASP I 117 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN I 126 " --> pdb=" O GLN I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 160 Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 196 through 207 removed outlier: 3.969A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 217 removed outlier: 3.595A pdb=" N GLY I 213 " --> pdb=" O PRO I 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 108 removed outlier: 3.701A pdb=" N ILE J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLU J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLN J 66 " --> pdb=" O LYS J 62 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN J 71 " --> pdb=" O GLN J 67 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS J 104 " --> pdb=" O GLN J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 128 removed outlier: 3.554A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU J 121 " --> pdb=" O ASP J 117 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN J 126 " --> pdb=" O GLN J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 160 removed outlier: 3.520A pdb=" N ALA J 146 " --> pdb=" O PRO J 142 " (cutoff:3.500A) Proline residue: J 153 - end of helix Processing helix chain 'J' and resid 196 through 207 removed outlier: 3.604A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 207 through 217 Processing helix chain 'K' and resid 10 through 108 removed outlier: 3.994A pdb=" N HIS K 14 " --> pdb=" O LYS K 10 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU K 35 " --> pdb=" O ASP K 31 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN K 47 " --> pdb=" O GLY K 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS K 62 " --> pdb=" O GLU K 58 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN K 63 " --> pdb=" O LYS K 59 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL K 83 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 128 removed outlier: 3.692A pdb=" N VAL K 114 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU K 121 " --> pdb=" O ASP K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 139 No H-bonds generated for 'chain 'K' and resid 137 through 139' Processing helix chain 'K' and resid 140 through 160 Proline residue: K 153 - end of helix Processing helix chain 'K' and resid 196 through 217 removed outlier: 3.712A pdb=" N GLN K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Proline residue: K 209 - end of helix Processing helix chain 'L' and resid 13 through 19 Processing helix chain 'L' and resid 44 through 56 Processing helix chain 'L' and resid 68 through 72 Processing helix chain 'L' and resid 74 through 80 removed outlier: 3.617A pdb=" N ALA L 80 " --> pdb=" O HIS L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 109 Processing helix chain 'M' and resid 7 through 90 removed outlier: 3.740A pdb=" N LYS M 27 " --> pdb=" O SER M 23 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS M 29 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASN M 30 " --> pdb=" O ARG M 26 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN M 41 " --> pdb=" O LYS M 37 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 104 removed outlier: 3.567A pdb=" N ALA M 101 " --> pdb=" O ASP M 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 70 removed outlier: 3.891A pdb=" N LYS N 37 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N HIS N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 90 removed outlier: 4.467A pdb=" N LYS N 75 " --> pdb=" O SER N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 105 removed outlier: 3.612A pdb=" N ALA N 101 " --> pdb=" O ASP N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 105 removed outlier: 4.534A pdb=" N LYS O 34 " --> pdb=" O ASN O 30 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN O 35 " --> pdb=" O ARG O 31 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS O 37 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU O 45 " --> pdb=" O GLN O 41 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN O 46 " --> pdb=" O ALA O 42 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS O 75 " --> pdb=" O SER O 71 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU O 76 " --> pdb=" O GLU O 72 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN O 78 " --> pdb=" O GLU O 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN O 91 " --> pdb=" O TYR O 87 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASP O 93 " --> pdb=" O GLU O 89 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU O 94 " --> pdb=" O GLN O 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 27 removed outlier: 3.864A pdb=" N GLU P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 39 removed outlier: 3.548A pdb=" N TYR P 36 " --> pdb=" O ASN P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 56 Processing helix chain 'P' and resid 58 through 83 removed outlier: 7.548A pdb=" N SER P 71 " --> pdb=" O GLN P 67 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLN P 72 " --> pdb=" O THR P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 104 removed outlier: 3.595A pdb=" N ASN P 104 " --> pdb=" O MET P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 118 removed outlier: 3.947A pdb=" N PHE P 111 " --> pdb=" O ARG P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 132 removed outlier: 4.660A pdb=" N LEU P 127 " --> pdb=" O PRO P 124 " (cutoff:3.500A) Proline residue: P 128 - end of helix Processing helix chain 'P' and resid 134 through 152 Processing helix chain 'P' and resid 157 through 173 Processing helix chain 'P' and resid 193 through 210 removed outlier: 4.370A pdb=" N CYS P 200 " --> pdb=" O GLN P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 221 removed outlier: 3.679A pdb=" N ARG P 215 " --> pdb=" O VAL P 211 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE P 216 " --> pdb=" O ASN P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 233 Processing helix chain 'P' and resid 236 through 251 Processing helix chain 'P' and resid 253 through 261 removed outlier: 4.259A pdb=" N ARG P 261 " --> pdb=" O CYS P 257 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 276 removed outlier: 4.430A pdb=" N VAL P 268 " --> pdb=" O ASN P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 278 through 295 Processing helix chain 'P' and resid 298 through 312 Processing helix chain 'P' and resid 313 through 324 removed outlier: 3.762A pdb=" N GLN P 317 " --> pdb=" O LYS P 313 " (cutoff:3.500A) Processing helix chain 'P' and resid 328 through 350 removed outlier: 4.483A pdb=" N ASP P 334 " --> pdb=" O ASP P 330 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER P 345 " --> pdb=" O LYS P 341 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLN P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP P 348 " --> pdb=" O GLU P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 352 through 362 removed outlier: 3.768A pdb=" N SER P 356 " --> pdb=" O PHE P 352 " (cutoff:3.500A) Processing helix chain 'P' and resid 367 through 372 Processing helix chain 'P' and resid 372 through 380 removed outlier: 4.369A pdb=" N TRP P 376 " --> pdb=" O SER P 372 " (cutoff:3.500A) Processing helix chain 'P' and resid 381 through 383 No H-bonds generated for 'chain 'P' and resid 381 through 383' Processing helix chain 'P' and resid 384 through 401 removed outlier: 6.230A pdb=" N LEU P 390 " --> pdb=" O LYS P 386 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU P 391 " --> pdb=" O ASN P 387 " (cutoff:3.500A) Processing helix chain 'P' and resid 403 through 421 Processing helix chain 'P' and resid 422 through 432 removed outlier: 4.110A pdb=" N ARG P 426 " --> pdb=" O PRO P 422 " (cutoff:3.500A) Processing helix chain 'P' and resid 433 through 441 removed outlier: 3.616A pdb=" N VAL P 437 " --> pdb=" O GLY P 433 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 461 Processing helix chain 'Q' and resid 14 through 37 removed outlier: 3.508A pdb=" N THR Q 35 " --> pdb=" O ARG Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 48 removed outlier: 4.293A pdb=" N ASP Q 48 " --> pdb=" O LYS Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 54 Processing helix chain 'Q' and resid 62 through 71 Processing helix chain 'Q' and resid 77 through 97 removed outlier: 3.863A pdb=" N LEU Q 91 " --> pdb=" O ILE Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 118 Processing helix chain 'Q' and resid 120 through 123 Processing helix chain 'Q' and resid 124 through 140 removed outlier: 3.509A pdb=" N LEU Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 167 Processing helix chain 'Q' and resid 172 through 188 removed outlier: 4.364A pdb=" N LYS Q 180 " --> pdb=" O ASN Q 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 192 through 207 Processing helix chain 'Q' and resid 218 through 234 removed outlier: 3.676A pdb=" N TYR Q 232 " --> pdb=" O THR Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 250 Processing helix chain 'Q' and resid 256 through 273 Processing helix chain 'R' and resid 14 through 37 Processing helix chain 'R' and resid 42 through 57 removed outlier: 4.055A pdb=" N ASP R 48 " --> pdb=" O LYS R 44 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA R 56 " --> pdb=" O VAL R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 71 Processing helix chain 'R' and resid 77 through 98 removed outlier: 3.588A pdb=" N LEU R 94 " --> pdb=" O GLU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 117 Processing helix chain 'R' and resid 120 through 123 Processing helix chain 'R' and resid 124 through 141 removed outlier: 3.959A pdb=" N TYR R 139 " --> pdb=" O GLN R 135 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS R 141 " --> pdb=" O THR R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 167 Processing helix chain 'R' and resid 172 through 188 Processing helix chain 'R' and resid 192 through 207 Processing helix chain 'R' and resid 218 through 234 Processing helix chain 'R' and resid 235 through 237 No H-bonds generated for 'chain 'R' and resid 235 through 237' Processing helix chain 'R' and resid 239 through 248 Processing helix chain 'R' and resid 249 through 252 Processing helix chain 'R' and resid 256 through 274 removed outlier: 3.682A pdb=" N LEU R 260 " --> pdb=" O THR R 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 37 Processing helix chain 'S' and resid 42 through 49 Processing helix chain 'S' and resid 49 through 54 Processing helix chain 'S' and resid 61 through 71 Processing helix chain 'S' and resid 77 through 98 removed outlier: 3.544A pdb=" N LEU S 88 " --> pdb=" O ARG S 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU S 94 " --> pdb=" O GLU S 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'S' and resid 120 through 123 Processing helix chain 'S' and resid 124 through 141 removed outlier: 3.739A pdb=" N TYR S 139 " --> pdb=" O GLN S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 167 Processing helix chain 'S' and resid 172 through 188 Processing helix chain 'S' and resid 192 through 207 Processing helix chain 'S' and resid 218 through 234 removed outlier: 3.712A pdb=" N TYR S 232 " --> pdb=" O THR S 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 250 removed outlier: 3.570A pdb=" N GLN S 243 " --> pdb=" O SER S 239 " (cutoff:3.500A) Processing helix chain 'S' and resid 256 through 274 Processing helix chain 'T' and resid 63 through 72 removed outlier: 3.617A pdb=" N GLN T 69 " --> pdb=" O MET T 65 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG T 72 " --> pdb=" O GLU T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 25 removed outlier: 6.697A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 28 through 32 current: chain 'A' and resid 50 through 58 removed outlier: 6.527A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 61 through 66 current: chain 'B' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 28 through 32 current: chain 'B' and resid 50 through 58 removed outlier: 6.625A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 61 through 66 current: chain 'C' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 28 through 32 current: chain 'C' and resid 50 through 58 removed outlier: 6.643A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 61 through 66 current: chain 'D' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 60 current: chain 'D' and resid 81 through 90 removed outlier: 6.667A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 93 through 98 current: chain 'E' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 60 current: chain 'E' and resid 81 through 90 removed outlier: 5.578A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 93 through 98 current: chain 'F' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 57 through 60 current: chain 'F' and resid 81 through 90 removed outlier: 5.759A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 93 through 98 current: chain 'I' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 164 through 167 current: chain 'I' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 190 through 195 current: chain 'J' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 164 through 167 current: chain 'J' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 190 through 195 current: chain 'K' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 164 through 167 current: chain 'K' and resid 190 through 195 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 98 through 100 current: chain 'A' and resid 309 through 315 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 309 through 315 current: chain 'A' and resid 401 through 410 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 401 through 410 current: chain 'A' and resid 454 through 455 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 167 removed outlier: 3.506A pdb=" N GLY A 154 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 6.397A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 98 through 99 current: chain 'B' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 309 through 312 current: chain 'B' and resid 401 through 410 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 401 through 410 current: chain 'B' and resid 454 through 455 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 167 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.579A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 226 through 227 removed outlier: 4.807A pdb=" N CYS B 240 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AB4, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AB5, first strand: chain 'C' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 98 through 100 current: chain 'C' and resid 309 through 314 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 309 through 314 current: chain 'C' and resid 401 through 410 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 401 through 410 current: chain 'C' and resid 454 through 455 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 163 through 167 removed outlier: 5.392A pdb=" N GLU C 134 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.330A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 123 Processing sheet with id=AC1, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AC2, first strand: chain 'D' and resid 163 through 164 removed outlier: 4.453A pdb=" N ARG D 340 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 183 through 184 removed outlier: 4.493A pdb=" N ILE D 183 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AC5, first strand: chain 'E' and resid 131 through 133 removed outlier: 6.498A pdb=" N ILE E 191 " --> pdb=" O LEU E 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 163 through 164 removed outlier: 4.237A pdb=" N ARG E 340 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 183 through 184 removed outlier: 4.720A pdb=" N ILE E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 120 through 123 Processing sheet with id=AC9, first strand: chain 'F' and resid 130 through 133 removed outlier: 6.666A pdb=" N ARG F 130 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU F 261 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE F 132 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU F 263 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 297 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE F 191 " --> pdb=" O LEU F 354 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 163 through 164 removed outlier: 4.271A pdb=" N ARG F 340 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 183 through 184 removed outlier: 4.401A pdb=" N ILE F 183 " --> pdb=" O ILE F 170 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 33 through 38 removed outlier: 4.615A pdb=" N ALA G 318 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU G 3 " --> pdb=" O PRO G 323 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL G 370 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AD5, first strand: chain 'G' and resid 214 through 218 removed outlier: 3.729A pdb=" N ASN G 214 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU G 224 " --> pdb=" O LEU G 216 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLU G 218 " --> pdb=" O SER G 222 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER G 222 " --> pdb=" O GLU G 218 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 92 through 101 Processing sheet with id=AD7, first strand: chain 'L' and resid 36 through 38 removed outlier: 8.713A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU L 7 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU L 65 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA L 9 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ASN L 67 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE L 11 " --> pdb=" O ASN L 67 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY L 62 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU L 89 " --> pdb=" O GLY L 62 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE L 64 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE L 91 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE L 66 " --> pdb=" O ILE L 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'T' and resid 83 through 88 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 83 through 88 current: chain 'T' and resid 121 through 126 removed outlier: 4.405A pdb=" N ILE T 121 " --> pdb=" O PHE T 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 151 through 155 current: chain 'T' and resid 170 through 173 removed outlier: 6.367A pdb=" N HIS T 190 " --> pdb=" O ASP T 185 " (cutoff:3.500A) 2715 hydrogen bonds defined for protein. 7917 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: 19.16 Time building geometry restraints manager: 14.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10159 1.32 - 1.45: 10808 1.45 - 1.57: 29071 1.57 - 1.70: 1 1.70 - 1.83: 447 Bond restraints: 50486 Sorted by residual: bond pdb=" C4 ADP C 701 " pdb=" C5 ADP C 701 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C5 ADP C 701 " pdb=" C6 ADP C 701 " ideal model delta sigma weight residual 1.490 1.387 0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" CZ ARG B 338 " pdb=" NH2 ARG B 338 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.30e-02 5.92e+03 1.28e+01 bond pdb=" CZ ARG A 338 " pdb=" NH2 ARG A 338 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" CA PRO B 169 " pdb=" C PRO B 169 " ideal model delta sigma weight residual 1.514 1.534 -0.019 5.50e-03 3.31e+04 1.25e+01 ... (remaining 50481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 59250 2.64 - 5.28: 8603 5.28 - 7.93: 241 7.93 - 10.57: 13 10.57 - 13.21: 2 Bond angle restraints: 68109 Sorted by residual: angle pdb=" CA ASP L 60 " pdb=" CB ASP L 60 " pdb=" CG ASP L 60 " ideal model delta sigma weight residual 112.60 120.02 -7.42 1.00e+00 1.00e+00 5.51e+01 angle pdb=" CA ASN L 67 " pdb=" CB ASN L 67 " pdb=" CG ASN L 67 " ideal model delta sigma weight residual 112.60 119.18 -6.58 1.00e+00 1.00e+00 4.33e+01 angle pdb=" CA ASP B 466 " pdb=" CB ASP B 466 " pdb=" CG ASP B 466 " ideal model delta sigma weight residual 112.60 119.10 -6.50 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA ASP C 186 " pdb=" CB ASP C 186 " pdb=" CG ASP C 186 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 angle pdb=" CA ASP E 359 " pdb=" CB ASP E 359 " pdb=" CG ASP E 359 " ideal model delta sigma weight residual 112.60 118.74 -6.14 1.00e+00 1.00e+00 3.77e+01 ... (remaining 68104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 30567 35.99 - 71.97: 439 71.97 - 107.96: 70 107.96 - 143.94: 1 143.94 - 179.93: 1 Dihedral angle restraints: 31078 sinusoidal: 12891 harmonic: 18187 Sorted by residual: dihedral pdb=" O1B ADP C 701 " pdb=" O3A ADP C 701 " pdb=" PB ADP C 701 " pdb=" PA ADP C 701 " ideal model delta sinusoidal sigma weight residual 300.00 120.07 179.93 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA LEU H 202 " pdb=" C LEU H 202 " pdb=" N LYS H 203 " pdb=" CA LYS H 203 " ideal model delta harmonic sigma weight residual 180.00 150.68 29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLU G 12 " pdb=" C GLU G 12 " pdb=" N LYS G 13 " pdb=" CA LYS G 13 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 31075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 5929 0.103 - 0.206: 1499 0.206 - 0.309: 150 0.309 - 0.412: 27 0.412 - 0.515: 4 Chirality restraints: 7609 Sorted by residual: chirality pdb=" CA ASP F 299 " pdb=" N ASP F 299 " pdb=" C ASP F 299 " pdb=" CB ASP F 299 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CA ASP E 299 " pdb=" N ASP E 299 " pdb=" C ASP E 299 " pdb=" CB ASP E 299 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA TYR A 40 " pdb=" N TYR A 40 " pdb=" C TYR A 40 " pdb=" CB TYR A 40 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 7606 not shown) Planarity restraints: 8813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP T 218 " 0.171 2.00e-02 2.50e+03 9.39e-02 2.21e+02 pdb=" CG TRP T 218 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP T 218 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP T 218 " -0.104 2.00e-02 2.50e+03 pdb=" NE1 TRP T 218 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TRP T 218 " -0.050 2.00e-02 2.50e+03 pdb=" CE3 TRP T 218 " -0.126 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 218 " 0.091 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 218 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP T 218 " 0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 122 " -0.138 2.00e-02 2.50e+03 7.88e-02 1.55e+02 pdb=" CG TRP R 122 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP R 122 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP R 122 " 0.065 2.00e-02 2.50e+03 pdb=" NE1 TRP R 122 " 0.073 2.00e-02 2.50e+03 pdb=" CE2 TRP R 122 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP R 122 " 0.114 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 122 " -0.093 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 122 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP R 122 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 114 " 0.158 2.00e-02 2.50e+03 8.78e-02 1.54e+02 pdb=" CG TYR O 114 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR O 114 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TYR O 114 " -0.073 2.00e-02 2.50e+03 pdb=" CE1 TYR O 114 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR O 114 " -0.048 2.00e-02 2.50e+03 pdb=" CZ TYR O 114 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR O 114 " 0.138 2.00e-02 2.50e+03 ... (remaining 8810 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 18336 2.91 - 3.41: 49483 3.41 - 3.91: 83452 3.91 - 4.40: 93042 4.40 - 4.90: 160485 Nonbonded interactions: 404798 Sorted by model distance: nonbonded pdb=" OG1 THR C 257 " pdb="MG MG C 702 " model vdw 2.417 2.170 nonbonded pdb=" O2B ADP C 701 " pdb="MG MG C 702 " model vdw 2.442 2.170 nonbonded pdb=" OH TYR F 303 " pdb=" OD1 ASP F 330 " model vdw 2.500 3.040 nonbonded pdb=" OH TYR D 303 " pdb=" OD1 ASP D 330 " model vdw 2.513 3.040 nonbonded pdb=" OH TYR E 303 " pdb=" OD1 ASP E 330 " model vdw 2.541 3.040 ... (remaining 404793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 16 through 250 or resid 258 through 412 or resid 418 throu \ gh 615)) selection = (chain 'C' and (resid 16 through 250 or resid 258 through 412 or resid 418 throu \ gh 615)) } ncs_group { reference = (chain 'D' and (resid 38 through 213 or resid 226 through 506)) selection = (chain 'E' and (resid 38 through 213 or resid 226 through 506)) selection = chain 'F' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 9 through 226) selection = chain 'K' } ncs_group { reference = chain 'M' selection = (chain 'N' and resid 6 through 116) selection = (chain 'O' and resid 6 through 116) } ncs_group { reference = chain 'Q' selection = (chain 'R' and resid 13 through 274) selection = (chain 'S' and resid 13 through 274) } 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: 2.250 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: 0.030 Extract box with map and model: 1.940 Check model and map are aligned: 0.340 Set scattering table: 0.410 Process input model: 101.040 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 111.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.142 50486 Z= 0.780 Angle : 1.742 13.209 68109 Z= 1.182 Chirality : 0.088 0.515 7609 Planarity : 0.015 0.189 8813 Dihedral : 13.567 179.929 19334 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.11 % Favored : 96.66 % Rotamer: Outliers : 0.68 % Allowed : 2.98 % Favored : 96.34 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.10), residues: 6176 helix: -0.46 (0.08), residues: 3234 sheet: 0.09 (0.19), residues: 660 loop : -0.39 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.171 0.028 TRP T 218 HIS 0.018 0.003 HIS L 33 PHE 0.111 0.012 PHE P 49 TYR 0.158 0.021 TYR O 114 ARG 0.015 0.001 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1433 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 1396 time to evaluate : 5.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7730 (tt0) cc_final: 0.7517 (tt0) REVERT: A 359 ARG cc_start: 0.9120 (ttp-170) cc_final: 0.8460 (ttp-170) REVERT: A 384 SER cc_start: 0.8954 (t) cc_final: 0.8662 (p) REVERT: A 467 LYS cc_start: 0.8138 (tttt) cc_final: 0.7840 (tppp) REVERT: B 167 MET cc_start: 0.9319 (mtm) cc_final: 0.9111 (mtp) REVERT: B 197 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8112 (tm-30) REVERT: B 443 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8551 (mmtm) REVERT: B 550 MET cc_start: 0.7769 (mmm) cc_final: 0.7175 (mtt) REVERT: B 574 MET cc_start: 0.7816 (mtp) cc_final: 0.7609 (mtt) REVERT: B 604 LEU cc_start: 0.8078 (mp) cc_final: 0.7838 (mp) REVERT: B 605 LEU cc_start: 0.8467 (tp) cc_final: 0.7837 (tp) REVERT: B 609 GLN cc_start: 0.8582 (mt0) cc_final: 0.8016 (mt0) REVERT: C 61 MET cc_start: 0.8676 (mtt) cc_final: 0.8274 (mtm) REVERT: C 95 MET cc_start: 0.9489 (mmp) cc_final: 0.9207 (mmp) REVERT: C 468 HIS cc_start: 0.8833 (m-70) cc_final: 0.8386 (m170) REVERT: C 471 GLU cc_start: 0.7805 (pm20) cc_final: 0.7536 (pm20) REVERT: C 485 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7300 (mt-10) REVERT: C 550 MET cc_start: 0.7319 (mmm) cc_final: 0.6908 (mtt) REVERT: C 584 MET cc_start: 0.8920 (mtm) cc_final: 0.8539 (mtp) REVERT: C 598 LYS cc_start: 0.7545 (mtmt) cc_final: 0.7282 (mtmm) REVERT: C 607 ASP cc_start: 0.6734 (m-30) cc_final: 0.6327 (m-30) REVERT: D 106 ASP cc_start: 0.8861 (p0) cc_final: 0.8600 (p0) REVERT: D 251 ASN cc_start: 0.7699 (t0) cc_final: 0.7221 (t0) REVERT: D 345 ASN cc_start: 0.8364 (t0) cc_final: 0.7944 (t0) REVERT: E 127 MET cc_start: 0.8978 (mtp) cc_final: 0.8700 (mtt) REVERT: E 410 MET cc_start: 0.9268 (mtm) cc_final: 0.9058 (mtm) REVERT: F 249 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7731 (mt-10) REVERT: F 365 ILE cc_start: 0.9341 (mt) cc_final: 0.9016 (mt) REVERT: F 369 THR cc_start: 0.9515 (m) cc_final: 0.9215 (m) REVERT: F 387 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8298 (mp10) REVERT: F 485 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7747 (mtt90) REVERT: F 491 MET cc_start: 0.8699 (mtp) cc_final: 0.8467 (mtp) REVERT: H 27 GLN cc_start: 0.7660 (mt0) cc_final: 0.6865 (mt0) REVERT: I 89 ASP cc_start: 0.7531 (m-30) cc_final: 0.7307 (m-30) REVERT: I 93 ASP cc_start: 0.7924 (m-30) cc_final: 0.7695 (m-30) REVERT: I 108 ASP cc_start: 0.7821 (t0) cc_final: 0.7293 (t0) REVERT: I 125 TYR cc_start: 0.9339 (m-10) cc_final: 0.9086 (m-10) REVERT: I 132 MET cc_start: 0.8893 (mtm) cc_final: 0.8535 (mtm) REVERT: I 154 MET cc_start: 0.8775 (mtm) cc_final: 0.8545 (mtm) REVERT: J 19 ILE cc_start: 0.9548 (mt) cc_final: 0.9044 (mm) REVERT: J 24 ASN cc_start: 0.9592 (m-40) cc_final: 0.8657 (m110) REVERT: J 25 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8499 (tm-30) REVERT: J 29 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7761 (mm-30) REVERT: J 54 MET cc_start: 0.8662 (ttm) cc_final: 0.8336 (ttp) REVERT: J 57 TYR cc_start: 0.8146 (m-80) cc_final: 0.7742 (m-80) REVERT: J 97 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7696 (mm-30) REVERT: J 141 PHE cc_start: 0.8657 (t80) cc_final: 0.8307 (t80) REVERT: K 18 PHE cc_start: 0.9315 (t80) cc_final: 0.8872 (t80) REVERT: K 58 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8230 (mt-10) REVERT: K 69 LYS cc_start: 0.7370 (mttt) cc_final: 0.7084 (mtmt) REVERT: L 112 MET cc_start: 0.6076 (ttm) cc_final: 0.5489 (mpp) REVERT: O 98 ASN cc_start: 0.8313 (m-40) cc_final: 0.8036 (m-40) REVERT: O 102 PHE cc_start: 0.7952 (m-80) cc_final: 0.7282 (m-10) REVERT: O 104 CYS cc_start: 0.8507 (m) cc_final: 0.8097 (m) REVERT: O 105 ASP cc_start: 0.8078 (t0) cc_final: 0.7840 (t70) REVERT: P 156 MET cc_start: 0.0091 (mtp) cc_final: -0.2121 (mmt) REVERT: P 391 LEU cc_start: 0.9341 (mt) cc_final: 0.9041 (mt) REVERT: P 434 LYS cc_start: 0.9352 (pttp) cc_final: 0.9075 (mtpt) REVERT: P 451 ASN cc_start: 0.9181 (m-40) cc_final: 0.8590 (t0) REVERT: Q 98 ILE cc_start: 0.7977 (mt) cc_final: 0.7763 (mt) REVERT: Q 101 PHE cc_start: 0.8670 (m-80) cc_final: 0.8445 (m-10) REVERT: Q 103 MET cc_start: 0.7713 (mtp) cc_final: 0.7471 (ttm) REVERT: Q 107 LEU cc_start: 0.8720 (mt) cc_final: 0.8290 (mt) REVERT: Q 188 MET cc_start: 0.7145 (ttm) cc_final: 0.6802 (ttm) REVERT: Q 229 MET cc_start: 0.8946 (tpp) cc_final: 0.7983 (mmt) REVERT: R 96 SER cc_start: 0.9039 (m) cc_final: 0.8774 (p) REVERT: R 125 ASP cc_start: 0.8290 (m-30) cc_final: 0.8074 (t70) REVERT: R 168 ILE cc_start: 0.8752 (mm) cc_final: 0.8534 (pt) REVERT: R 205 LYS cc_start: 0.8469 (tptt) cc_final: 0.7918 (mmmt) REVERT: R 213 PHE cc_start: 0.8533 (m-80) cc_final: 0.8235 (m-10) REVERT: R 234 MET cc_start: 0.8486 (ttm) cc_final: 0.7942 (mmm) REVERT: S 60 TYR cc_start: 0.4011 (p90) cc_final: 0.3667 (p90) REVERT: S 129 LYS cc_start: 0.8676 (mttp) cc_final: 0.8427 (ttmm) REVERT: S 188 MET cc_start: 0.7253 (tpp) cc_final: 0.6818 (ttm) REVERT: S 197 TYR cc_start: 0.7098 (m-80) cc_final: 0.6892 (t80) REVERT: S 229 MET cc_start: 0.8143 (tpp) cc_final: 0.7736 (mmm) REVERT: S 255 LEU cc_start: 0.8418 (tp) cc_final: 0.8149 (tp) REVERT: T 90 LEU cc_start: 0.9013 (tp) cc_final: 0.8604 (mt) REVERT: T 117 MET cc_start: 0.8710 (mmt) cc_final: 0.8297 (mmt) REVERT: T 118 ASP cc_start: 0.8274 (m-30) cc_final: 0.8016 (m-30) outliers start: 37 outliers final: 8 residues processed: 1417 average time/residue: 0.7243 time to fit residues: 1623.5541 Evaluate side-chains 898 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 889 time to evaluate : 5.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain P residue 256 MET Chi-restraints excluded: chain P residue 447 GLN Chi-restraints excluded: chain T residue 77 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 5.9990 chunk 466 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 314 optimal weight: 0.9990 chunk 249 optimal weight: 0.8980 chunk 482 optimal weight: 40.0000 chunk 186 optimal weight: 0.9980 chunk 293 optimal weight: 0.6980 chunk 359 optimal weight: 1.9990 chunk 559 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 468 HIS A 609 GLN B 213 GLN B 610 ASN C 430 GLN C 468 HIS D 38 ASN D 482 GLN G 286 ASN I 139 GLN J 96 ASN K 49 GLN L 96 HIS N 66 HIS N 85 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 GLN P 451 ASN P 457 GLN Q 198 HIS Q 207 GLN Q 274 ASN T 135 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 50486 Z= 0.216 Angle : 0.647 9.394 68109 Z= 0.344 Chirality : 0.044 0.178 7609 Planarity : 0.005 0.058 8813 Dihedral : 6.208 173.505 6820 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.20 % Favored : 97.78 % Rotamer: Outliers : 1.90 % Allowed : 8.14 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.10), residues: 6176 helix: 1.22 (0.09), residues: 3177 sheet: 0.07 (0.18), residues: 711 loop : -0.03 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 567 HIS 0.016 0.001 HIS A 573 PHE 0.026 0.002 PHE P 49 TYR 0.034 0.002 TYR K 57 ARG 0.009 0.001 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 939 time to evaluate : 6.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.9254 (p) cc_final: 0.9039 (m) REVERT: A 268 ASN cc_start: 0.7542 (m-40) cc_final: 0.7337 (m-40) REVERT: A 384 SER cc_start: 0.8882 (t) cc_final: 0.8563 (p) REVERT: A 442 ARG cc_start: 0.6813 (mtt90) cc_final: 0.6294 (mpt180) REVERT: A 483 LEU cc_start: 0.8634 (mt) cc_final: 0.8220 (mt) REVERT: A 501 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7997 (tt) REVERT: A 578 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7868 (pp) REVERT: B 213 GLN cc_start: 0.8525 (mt0) cc_final: 0.8315 (mt0) REVERT: B 283 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: B 443 LYS cc_start: 0.8967 (mmtm) cc_final: 0.8702 (mmmm) REVERT: B 471 GLU cc_start: 0.7864 (pm20) cc_final: 0.7574 (pm20) REVERT: B 550 MET cc_start: 0.7603 (mmm) cc_final: 0.7207 (mtt) REVERT: B 603 GLN cc_start: 0.8014 (tp40) cc_final: 0.7773 (tp40) REVERT: C 61 MET cc_start: 0.8616 (mtt) cc_final: 0.8273 (mtm) REVERT: C 95 MET cc_start: 0.9488 (mmp) cc_final: 0.9219 (mmp) REVERT: C 438 LYS cc_start: 0.8502 (mttt) cc_final: 0.8148 (mmtp) REVERT: C 485 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7281 (mt-10) REVERT: C 550 MET cc_start: 0.7066 (mmm) cc_final: 0.6658 (mtt) REVERT: C 584 MET cc_start: 0.8834 (mtm) cc_final: 0.8353 (mtp) REVERT: C 607 ASP cc_start: 0.6299 (m-30) cc_final: 0.6077 (m-30) REVERT: C 608 MET cc_start: 0.6729 (ptm) cc_final: 0.6454 (ptm) REVERT: D 141 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7823 (mtp-110) REVERT: D 238 MET cc_start: 0.8982 (tpp) cc_final: 0.8728 (tpp) REVERT: D 251 ASN cc_start: 0.7630 (t0) cc_final: 0.7157 (t0) REVERT: D 345 ASN cc_start: 0.8428 (t0) cc_final: 0.7953 (t0) REVERT: F 330 ASP cc_start: 0.8890 (t0) cc_final: 0.8677 (t0) REVERT: F 369 THR cc_start: 0.9512 (m) cc_final: 0.9222 (m) REVERT: G 338 LEU cc_start: 0.8626 (tp) cc_final: 0.8402 (tp) REVERT: G 377 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7494 (t0) REVERT: I 70 ILE cc_start: 0.7921 (mp) cc_final: 0.7670 (mp) REVERT: I 76 MET cc_start: 0.8315 (mmm) cc_final: 0.8086 (mmm) REVERT: I 129 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8184 (tp30) REVERT: J 24 ASN cc_start: 0.9414 (m-40) cc_final: 0.9136 (m110) REVERT: J 72 MET cc_start: 0.7905 (mmp) cc_final: 0.7568 (tpp) REVERT: J 75 LEU cc_start: 0.8577 (mm) cc_final: 0.7920 (pp) REVERT: J 96 ASN cc_start: 0.8007 (m110) cc_final: 0.7758 (m-40) REVERT: J 141 PHE cc_start: 0.8666 (t80) cc_final: 0.8355 (t80) REVERT: J 172 TYR cc_start: 0.8792 (m-80) cc_final: 0.8306 (m-80) REVERT: K 15 MET cc_start: 0.8181 (mtt) cc_final: 0.7714 (mmt) REVERT: K 18 PHE cc_start: 0.9315 (t80) cc_final: 0.8943 (t80) REVERT: K 52 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8780 (ptpp) REVERT: K 58 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8543 (tp30) REVERT: L 108 ARG cc_start: 0.7669 (mmt90) cc_final: 0.7352 (mtt180) REVERT: L 112 MET cc_start: 0.5928 (ttm) cc_final: 0.5486 (pmm) REVERT: M 74 GLU cc_start: 0.8395 (tp30) cc_final: 0.8177 (tm-30) REVERT: N 11 LEU cc_start: 0.8934 (mt) cc_final: 0.8620 (mt) REVERT: N 16 LYS cc_start: 0.9218 (mttt) cc_final: 0.8953 (mttp) REVERT: N 34 LYS cc_start: 0.9147 (ptpp) cc_final: 0.8931 (ptpp) REVERT: N 75 LYS cc_start: 0.8762 (tmmt) cc_final: 0.7962 (ptpp) REVERT: O 102 PHE cc_start: 0.7763 (m-80) cc_final: 0.7022 (m-10) REVERT: O 104 CYS cc_start: 0.8067 (m) cc_final: 0.7692 (m) REVERT: P 100 MET cc_start: -0.0420 (ppp) cc_final: -0.0699 (ppp) REVERT: P 156 MET cc_start: -0.0653 (mtp) cc_final: -0.2240 (mmt) REVERT: P 309 MET cc_start: 0.7579 (mtm) cc_final: 0.6607 (mpp) REVERT: P 391 LEU cc_start: 0.9284 (mt) cc_final: 0.8898 (mt) REVERT: P 451 ASN cc_start: 0.9257 (m110) cc_final: 0.8815 (t0) REVERT: Q 34 GLN cc_start: 0.8331 (tm-30) cc_final: 0.8120 (tm-30) REVERT: Q 60 TYR cc_start: 0.8426 (m-80) cc_final: 0.8165 (m-80) REVERT: Q 181 LEU cc_start: 0.8481 (mm) cc_final: 0.8144 (tp) REVERT: Q 188 MET cc_start: 0.7143 (ttm) cc_final: 0.6648 (ttm) REVERT: R 96 SER cc_start: 0.9059 (m) cc_final: 0.8823 (p) REVERT: R 109 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7574 (tm-30) REVERT: R 161 MET cc_start: 0.8532 (tmm) cc_final: 0.8226 (tmm) REVERT: R 199 LEU cc_start: 0.8924 (tp) cc_final: 0.8714 (tt) REVERT: R 205 LYS cc_start: 0.8438 (tptt) cc_final: 0.7929 (mmmt) REVERT: R 256 THR cc_start: 0.8679 (p) cc_final: 0.8413 (t) REVERT: S 10 MET cc_start: 0.7111 (mtm) cc_final: 0.6909 (mtt) REVERT: S 60 TYR cc_start: 0.4585 (OUTLIER) cc_final: 0.4382 (p90) REVERT: S 103 MET cc_start: 0.6701 (mtp) cc_final: 0.6435 (ttm) REVERT: S 168 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8277 (pt) REVERT: S 188 MET cc_start: 0.7235 (tpp) cc_final: 0.6754 (ttm) REVERT: S 232 TYR cc_start: 0.7502 (t80) cc_final: 0.6408 (t80) REVERT: T 90 LEU cc_start: 0.8980 (tp) cc_final: 0.8510 (mt) outliers start: 103 outliers final: 51 residues processed: 992 average time/residue: 0.6454 time to fit residues: 1036.9882 Evaluate side-chains 845 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 788 time to evaluate : 5.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain T residue 170 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 310 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 465 optimal weight: 5.9990 chunk 380 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 560 optimal weight: 3.9990 chunk 605 optimal weight: 0.8980 chunk 499 optimal weight: 9.9990 chunk 555 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 449 optimal weight: 30.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 HIS A 468 HIS B 164 HIS B 573 HIS B 610 ASN C 164 HIS F 226 ASN F 345 ASN K 96 ASN L 67 ASN Q 41 ASN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 198 HIS Q 222 GLN S 59 ASN T 213 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 50486 Z= 0.341 Angle : 0.632 11.768 68109 Z= 0.331 Chirality : 0.045 0.241 7609 Planarity : 0.005 0.047 8813 Dihedral : 5.753 171.953 6801 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.06 % Allowed : 9.83 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.11), residues: 6176 helix: 1.51 (0.09), residues: 3172 sheet: -0.12 (0.19), residues: 664 loop : -0.27 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 197 HIS 0.014 0.001 HIS Q 198 PHE 0.029 0.002 PHE G 230 TYR 0.043 0.002 TYR M 47 ARG 0.007 0.001 ARG C 553 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 820 time to evaluate : 6.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.9297 (p) cc_final: 0.9058 (m) REVERT: A 297 GLU cc_start: 0.7477 (tt0) cc_final: 0.7062 (tt0) REVERT: A 384 SER cc_start: 0.9025 (t) cc_final: 0.8666 (p) REVERT: A 483 LEU cc_start: 0.8595 (mt) cc_final: 0.8308 (mt) REVERT: A 501 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8087 (tt) REVERT: A 518 ASP cc_start: 0.6453 (m-30) cc_final: 0.6251 (t0) REVERT: A 523 ASN cc_start: 0.7208 (t0) cc_final: 0.6682 (t0) REVERT: B 443 LYS cc_start: 0.9124 (mmtm) cc_final: 0.8881 (mmmm) REVERT: B 471 GLU cc_start: 0.7819 (pm20) cc_final: 0.7385 (pm20) REVERT: B 486 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8257 (tm-30) REVERT: B 530 ARG cc_start: 0.7888 (ptp90) cc_final: 0.7646 (ptm-80) REVERT: B 550 MET cc_start: 0.7788 (mmm) cc_final: 0.7132 (mtt) REVERT: B 552 ARG cc_start: 0.8033 (ttt-90) cc_final: 0.7716 (ttt90) REVERT: B 603 GLN cc_start: 0.8036 (tp40) cc_final: 0.7816 (tp40) REVERT: B 604 LEU cc_start: 0.7808 (tp) cc_final: 0.7414 (tt) REVERT: B 609 GLN cc_start: 0.8910 (mt0) cc_final: 0.8550 (mm-40) REVERT: C 61 MET cc_start: 0.8643 (mtt) cc_final: 0.8362 (mtm) REVERT: C 95 MET cc_start: 0.9482 (mmp) cc_final: 0.9221 (mmp) REVERT: C 485 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7384 (mt-10) REVERT: C 550 MET cc_start: 0.7028 (mmm) cc_final: 0.6741 (mtt) REVERT: C 607 ASP cc_start: 0.6439 (m-30) cc_final: 0.6198 (m-30) REVERT: D 251 ASN cc_start: 0.7623 (t0) cc_final: 0.7139 (t0) REVERT: D 345 ASN cc_start: 0.8349 (t0) cc_final: 0.7786 (t0) REVERT: D 410 MET cc_start: 0.7751 (mmm) cc_final: 0.7503 (mpp) REVERT: E 54 ASN cc_start: 0.8799 (t0) cc_final: 0.8492 (t0) REVERT: E 475 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: F 226 ASN cc_start: 0.7492 (OUTLIER) cc_final: 0.7175 (m110) REVERT: F 330 ASP cc_start: 0.8818 (t0) cc_final: 0.8606 (t0) REVERT: F 369 THR cc_start: 0.9585 (m) cc_final: 0.9320 (m) REVERT: F 485 ARG cc_start: 0.8451 (ttm110) cc_final: 0.8161 (ttm170) REVERT: I 72 MET cc_start: 0.8101 (tpp) cc_final: 0.7897 (mmt) REVERT: I 76 MET cc_start: 0.8357 (mmm) cc_final: 0.8147 (mmm) REVERT: I 154 MET cc_start: 0.9015 (mtm) cc_final: 0.8791 (mtm) REVERT: J 21 GLN cc_start: 0.9071 (tp40) cc_final: 0.8865 (tp40) REVERT: J 24 ASN cc_start: 0.9423 (m-40) cc_final: 0.9110 (m110) REVERT: J 96 ASN cc_start: 0.8147 (m110) cc_final: 0.7895 (m-40) REVERT: J 141 PHE cc_start: 0.8688 (t80) cc_final: 0.8315 (t80) REVERT: J 155 TYR cc_start: 0.9378 (t80) cc_final: 0.9099 (t80) REVERT: J 172 TYR cc_start: 0.8852 (m-80) cc_final: 0.8379 (m-10) REVERT: K 15 MET cc_start: 0.8431 (mtt) cc_final: 0.7886 (mmt) REVERT: K 18 PHE cc_start: 0.9305 (t80) cc_final: 0.8952 (t80) REVERT: K 52 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8842 (mttt) REVERT: K 58 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8362 (mt-10) REVERT: L 108 ARG cc_start: 0.7630 (mmt90) cc_final: 0.7157 (mtt180) REVERT: L 112 MET cc_start: 0.5761 (ttm) cc_final: 0.5126 (pmm) REVERT: M 74 GLU cc_start: 0.8386 (tp30) cc_final: 0.8125 (tm-30) REVERT: N 16 LYS cc_start: 0.9172 (mttt) cc_final: 0.8891 (mttt) REVERT: N 26 ARG cc_start: 0.8558 (ptp-110) cc_final: 0.8245 (mtt-85) REVERT: O 81 MET cc_start: 0.7874 (mtp) cc_final: 0.7633 (mtm) REVERT: O 104 CYS cc_start: 0.8166 (m) cc_final: 0.7796 (m) REVERT: P 96 MET cc_start: 0.5251 (mtp) cc_final: 0.4886 (ptp) REVERT: P 156 MET cc_start: -0.0661 (mtp) cc_final: -0.2302 (mmt) REVERT: P 309 MET cc_start: 0.7774 (mtm) cc_final: 0.6838 (mpp) REVERT: P 391 LEU cc_start: 0.9301 (mt) cc_final: 0.9044 (mt) REVERT: P 451 ASN cc_start: 0.9217 (m110) cc_final: 0.8821 (t0) REVERT: Q 46 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7390 (mtt180) REVERT: Q 90 GLU cc_start: 0.8948 (tp30) cc_final: 0.8327 (tp30) REVERT: Q 115 MET cc_start: 0.7477 (mmt) cc_final: 0.7164 (mmt) REVERT: Q 126 TYR cc_start: 0.5010 (t80) cc_final: 0.4768 (t80) REVERT: Q 161 MET cc_start: 0.8848 (tmm) cc_final: 0.8599 (tmm) REVERT: Q 178 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8114 (tt) REVERT: Q 181 LEU cc_start: 0.8700 (mm) cc_final: 0.8141 (tp) REVERT: Q 188 MET cc_start: 0.7430 (ttm) cc_final: 0.6859 (ttm) REVERT: R 96 SER cc_start: 0.9060 (m) cc_final: 0.8835 (p) REVERT: R 109 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7403 (tm-30) REVERT: R 146 THR cc_start: 0.8368 (t) cc_final: 0.8144 (t) REVERT: R 161 MET cc_start: 0.8454 (tmm) cc_final: 0.8043 (tmm) REVERT: R 199 LEU cc_start: 0.8919 (tp) cc_final: 0.8717 (tt) REVERT: R 205 LYS cc_start: 0.8595 (tptt) cc_final: 0.8134 (mmmt) REVERT: S 93 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8639 (ttp80) REVERT: S 103 MET cc_start: 0.6830 (mtp) cc_final: 0.6493 (ttm) REVERT: S 170 GLU cc_start: 0.8075 (tp30) cc_final: 0.7867 (tp30) REVERT: S 188 MET cc_start: 0.7286 (tpp) cc_final: 0.6766 (ttm) REVERT: S 197 TYR cc_start: 0.7291 (t80) cc_final: 0.6847 (t80) REVERT: T 90 LEU cc_start: 0.9129 (tp) cc_final: 0.8705 (mt) outliers start: 112 outliers final: 73 residues processed: 885 average time/residue: 0.6622 time to fit residues: 949.2518 Evaluate side-chains 845 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 768 time to evaluate : 6.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 178 LEU Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 209 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 553 optimal weight: 8.9990 chunk 421 optimal weight: 0.9980 chunk 290 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 376 optimal weight: 2.9990 chunk 562 optimal weight: 1.9990 chunk 595 optimal weight: 20.0000 chunk 293 optimal weight: 3.9990 chunk 533 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 444 HIS B 157 ASN F 181 ASN F 226 ASN K 126 GLN P 347 GLN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 ASN Q 198 HIS S 59 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 50486 Z= 0.349 Angle : 0.613 12.886 68109 Z= 0.318 Chirality : 0.044 0.193 7609 Planarity : 0.004 0.047 8813 Dihedral : 5.568 169.014 6801 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.41 % Allowed : 10.66 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.11), residues: 6176 helix: 1.67 (0.09), residues: 3173 sheet: -0.18 (0.19), residues: 696 loop : -0.36 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 567 HIS 0.009 0.001 HIS A 444 PHE 0.023 0.002 PHE P 49 TYR 0.025 0.002 TYR S 197 ARG 0.008 0.001 ARG N 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 812 time to evaluate : 5.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.9298 (p) cc_final: 0.9056 (m) REVERT: A 384 SER cc_start: 0.9042 (t) cc_final: 0.8672 (p) REVERT: A 518 ASP cc_start: 0.6404 (m-30) cc_final: 0.6201 (t0) REVERT: A 523 ASN cc_start: 0.7322 (t0) cc_final: 0.6918 (t0) REVERT: B 197 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 291 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: B 443 LYS cc_start: 0.9202 (mmtm) cc_final: 0.8953 (mmmm) REVERT: B 471 GLU cc_start: 0.7911 (pm20) cc_final: 0.7468 (pm20) REVERT: B 486 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8205 (tm-30) REVERT: B 550 MET cc_start: 0.7725 (mmm) cc_final: 0.7130 (mtt) REVERT: B 580 LYS cc_start: 0.8588 (mmtp) cc_final: 0.8188 (mtpp) REVERT: B 604 LEU cc_start: 0.7955 (tp) cc_final: 0.7583 (tt) REVERT: B 609 GLN cc_start: 0.8990 (mt0) cc_final: 0.8585 (mm-40) REVERT: C 61 MET cc_start: 0.8694 (mtt) cc_final: 0.8480 (mtm) REVERT: C 103 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8918 (tt0) REVERT: C 308 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8442 (ptt-90) REVERT: C 484 GLN cc_start: 0.8231 (tp40) cc_final: 0.7787 (tt0) REVERT: C 550 MET cc_start: 0.6997 (mmm) cc_final: 0.6786 (mtt) REVERT: C 571 ARG cc_start: 0.8782 (ptm-80) cc_final: 0.8550 (tmm-80) REVERT: C 607 ASP cc_start: 0.6613 (m-30) cc_final: 0.6198 (m-30) REVERT: D 149 ASP cc_start: 0.8343 (t0) cc_final: 0.8123 (t0) REVERT: D 251 ASN cc_start: 0.7610 (t0) cc_final: 0.7223 (t0) REVERT: D 299 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: D 345 ASN cc_start: 0.8356 (t0) cc_final: 0.7799 (t0) REVERT: E 54 ASN cc_start: 0.8892 (t0) cc_final: 0.8585 (t0) REVERT: E 475 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: F 321 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8263 (mmt-90) REVERT: F 330 ASP cc_start: 0.8841 (t0) cc_final: 0.8612 (t0) REVERT: F 408 GLU cc_start: 0.8892 (tp30) cc_final: 0.8678 (tp30) REVERT: H 170 ASN cc_start: 0.8790 (m-40) cc_final: 0.8481 (m-40) REVERT: I 72 MET cc_start: 0.8001 (tpp) cc_final: 0.7668 (mmm) REVERT: I 76 MET cc_start: 0.8346 (mmm) cc_final: 0.8074 (mmm) REVERT: I 78 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: I 129 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8430 (tp30) REVERT: I 155 TYR cc_start: 0.9020 (t80) cc_final: 0.8759 (t80) REVERT: J 21 GLN cc_start: 0.9105 (tp40) cc_final: 0.8904 (tp40) REVERT: J 24 ASN cc_start: 0.9414 (m-40) cc_final: 0.9100 (m110) REVERT: J 52 LYS cc_start: 0.8946 (tppp) cc_final: 0.8607 (tppp) REVERT: J 80 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7443 (ttp-170) REVERT: J 96 ASN cc_start: 0.8222 (m110) cc_final: 0.7860 (m110) REVERT: J 141 PHE cc_start: 0.8743 (t80) cc_final: 0.8313 (t80) REVERT: J 172 TYR cc_start: 0.8861 (m-80) cc_final: 0.8412 (m-10) REVERT: K 15 MET cc_start: 0.8693 (mtt) cc_final: 0.8335 (mmt) REVERT: K 18 PHE cc_start: 0.9295 (t80) cc_final: 0.9083 (t80) REVERT: K 58 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8592 (tp30) REVERT: L 108 ARG cc_start: 0.7580 (mmt90) cc_final: 0.7093 (mtt180) REVERT: O 15 GLU cc_start: 0.8231 (tt0) cc_final: 0.7814 (mm-30) REVERT: O 104 CYS cc_start: 0.8228 (m) cc_final: 0.7838 (m) REVERT: P 156 MET cc_start: -0.0742 (mtp) cc_final: -0.2346 (mmt) REVERT: P 208 MET cc_start: 0.5338 (mmm) cc_final: 0.4969 (mmm) REVERT: P 309 MET cc_start: 0.7873 (mtm) cc_final: 0.6944 (mpp) REVERT: Q 115 MET cc_start: 0.7510 (mmt) cc_final: 0.7275 (mmt) REVERT: Q 139 TYR cc_start: 0.8490 (t80) cc_final: 0.8256 (t80) REVERT: Q 161 MET cc_start: 0.8798 (tmm) cc_final: 0.8243 (tmm) REVERT: Q 181 LEU cc_start: 0.8706 (mm) cc_final: 0.8088 (tp) REVERT: Q 188 MET cc_start: 0.7412 (ttm) cc_final: 0.6820 (ttm) REVERT: R 109 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7368 (tm-30) REVERT: R 146 THR cc_start: 0.8439 (t) cc_final: 0.8206 (t) REVERT: R 161 MET cc_start: 0.8440 (tmm) cc_final: 0.8018 (tmm) REVERT: R 199 LEU cc_start: 0.8864 (tp) cc_final: 0.8663 (tt) REVERT: R 205 LYS cc_start: 0.8596 (tptt) cc_final: 0.8143 (mmtt) REVERT: S 103 MET cc_start: 0.6789 (mtp) cc_final: 0.6369 (ttm) REVERT: S 170 GLU cc_start: 0.8148 (tp30) cc_final: 0.7463 (tm-30) REVERT: S 188 MET cc_start: 0.7294 (tpp) cc_final: 0.6876 (ttm) REVERT: S 197 TYR cc_start: 0.7255 (t80) cc_final: 0.7015 (t80) REVERT: T 90 LEU cc_start: 0.9126 (tp) cc_final: 0.8731 (mt) outliers start: 131 outliers final: 84 residues processed: 893 average time/residue: 0.6392 time to fit residues: 926.3271 Evaluate side-chains 856 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 765 time to evaluate : 6.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 210 GLU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 184 HIS Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 209 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 495 optimal weight: 40.0000 chunk 337 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 443 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 508 optimal weight: 40.0000 chunk 411 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 304 optimal weight: 3.9990 chunk 534 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN D 358 ASN D 482 GLN G 252 GLN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 HIS ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 50486 Z= 0.344 Angle : 0.614 11.291 68109 Z= 0.317 Chirality : 0.044 0.317 7609 Planarity : 0.004 0.048 8813 Dihedral : 5.471 167.779 6801 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.32 % Allowed : 11.60 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.11), residues: 6176 helix: 1.76 (0.09), residues: 3175 sheet: -0.31 (0.19), residues: 708 loop : -0.42 (0.13), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 450 HIS 0.009 0.001 HIS A 444 PHE 0.025 0.002 PHE Q 200 TYR 0.022 0.002 TYR S 60 ARG 0.012 0.001 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 803 time to evaluate : 6.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.9283 (p) cc_final: 0.9016 (m) REVERT: A 297 GLU cc_start: 0.7585 (tt0) cc_final: 0.7180 (tt0) REVERT: A 384 SER cc_start: 0.9052 (t) cc_final: 0.8693 (p) REVERT: A 518 ASP cc_start: 0.6389 (m-30) cc_final: 0.6186 (t0) REVERT: A 523 ASN cc_start: 0.7403 (t0) cc_final: 0.6974 (t0) REVERT: B 197 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 291 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: B 443 LYS cc_start: 0.9227 (mmtm) cc_final: 0.8982 (mmmm) REVERT: B 471 GLU cc_start: 0.7984 (pm20) cc_final: 0.7597 (pm20) REVERT: B 486 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8149 (tm-30) REVERT: B 523 ASN cc_start: 0.8303 (t0) cc_final: 0.8077 (t0) REVERT: B 550 MET cc_start: 0.7740 (mmm) cc_final: 0.7284 (mtt) REVERT: B 580 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8220 (mtpp) REVERT: B 604 LEU cc_start: 0.7985 (tp) cc_final: 0.7658 (tt) REVERT: C 61 MET cc_start: 0.8706 (mtt) cc_final: 0.8498 (mtm) REVERT: C 103 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8924 (tt0) REVERT: C 308 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8423 (ptt-90) REVERT: C 438 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7864 (mttt) REVERT: C 484 GLN cc_start: 0.8248 (tp40) cc_final: 0.7852 (tt0) REVERT: C 571 ARG cc_start: 0.8813 (ptm-80) cc_final: 0.8481 (tmm-80) REVERT: C 584 MET cc_start: 0.8895 (mtm) cc_final: 0.8665 (ttm) REVERT: C 603 GLN cc_start: 0.7436 (tp40) cc_final: 0.6660 (tp40) REVERT: C 607 ASP cc_start: 0.6689 (m-30) cc_final: 0.6275 (m-30) REVERT: D 149 ASP cc_start: 0.8346 (t0) cc_final: 0.8121 (t0) REVERT: D 167 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7571 (mt-10) REVERT: D 251 ASN cc_start: 0.7594 (t0) cc_final: 0.7232 (t0) REVERT: D 299 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: D 345 ASN cc_start: 0.8347 (t0) cc_final: 0.7782 (t0) REVERT: D 380 ASP cc_start: 0.8733 (t0) cc_final: 0.8498 (t0) REVERT: E 54 ASN cc_start: 0.8904 (t0) cc_final: 0.8463 (t0) REVERT: E 475 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: F 256 ASN cc_start: 0.8076 (t0) cc_final: 0.7622 (t0) REVERT: F 321 ARG cc_start: 0.8687 (mmm-85) cc_final: 0.8310 (mmt-90) REVERT: F 408 GLU cc_start: 0.8910 (tp30) cc_final: 0.8662 (tp30) REVERT: H 163 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7706 (mppt) REVERT: H 170 ASN cc_start: 0.8804 (m-40) cc_final: 0.8557 (m-40) REVERT: I 72 MET cc_start: 0.8027 (tpp) cc_final: 0.7695 (mmm) REVERT: I 76 MET cc_start: 0.8353 (mmm) cc_final: 0.8079 (mmm) REVERT: I 78 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7633 (mp10) REVERT: I 117 ASP cc_start: 0.7315 (m-30) cc_final: 0.7098 (m-30) REVERT: I 155 TYR cc_start: 0.9039 (t80) cc_final: 0.8816 (t80) REVERT: I 226 ASP cc_start: 0.7866 (t0) cc_final: 0.7366 (m-30) REVERT: J 24 ASN cc_start: 0.9403 (m-40) cc_final: 0.9072 (m110) REVERT: J 52 LYS cc_start: 0.8925 (tppp) cc_final: 0.8668 (tppp) REVERT: J 80 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7442 (ttp-170) REVERT: J 94 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8550 (tt) REVERT: J 141 PHE cc_start: 0.8755 (t80) cc_final: 0.8331 (t80) REVERT: J 172 TYR cc_start: 0.8879 (m-80) cc_final: 0.8449 (m-80) REVERT: K 18 PHE cc_start: 0.9404 (t80) cc_final: 0.9098 (t80) REVERT: K 58 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8572 (tp30) REVERT: L 108 ARG cc_start: 0.7510 (mmt90) cc_final: 0.7075 (mtt180) REVERT: N 34 LYS cc_start: 0.9143 (ptpp) cc_final: 0.8769 (ptpp) REVERT: O 15 GLU cc_start: 0.8274 (tt0) cc_final: 0.7907 (tp30) REVERT: O 102 PHE cc_start: 0.7636 (m-80) cc_final: 0.7252 (t80) REVERT: O 104 CYS cc_start: 0.8208 (m) cc_final: 0.7831 (m) REVERT: P 96 MET cc_start: 0.4657 (mtp) cc_final: 0.4362 (ptp) REVERT: P 156 MET cc_start: -0.0777 (mtp) cc_final: -0.2375 (mmt) REVERT: P 208 MET cc_start: 0.5316 (mmm) cc_final: 0.5052 (mmm) REVERT: P 309 MET cc_start: 0.7906 (mtm) cc_final: 0.6994 (mpp) REVERT: P 426 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.8193 (ptm-80) REVERT: P 451 ASN cc_start: 0.8991 (m-40) cc_final: 0.8527 (t0) REVERT: Q 46 ARG cc_start: 0.7690 (mtp85) cc_final: 0.7466 (mtt180) REVERT: Q 115 MET cc_start: 0.7492 (mmt) cc_final: 0.7282 (mmt) REVERT: Q 161 MET cc_start: 0.8777 (tmm) cc_final: 0.8174 (tmm) REVERT: Q 178 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8286 (tt) REVERT: Q 188 MET cc_start: 0.7361 (ttm) cc_final: 0.6775 (ttm) REVERT: Q 242 LEU cc_start: 0.8959 (mt) cc_final: 0.8372 (mt) REVERT: R 109 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7345 (tm-30) REVERT: R 146 THR cc_start: 0.8230 (t) cc_final: 0.7988 (t) REVERT: R 161 MET cc_start: 0.8434 (tmm) cc_final: 0.8041 (tmm) REVERT: R 205 LYS cc_start: 0.8592 (tptt) cc_final: 0.8133 (mmtt) REVERT: R 207 GLN cc_start: 0.7420 (tp40) cc_final: 0.6672 (tm-30) REVERT: R 256 THR cc_start: 0.8919 (p) cc_final: 0.8689 (t) REVERT: S 170 GLU cc_start: 0.8163 (tp30) cc_final: 0.7469 (tm-30) REVERT: S 188 MET cc_start: 0.7346 (tpp) cc_final: 0.6861 (ttm) REVERT: T 90 LEU cc_start: 0.9116 (tp) cc_final: 0.8755 (mt) outliers start: 126 outliers final: 89 residues processed: 879 average time/residue: 0.6524 time to fit residues: 932.1936 Evaluate side-chains 851 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 751 time to evaluate : 5.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 210 GLU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 102 PHE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 58 LYS Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 178 LEU Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 184 HIS Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 209 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 200 optimal weight: 0.9990 chunk 536 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 349 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 596 optimal weight: 30.0000 chunk 494 optimal weight: 9.9990 chunk 275 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 312 optimal weight: 0.0370 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS B 157 ASN C 140 ASN C 573 HIS F 54 ASN F 256 ASN I 66 GLN J 96 ASN K 71 GLN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 405 GLN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 50486 Z= 0.244 Angle : 0.575 13.103 68109 Z= 0.297 Chirality : 0.042 0.322 7609 Planarity : 0.004 0.048 8813 Dihedral : 5.285 168.075 6801 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.32 % Allowed : 11.91 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.11), residues: 6176 helix: 1.91 (0.09), residues: 3172 sheet: -0.38 (0.19), residues: 700 loop : -0.40 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 197 HIS 0.008 0.001 HIS A 444 PHE 0.026 0.001 PHE S 200 TYR 0.021 0.001 TYR S 60 ARG 0.011 0.000 ARG N 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 804 time to evaluate : 5.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.9271 (p) cc_final: 0.9035 (m) REVERT: A 297 GLU cc_start: 0.7625 (tt0) cc_final: 0.7201 (tt0) REVERT: A 384 SER cc_start: 0.9022 (t) cc_final: 0.8667 (p) REVERT: A 518 ASP cc_start: 0.6735 (m-30) cc_final: 0.6313 (t0) REVERT: A 523 ASN cc_start: 0.7291 (t0) cc_final: 0.6881 (t0) REVERT: B 197 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 291 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: B 443 LYS cc_start: 0.9251 (mmtm) cc_final: 0.9002 (mmmm) REVERT: B 471 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: B 486 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8144 (tm-30) REVERT: B 523 ASN cc_start: 0.8281 (t0) cc_final: 0.8069 (t0) REVERT: B 530 ARG cc_start: 0.7976 (ptp90) cc_final: 0.7532 (ptt-90) REVERT: B 550 MET cc_start: 0.7742 (mmm) cc_final: 0.7326 (mtt) REVERT: B 580 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8256 (mtpp) REVERT: B 604 LEU cc_start: 0.7986 (tp) cc_final: 0.7718 (tt) REVERT: C 103 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8913 (tt0) REVERT: C 438 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7855 (mttt) REVERT: C 484 GLN cc_start: 0.8165 (tp40) cc_final: 0.7946 (tt0) REVERT: C 571 ARG cc_start: 0.8827 (ptm-80) cc_final: 0.8464 (tmm-80) REVERT: C 584 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8636 (ttm) REVERT: C 603 GLN cc_start: 0.7544 (tp40) cc_final: 0.6594 (tp40) REVERT: C 607 ASP cc_start: 0.6639 (m-30) cc_final: 0.6073 (m-30) REVERT: D 238 MET cc_start: 0.9012 (tpp) cc_final: 0.8770 (tpt) REVERT: D 251 ASN cc_start: 0.7551 (t0) cc_final: 0.7164 (t0) REVERT: D 299 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: D 345 ASN cc_start: 0.8330 (t0) cc_final: 0.7722 (t0) REVERT: D 388 ILE cc_start: 0.8741 (mm) cc_final: 0.8499 (mt) REVERT: E 54 ASN cc_start: 0.8801 (t0) cc_final: 0.8377 (t0) REVERT: E 358 ASN cc_start: 0.8816 (t0) cc_final: 0.8359 (t0) REVERT: E 475 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: F 321 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8305 (mmt-90) REVERT: F 369 THR cc_start: 0.9565 (m) cc_final: 0.9326 (m) REVERT: G 204 LEU cc_start: 0.8543 (pt) cc_final: 0.8301 (pp) REVERT: H 163 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7650 (mppt) REVERT: H 170 ASN cc_start: 0.8838 (m-40) cc_final: 0.8450 (m-40) REVERT: I 70 ILE cc_start: 0.7857 (mp) cc_final: 0.7624 (mp) REVERT: I 72 MET cc_start: 0.8063 (tpp) cc_final: 0.7590 (mmm) REVERT: I 76 MET cc_start: 0.8355 (mmm) cc_final: 0.8026 (mmm) REVERT: I 78 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7610 (mp10) REVERT: I 117 ASP cc_start: 0.7326 (m-30) cc_final: 0.7077 (m-30) REVERT: I 155 TYR cc_start: 0.9037 (t80) cc_final: 0.8820 (t80) REVERT: I 226 ASP cc_start: 0.7885 (t0) cc_final: 0.7412 (m-30) REVERT: J 15 MET cc_start: 0.9281 (ppp) cc_final: 0.9056 (ppp) REVERT: J 16 MET cc_start: 0.8875 (ppp) cc_final: 0.8582 (ppp) REVERT: J 24 ASN cc_start: 0.9385 (m-40) cc_final: 0.9087 (m110) REVERT: J 25 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8641 (pp20) REVERT: J 52 LYS cc_start: 0.8939 (tppp) cc_final: 0.8669 (tppp) REVERT: J 80 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7444 (ttp-170) REVERT: J 94 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8568 (tt) REVERT: J 141 PHE cc_start: 0.8715 (t80) cc_final: 0.8331 (t80) REVERT: J 172 TYR cc_start: 0.8896 (m-80) cc_final: 0.8498 (m-80) REVERT: K 18 PHE cc_start: 0.9410 (t80) cc_final: 0.9114 (t80) REVERT: K 58 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8530 (tp30) REVERT: L 108 ARG cc_start: 0.7391 (mmt90) cc_final: 0.7008 (mtt180) REVERT: M 102 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7874 (t80) REVERT: O 15 GLU cc_start: 0.8311 (tt0) cc_final: 0.7910 (tp30) REVERT: O 102 PHE cc_start: 0.7636 (m-80) cc_final: 0.7283 (t80) REVERT: O 104 CYS cc_start: 0.8174 (m) cc_final: 0.7788 (m) REVERT: P 96 MET cc_start: 0.4427 (mtp) cc_final: 0.4206 (ptp) REVERT: P 156 MET cc_start: -0.0749 (mtp) cc_final: -0.2345 (mmt) REVERT: P 208 MET cc_start: 0.5384 (mmm) cc_final: 0.5142 (mmm) REVERT: P 309 MET cc_start: 0.7948 (mtm) cc_final: 0.7034 (mpp) REVERT: P 426 ARG cc_start: 0.8591 (ptm-80) cc_final: 0.8377 (ptm-80) REVERT: P 451 ASN cc_start: 0.9000 (m-40) cc_final: 0.8584 (t0) REVERT: Q 115 MET cc_start: 0.7549 (mmt) cc_final: 0.7147 (mmt) REVERT: Q 161 MET cc_start: 0.8754 (tmm) cc_final: 0.7893 (tmm) REVERT: Q 162 GLN cc_start: 0.8459 (mt0) cc_final: 0.8235 (mm-40) REVERT: Q 188 MET cc_start: 0.7467 (ttm) cc_final: 0.6914 (ttm) REVERT: R 15 SER cc_start: 0.7405 (m) cc_final: 0.7172 (t) REVERT: R 32 CYS cc_start: 0.8699 (m) cc_final: 0.8254 (m) REVERT: R 103 MET cc_start: 0.8471 (mtp) cc_final: 0.7368 (mmt) REVERT: R 146 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7981 (t) REVERT: R 161 MET cc_start: 0.8485 (tmm) cc_final: 0.7975 (tmm) REVERT: R 205 LYS cc_start: 0.8582 (tptt) cc_final: 0.8218 (mmtt) REVERT: R 207 GLN cc_start: 0.7597 (tp40) cc_final: 0.6837 (tm-30) REVERT: R 256 THR cc_start: 0.8882 (p) cc_final: 0.8422 (t) REVERT: S 93 ARG cc_start: 0.8911 (ttp80) cc_final: 0.8395 (ttp80) REVERT: S 170 GLU cc_start: 0.8145 (tp30) cc_final: 0.7481 (tm-30) REVERT: S 188 MET cc_start: 0.7349 (tpp) cc_final: 0.6883 (ttm) REVERT: T 90 LEU cc_start: 0.9090 (tp) cc_final: 0.8741 (mt) outliers start: 126 outliers final: 75 residues processed: 884 average time/residue: 0.6687 time to fit residues: 968.5130 Evaluate side-chains 846 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 758 time to evaluate : 6.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 102 PHE Chi-restraints excluded: chain N residue 58 LYS Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain P residue 349 LEU Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 170 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 574 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 339 optimal weight: 0.8980 chunk 435 optimal weight: 8.9990 chunk 337 optimal weight: 6.9990 chunk 501 optimal weight: 40.0000 chunk 332 optimal weight: 9.9990 chunk 593 optimal weight: 0.5980 chunk 371 optimal weight: 9.9990 chunk 361 optimal weight: 20.0000 chunk 274 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS B 157 ASN C 140 ASN C 261 GLN D 482 GLN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 50486 Z= 0.297 Angle : 0.593 14.441 68109 Z= 0.305 Chirality : 0.043 0.294 7609 Planarity : 0.004 0.051 8813 Dihedral : 5.251 168.001 6801 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.28 % Allowed : 12.79 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.11), residues: 6176 helix: 1.96 (0.09), residues: 3171 sheet: -0.44 (0.19), residues: 696 loop : -0.44 (0.13), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 197 HIS 0.008 0.001 HIS A 444 PHE 0.027 0.001 PHE S 200 TYR 0.024 0.002 TYR G 75 ARG 0.011 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 789 time to evaluate : 5.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.9274 (p) cc_final: 0.9024 (m) REVERT: A 297 GLU cc_start: 0.7630 (tt0) cc_final: 0.7198 (tt0) REVERT: A 384 SER cc_start: 0.9051 (t) cc_final: 0.8698 (p) REVERT: A 442 ARG cc_start: 0.7280 (mtt90) cc_final: 0.6819 (mpt180) REVERT: A 518 ASP cc_start: 0.6744 (m-30) cc_final: 0.6318 (t0) REVERT: A 523 ASN cc_start: 0.7301 (t0) cc_final: 0.6896 (t0) REVERT: A 540 MET cc_start: 0.8010 (mtm) cc_final: 0.7544 (mtp) REVERT: B 197 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 291 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: B 443 LYS cc_start: 0.9283 (mmtm) cc_final: 0.8900 (mmmm) REVERT: B 471 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7606 (pm20) REVERT: B 486 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8144 (tm-30) REVERT: B 523 ASN cc_start: 0.8297 (t0) cc_final: 0.8079 (t0) REVERT: B 530 ARG cc_start: 0.8005 (ptp90) cc_final: 0.7557 (ptt-90) REVERT: B 550 MET cc_start: 0.7726 (mmm) cc_final: 0.7324 (mtt) REVERT: B 552 ARG cc_start: 0.8032 (ttt-90) cc_final: 0.7702 (ttt90) REVERT: B 580 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8308 (mtpp) REVERT: B 604 LEU cc_start: 0.8124 (tp) cc_final: 0.7848 (tt) REVERT: C 103 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8903 (tt0) REVERT: C 438 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7872 (mttt) REVERT: C 484 GLN cc_start: 0.8148 (tp40) cc_final: 0.7918 (tt0) REVERT: C 571 ARG cc_start: 0.8808 (ptm-80) cc_final: 0.8451 (tmm-80) REVERT: C 584 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8624 (ttm) REVERT: C 603 GLN cc_start: 0.7691 (tp40) cc_final: 0.6718 (tp40) REVERT: C 607 ASP cc_start: 0.6705 (m-30) cc_final: 0.6130 (m-30) REVERT: C 610 ASN cc_start: 0.7062 (m-40) cc_final: 0.6610 (m-40) REVERT: D 251 ASN cc_start: 0.7559 (t0) cc_final: 0.7179 (t0) REVERT: D 299 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7091 (m-30) REVERT: D 345 ASN cc_start: 0.8328 (t0) cc_final: 0.7725 (t0) REVERT: D 388 ILE cc_start: 0.8759 (mm) cc_final: 0.8536 (mt) REVERT: E 54 ASN cc_start: 0.8863 (t0) cc_final: 0.8449 (t0) REVERT: E 358 ASN cc_start: 0.8826 (t0) cc_final: 0.8378 (t0) REVERT: E 475 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: F 321 ARG cc_start: 0.8651 (mmm-85) cc_final: 0.8311 (mmt-90) REVERT: F 330 ASP cc_start: 0.8827 (t70) cc_final: 0.8548 (t0) REVERT: F 369 THR cc_start: 0.9566 (m) cc_final: 0.9322 (m) REVERT: F 408 GLU cc_start: 0.8892 (tp30) cc_final: 0.8653 (tp30) REVERT: G 258 MET cc_start: 0.8420 (mmp) cc_final: 0.8177 (mmm) REVERT: H 163 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7651 (mppt) REVERT: H 170 ASN cc_start: 0.8842 (m-40) cc_final: 0.8443 (m-40) REVERT: I 70 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7603 (mp) REVERT: I 72 MET cc_start: 0.8101 (tpp) cc_final: 0.7677 (mmm) REVERT: I 76 MET cc_start: 0.8388 (mmm) cc_final: 0.8135 (mmm) REVERT: I 78 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: I 117 ASP cc_start: 0.7346 (m-30) cc_final: 0.7071 (m-30) REVERT: I 155 TYR cc_start: 0.9067 (t80) cc_final: 0.8828 (t80) REVERT: I 226 ASP cc_start: 0.7882 (t0) cc_final: 0.7413 (m-30) REVERT: J 16 MET cc_start: 0.8901 (ppp) cc_final: 0.8667 (ppp) REVERT: J 24 ASN cc_start: 0.9370 (m-40) cc_final: 0.9057 (m-40) REVERT: J 25 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8480 (pp20) REVERT: J 80 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7449 (ttp-170) REVERT: J 94 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8589 (tt) REVERT: J 172 TYR cc_start: 0.8900 (m-80) cc_final: 0.8500 (m-80) REVERT: K 18 PHE cc_start: 0.9388 (t80) cc_final: 0.9123 (t80) REVERT: K 52 LYS cc_start: 0.8901 (ptpp) cc_final: 0.8662 (pttm) REVERT: K 58 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8483 (tp30) REVERT: L 108 ARG cc_start: 0.7379 (mmt90) cc_final: 0.7028 (mtt180) REVERT: M 102 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7926 (t80) REVERT: N 12 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8737 (mm) REVERT: N 16 LYS cc_start: 0.9118 (mttt) cc_final: 0.8798 (mttt) REVERT: N 58 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8977 (tppt) REVERT: O 15 GLU cc_start: 0.8332 (tt0) cc_final: 0.7840 (tp30) REVERT: O 102 PHE cc_start: 0.7599 (m-80) cc_final: 0.7249 (t80) REVERT: O 104 CYS cc_start: 0.8218 (m) cc_final: 0.7854 (m) REVERT: P 96 MET cc_start: 0.4445 (mtp) cc_final: 0.4171 (ptp) REVERT: P 156 MET cc_start: -0.0900 (mtp) cc_final: -0.2438 (mmt) REVERT: P 208 MET cc_start: 0.5460 (mmm) cc_final: 0.5235 (mmm) REVERT: P 309 MET cc_start: 0.7973 (mtm) cc_final: 0.7114 (mpp) REVERT: P 426 ARG cc_start: 0.8625 (ptm-80) cc_final: 0.8394 (ptm-80) REVERT: P 451 ASN cc_start: 0.9046 (m-40) cc_final: 0.8627 (t0) REVERT: Q 115 MET cc_start: 0.7597 (mmt) cc_final: 0.7000 (mmt) REVERT: Q 161 MET cc_start: 0.8733 (tmm) cc_final: 0.8068 (tmm) REVERT: Q 188 MET cc_start: 0.7475 (ttm) cc_final: 0.6919 (ttm) REVERT: Q 197 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.7278 (t80) REVERT: R 32 CYS cc_start: 0.8698 (m) cc_final: 0.8261 (m) REVERT: R 146 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7993 (t) REVERT: R 161 MET cc_start: 0.8508 (tmm) cc_final: 0.8008 (tmm) REVERT: R 194 ASP cc_start: 0.8650 (m-30) cc_final: 0.8249 (t70) REVERT: R 195 GLU cc_start: 0.7898 (mp0) cc_final: 0.7638 (mp0) REVERT: R 205 LYS cc_start: 0.8555 (tptt) cc_final: 0.8201 (mmtt) REVERT: R 207 GLN cc_start: 0.7667 (tp40) cc_final: 0.6900 (tm-30) REVERT: R 256 THR cc_start: 0.8962 (p) cc_final: 0.8674 (t) REVERT: S 93 ARG cc_start: 0.8908 (ttp80) cc_final: 0.8416 (ttp80) REVERT: S 170 GLU cc_start: 0.8182 (tp30) cc_final: 0.7514 (tm-30) REVERT: S 188 MET cc_start: 0.7331 (tpp) cc_final: 0.6918 (ttm) REVERT: T 90 LEU cc_start: 0.9100 (tp) cc_final: 0.8661 (mt) REVERT: T 214 ASP cc_start: 0.8679 (m-30) cc_final: 0.7529 (t0) outliers start: 124 outliers final: 83 residues processed: 861 average time/residue: 0.6463 time to fit residues: 903.4831 Evaluate side-chains 865 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 765 time to evaluate : 5.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 102 PHE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 58 LYS Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain P residue 349 LEU Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 184 HIS Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 209 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 367 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 chunk 354 optimal weight: 1.9990 chunk 178 optimal weight: 0.0770 chunk 116 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 377 optimal weight: 3.9990 chunk 404 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 466 optimal weight: 0.9980 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 573 HIS C 140 ASN D 482 GLN ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 50486 Z= 0.245 Angle : 0.579 13.824 68109 Z= 0.298 Chirality : 0.042 0.267 7609 Planarity : 0.004 0.053 8813 Dihedral : 5.158 168.153 6801 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.17 % Allowed : 13.11 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.11), residues: 6176 helix: 1.98 (0.09), residues: 3193 sheet: -0.48 (0.19), residues: 717 loop : -0.41 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP P 376 HIS 0.008 0.001 HIS A 444 PHE 0.032 0.001 PHE S 151 TYR 0.027 0.001 TYR S 139 ARG 0.013 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 787 time to evaluate : 5.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.9256 (p) cc_final: 0.8994 (m) REVERT: A 290 ASP cc_start: 0.8299 (t0) cc_final: 0.7975 (t0) REVERT: A 297 GLU cc_start: 0.7626 (tt0) cc_final: 0.7180 (tt0) REVERT: A 306 MET cc_start: 0.9013 (tpt) cc_final: 0.8722 (tpt) REVERT: A 384 SER cc_start: 0.9036 (t) cc_final: 0.8682 (p) REVERT: A 518 ASP cc_start: 0.6753 (m-30) cc_final: 0.6317 (t0) REVERT: A 523 ASN cc_start: 0.7268 (t0) cc_final: 0.6894 (t0) REVERT: A 540 MET cc_start: 0.7969 (mtm) cc_final: 0.7574 (mtp) REVERT: B 197 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7763 (tm-30) REVERT: B 291 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: B 443 LYS cc_start: 0.9305 (mmtm) cc_final: 0.8925 (mmmm) REVERT: B 471 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: B 486 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8108 (tm-30) REVERT: B 523 ASN cc_start: 0.8310 (t0) cc_final: 0.8097 (t0) REVERT: B 530 ARG cc_start: 0.7985 (ptp90) cc_final: 0.7581 (ptt-90) REVERT: B 550 MET cc_start: 0.7816 (mmm) cc_final: 0.7365 (mtt) REVERT: B 552 ARG cc_start: 0.8040 (ttt-90) cc_final: 0.7710 (ttt90) REVERT: B 580 LYS cc_start: 0.8695 (mmtp) cc_final: 0.8311 (mtpp) REVERT: C 103 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8916 (tt0) REVERT: C 194 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8200 (pp) REVERT: C 438 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7877 (mttt) REVERT: C 484 GLN cc_start: 0.8186 (tp40) cc_final: 0.7978 (tt0) REVERT: C 553 ARG cc_start: 0.7420 (ttp80) cc_final: 0.7204 (ttp80) REVERT: C 571 ARG cc_start: 0.8778 (ptm-80) cc_final: 0.8433 (tmm-80) REVERT: C 584 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8568 (ttm) REVERT: C 603 GLN cc_start: 0.7696 (tp40) cc_final: 0.6720 (tp40) REVERT: C 607 ASP cc_start: 0.6696 (m-30) cc_final: 0.6117 (m-30) REVERT: C 610 ASN cc_start: 0.6996 (m-40) cc_final: 0.6507 (m-40) REVERT: D 238 MET cc_start: 0.8985 (tpp) cc_final: 0.8734 (tpt) REVERT: D 251 ASN cc_start: 0.7519 (t0) cc_final: 0.7040 (t0) REVERT: D 299 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6970 (m-30) REVERT: D 345 ASN cc_start: 0.8336 (t0) cc_final: 0.7732 (t0) REVERT: D 388 ILE cc_start: 0.8746 (mm) cc_final: 0.8546 (mt) REVERT: D 494 ARG cc_start: 0.8845 (mmp80) cc_final: 0.8461 (mmt180) REVERT: E 54 ASN cc_start: 0.8819 (t0) cc_final: 0.8414 (t0) REVERT: E 358 ASN cc_start: 0.8812 (t0) cc_final: 0.8373 (t0) REVERT: E 475 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: F 321 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8307 (mmt-90) REVERT: F 330 ASP cc_start: 0.8792 (t70) cc_final: 0.8503 (t0) REVERT: F 369 THR cc_start: 0.9560 (m) cc_final: 0.9335 (m) REVERT: F 408 GLU cc_start: 0.8890 (tp30) cc_final: 0.8631 (tp30) REVERT: H 163 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7667 (mppt) REVERT: H 170 ASN cc_start: 0.8846 (m-40) cc_final: 0.8402 (m-40) REVERT: I 70 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7596 (mp) REVERT: I 72 MET cc_start: 0.8081 (tpp) cc_final: 0.7673 (mmm) REVERT: I 76 MET cc_start: 0.8377 (mmm) cc_final: 0.8135 (mmm) REVERT: I 78 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: I 155 TYR cc_start: 0.9063 (t80) cc_final: 0.8834 (t80) REVERT: I 226 ASP cc_start: 0.7894 (t0) cc_final: 0.7376 (m-30) REVERT: J 24 ASN cc_start: 0.9366 (m-40) cc_final: 0.9064 (m-40) REVERT: J 25 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8489 (pp20) REVERT: J 80 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7464 (ttp-170) REVERT: J 94 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8693 (tt) REVERT: J 172 TYR cc_start: 0.8961 (m-80) cc_final: 0.8682 (m-80) REVERT: K 18 PHE cc_start: 0.9366 (t80) cc_final: 0.9122 (t80) REVERT: K 52 LYS cc_start: 0.8923 (ptpp) cc_final: 0.8602 (pttm) REVERT: K 55 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8769 (tm-30) REVERT: K 58 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8445 (tp30) REVERT: L 108 ARG cc_start: 0.7347 (mmt90) cc_final: 0.7027 (mtt180) REVERT: M 102 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7915 (t80) REVERT: N 58 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8958 (tppt) REVERT: O 15 GLU cc_start: 0.8337 (tt0) cc_final: 0.7988 (tp30) REVERT: O 102 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7282 (t80) REVERT: O 104 CYS cc_start: 0.8186 (m) cc_final: 0.7828 (m) REVERT: P 96 MET cc_start: 0.4363 (mtp) cc_final: 0.4117 (ptp) REVERT: P 156 MET cc_start: -0.0895 (mtp) cc_final: -0.2407 (mmt) REVERT: P 208 MET cc_start: 0.5477 (mmm) cc_final: 0.5246 (mmm) REVERT: P 309 MET cc_start: 0.7997 (mtm) cc_final: 0.7121 (mpp) REVERT: P 426 ARG cc_start: 0.8655 (ptm-80) cc_final: 0.8385 (ptm-80) REVERT: P 451 ASN cc_start: 0.9055 (m-40) cc_final: 0.8555 (t0) REVERT: Q 161 MET cc_start: 0.8725 (tmm) cc_final: 0.8043 (tmm) REVERT: Q 188 MET cc_start: 0.7425 (ttm) cc_final: 0.6869 (ttm) REVERT: Q 197 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7278 (t80) REVERT: R 32 CYS cc_start: 0.8712 (m) cc_final: 0.8276 (m) REVERT: R 103 MET cc_start: 0.8484 (mtp) cc_final: 0.7370 (mmt) REVERT: R 146 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7970 (t) REVERT: R 161 MET cc_start: 0.8507 (tmm) cc_final: 0.7999 (tmm) REVERT: R 194 ASP cc_start: 0.8562 (m-30) cc_final: 0.8226 (t70) REVERT: R 205 LYS cc_start: 0.8544 (tptt) cc_final: 0.8191 (mmtt) REVERT: R 207 GLN cc_start: 0.7684 (tp40) cc_final: 0.6952 (tm-30) REVERT: R 256 THR cc_start: 0.8945 (p) cc_final: 0.8643 (t) REVERT: S 93 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8377 (ttp80) REVERT: S 170 GLU cc_start: 0.8179 (tp30) cc_final: 0.7515 (tm-30) REVERT: S 188 MET cc_start: 0.7298 (tpp) cc_final: 0.6872 (ttm) REVERT: S 229 MET cc_start: 0.7904 (mmm) cc_final: 0.7584 (mmm) REVERT: T 90 LEU cc_start: 0.9083 (tp) cc_final: 0.8672 (mt) REVERT: T 214 ASP cc_start: 0.8688 (m-30) cc_final: 0.7547 (t0) outliers start: 118 outliers final: 78 residues processed: 855 average time/residue: 0.6368 time to fit residues: 887.7005 Evaluate side-chains 862 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 766 time to evaluate : 6.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 210 GLU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 102 PHE Chi-restraints excluded: chain N residue 58 LYS Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain O residue 102 PHE Chi-restraints excluded: chain P residue 349 LEU Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 184 HIS Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 209 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 540 optimal weight: 10.0000 chunk 568 optimal weight: 10.0000 chunk 518 optimal weight: 7.9990 chunk 553 optimal weight: 3.9990 chunk 333 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 434 optimal weight: 50.0000 chunk 169 optimal weight: 3.9990 chunk 499 optimal weight: 20.0000 chunk 523 optimal weight: 1.9990 chunk 551 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS B 157 ASN C 140 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 ASN S 59 ASN ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 50486 Z= 0.509 Angle : 0.697 14.861 68109 Z= 0.357 Chirality : 0.047 0.276 7609 Planarity : 0.005 0.062 8813 Dihedral : 5.462 166.126 6801 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.15 % Allowed : 13.33 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.11), residues: 6176 helix: 1.79 (0.09), residues: 3174 sheet: -0.71 (0.18), residues: 726 loop : -0.61 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 450 HIS 0.011 0.001 HIS T 58 PHE 0.033 0.002 PHE S 200 TYR 0.036 0.002 TYR Q 232 ARG 0.013 0.001 ARG N 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 767 time to evaluate : 6.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 GLU cc_start: 0.7689 (tt0) cc_final: 0.7237 (tt0) REVERT: A 384 SER cc_start: 0.9140 (t) cc_final: 0.8798 (p) REVERT: A 523 ASN cc_start: 0.7491 (t0) cc_final: 0.7054 (t0) REVERT: A 540 MET cc_start: 0.8049 (mtm) cc_final: 0.7498 (mtp) REVERT: B 167 MET cc_start: 0.9183 (mtm) cc_final: 0.8971 (mtm) REVERT: B 197 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 291 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: B 443 LYS cc_start: 0.9315 (mmtm) cc_final: 0.8964 (mmmm) REVERT: B 471 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: B 486 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8208 (tm-30) REVERT: B 523 ASN cc_start: 0.8363 (t0) cc_final: 0.8154 (t0) REVERT: B 530 ARG cc_start: 0.8036 (ptp90) cc_final: 0.7827 (ptm-80) REVERT: B 550 MET cc_start: 0.7721 (mmm) cc_final: 0.7332 (mtt) REVERT: C 103 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8934 (tt0) REVERT: C 438 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7928 (mttt) REVERT: C 484 GLN cc_start: 0.8297 (tp40) cc_final: 0.8030 (tt0) REVERT: C 571 ARG cc_start: 0.8782 (ptm-80) cc_final: 0.8473 (tmm-80) REVERT: C 584 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8697 (ttm) REVERT: C 603 GLN cc_start: 0.7721 (tp40) cc_final: 0.6737 (tp40) REVERT: C 607 ASP cc_start: 0.6804 (m-30) cc_final: 0.6215 (m-30) REVERT: C 610 ASN cc_start: 0.6996 (m-40) cc_final: 0.6551 (m-40) REVERT: D 251 ASN cc_start: 0.7604 (t0) cc_final: 0.7272 (t0) REVERT: D 345 ASN cc_start: 0.8342 (t0) cc_final: 0.7707 (t0) REVERT: D 453 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8504 (tm-30) REVERT: D 494 ARG cc_start: 0.8886 (mmp80) cc_final: 0.8668 (mmt-90) REVERT: E 54 ASN cc_start: 0.9044 (t0) cc_final: 0.8581 (t0) REVERT: E 358 ASN cc_start: 0.8810 (t0) cc_final: 0.8352 (t0) REVERT: E 475 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: F 256 ASN cc_start: 0.8088 (t0) cc_final: 0.7496 (t0) REVERT: F 330 ASP cc_start: 0.8820 (t70) cc_final: 0.8496 (t0) REVERT: F 408 GLU cc_start: 0.8954 (tp30) cc_final: 0.8597 (tp30) REVERT: H 163 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7742 (mtpt) REVERT: H 170 ASN cc_start: 0.8828 (m-40) cc_final: 0.8540 (m-40) REVERT: I 54 MET cc_start: 0.8987 (mmt) cc_final: 0.8721 (mpp) REVERT: I 70 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7579 (mp) REVERT: I 72 MET cc_start: 0.8097 (tpp) cc_final: 0.7662 (mmm) REVERT: I 76 MET cc_start: 0.8415 (mmm) cc_final: 0.8147 (mmm) REVERT: I 78 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: I 155 TYR cc_start: 0.9112 (t80) cc_final: 0.8859 (t80) REVERT: I 226 ASP cc_start: 0.7901 (t0) cc_final: 0.7381 (m-30) REVERT: J 15 MET cc_start: 0.9379 (ppp) cc_final: 0.8984 (ppp) REVERT: J 24 ASN cc_start: 0.9364 (m-40) cc_final: 0.9039 (m-40) REVERT: J 25 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8676 (tm-30) REVERT: J 80 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7408 (ttp-170) REVERT: J 94 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8621 (tt) REVERT: J 116 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8175 (mt) REVERT: J 133 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9024 (mp) REVERT: J 172 TYR cc_start: 0.8961 (m-80) cc_final: 0.8515 (m-10) REVERT: K 18 PHE cc_start: 0.9366 (t80) cc_final: 0.9127 (t80) REVERT: K 52 LYS cc_start: 0.8933 (ptpp) cc_final: 0.8423 (pttm) REVERT: K 55 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8545 (tm-30) REVERT: K 58 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8450 (tp30) REVERT: L 108 ARG cc_start: 0.7368 (mmt90) cc_final: 0.7033 (mtt180) REVERT: N 20 GLU cc_start: 0.8579 (pt0) cc_final: 0.8214 (pp20) REVERT: O 15 GLU cc_start: 0.8316 (tt0) cc_final: 0.7928 (tp30) REVERT: O 21 LYS cc_start: 0.9094 (mtmt) cc_final: 0.8484 (ptmt) REVERT: O 102 PHE cc_start: 0.7622 (m-80) cc_final: 0.7260 (t80) REVERT: O 104 CYS cc_start: 0.8328 (m) cc_final: 0.7982 (m) REVERT: P 96 MET cc_start: 0.4307 (mtp) cc_final: 0.4076 (ptp) REVERT: P 156 MET cc_start: -0.0919 (mtp) cc_final: -0.2439 (mmt) REVERT: P 208 MET cc_start: 0.5485 (mmm) cc_final: 0.5271 (mmm) REVERT: P 309 MET cc_start: 0.8021 (mtm) cc_final: 0.7189 (mpp) REVERT: P 426 ARG cc_start: 0.8699 (ptm-80) cc_final: 0.8441 (ptm-80) REVERT: P 451 ASN cc_start: 0.9051 (m-40) cc_final: 0.8658 (t0) REVERT: Q 115 MET cc_start: 0.7258 (mmt) cc_final: 0.6815 (mmt) REVERT: Q 161 MET cc_start: 0.8744 (tmm) cc_final: 0.8067 (tmm) REVERT: Q 188 MET cc_start: 0.7418 (ttm) cc_final: 0.6912 (ttm) REVERT: Q 197 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7343 (t80) REVERT: R 60 TYR cc_start: 0.7813 (m-80) cc_final: 0.7544 (m-80) REVERT: R 103 MET cc_start: 0.8533 (mtp) cc_final: 0.7389 (mmt) REVERT: R 146 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8099 (t) REVERT: R 161 MET cc_start: 0.8576 (tmm) cc_final: 0.8111 (tmm) REVERT: R 205 LYS cc_start: 0.8550 (tptt) cc_final: 0.8189 (mmtt) REVERT: R 256 THR cc_start: 0.8955 (p) cc_final: 0.8647 (t) REVERT: S 103 MET cc_start: 0.6772 (mtp) cc_final: 0.6539 (ttm) REVERT: S 170 GLU cc_start: 0.8230 (tp30) cc_final: 0.7977 (tp30) REVERT: S 188 MET cc_start: 0.7354 (tpp) cc_final: 0.6923 (ttm) REVERT: T 90 LEU cc_start: 0.9132 (tp) cc_final: 0.8829 (mt) REVERT: T 214 ASP cc_start: 0.8915 (m-30) cc_final: 0.8169 (m-30) outliers start: 117 outliers final: 90 residues processed: 837 average time/residue: 0.6729 time to fit residues: 919.1384 Evaluate side-chains 847 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 742 time to evaluate : 5.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 210 GLU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 58 LYS Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain P residue 349 LEU Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 184 HIS Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 209 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 363 optimal weight: 9.9990 chunk 585 optimal weight: 0.7980 chunk 357 optimal weight: 50.0000 chunk 277 optimal weight: 0.7980 chunk 406 optimal weight: 0.9980 chunk 613 optimal weight: 0.5980 chunk 564 optimal weight: 0.6980 chunk 488 optimal weight: 50.0000 chunk 50 optimal weight: 7.9990 chunk 377 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS B 157 ASN B 603 GLN C 140 ASN D 482 GLN ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 ASN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 50486 Z= 0.183 Angle : 0.588 13.992 68109 Z= 0.300 Chirality : 0.042 0.372 7609 Planarity : 0.004 0.052 8813 Dihedral : 5.087 167.323 6801 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.58 % Allowed : 14.18 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.11), residues: 6176 helix: 2.05 (0.09), residues: 3182 sheet: -0.60 (0.19), residues: 710 loop : -0.44 (0.13), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 450 HIS 0.009 0.001 HIS A 444 PHE 0.031 0.001 PHE S 200 TYR 0.033 0.001 TYR Q 232 ARG 0.014 0.001 ARG C 553 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 807 time to evaluate : 6.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8295 (t0) cc_final: 0.7923 (t0) REVERT: A 294 LEU cc_start: 0.8878 (mp) cc_final: 0.8485 (mt) REVERT: A 297 GLU cc_start: 0.7595 (tt0) cc_final: 0.7155 (tt0) REVERT: A 384 SER cc_start: 0.9026 (t) cc_final: 0.8679 (p) REVERT: A 518 ASP cc_start: 0.6623 (m-30) cc_final: 0.6350 (t0) REVERT: A 523 ASN cc_start: 0.7305 (t0) cc_final: 0.6968 (t0) REVERT: A 540 MET cc_start: 0.7942 (mtm) cc_final: 0.7607 (mtp) REVERT: B 197 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 266 TYR cc_start: 0.9033 (m-80) cc_final: 0.8826 (m-80) REVERT: B 291 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: B 368 MET cc_start: 0.8153 (mmm) cc_final: 0.7853 (mmm) REVERT: B 443 LYS cc_start: 0.9303 (mmtm) cc_final: 0.8967 (mmmm) REVERT: B 471 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: B 486 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 523 ASN cc_start: 0.8227 (t0) cc_final: 0.8012 (t0) REVERT: B 530 ARG cc_start: 0.7944 (ptp90) cc_final: 0.7613 (ptt-90) REVERT: B 550 MET cc_start: 0.7824 (mmm) cc_final: 0.7342 (mtt) REVERT: B 552 ARG cc_start: 0.8013 (ttt-90) cc_final: 0.7674 (ttt90) REVERT: C 194 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8173 (pp) REVERT: C 297 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: C 438 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7878 (mttt) REVERT: C 571 ARG cc_start: 0.8758 (ptm-80) cc_final: 0.8349 (tmm-80) REVERT: C 584 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8532 (ttm) REVERT: C 603 GLN cc_start: 0.7688 (tp40) cc_final: 0.6743 (tp40) REVERT: C 607 ASP cc_start: 0.6698 (m-30) cc_final: 0.6142 (m-30) REVERT: C 610 ASN cc_start: 0.7119 (m-40) cc_final: 0.6589 (m-40) REVERT: D 238 MET cc_start: 0.8939 (tpp) cc_final: 0.8712 (tpt) REVERT: D 251 ASN cc_start: 0.7671 (t0) cc_final: 0.7169 (t0) REVERT: D 345 ASN cc_start: 0.8326 (t0) cc_final: 0.7736 (t0) REVERT: D 494 ARG cc_start: 0.8851 (mmp80) cc_final: 0.8445 (mmt180) REVERT: E 54 ASN cc_start: 0.8828 (t0) cc_final: 0.8457 (t0) REVERT: E 358 ASN cc_start: 0.8680 (t0) cc_final: 0.8269 (t0) REVERT: E 475 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: F 256 ASN cc_start: 0.8129 (t0) cc_final: 0.7445 (t0) REVERT: F 330 ASP cc_start: 0.8755 (t70) cc_final: 0.8468 (t0) REVERT: F 369 THR cc_start: 0.9572 (m) cc_final: 0.9345 (m) REVERT: F 408 GLU cc_start: 0.8948 (tp30) cc_final: 0.8660 (tp30) REVERT: H 163 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7697 (mppt) REVERT: H 170 ASN cc_start: 0.8862 (m-40) cc_final: 0.8400 (m-40) REVERT: I 54 MET cc_start: 0.9033 (mmt) cc_final: 0.8773 (mpp) REVERT: I 70 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7649 (mp) REVERT: I 72 MET cc_start: 0.8111 (tpp) cc_final: 0.7647 (mmm) REVERT: I 76 MET cc_start: 0.8370 (mmm) cc_final: 0.8148 (mmm) REVERT: I 78 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: I 155 TYR cc_start: 0.9064 (t80) cc_final: 0.8829 (t80) REVERT: I 226 ASP cc_start: 0.7823 (t0) cc_final: 0.7332 (m-30) REVERT: J 15 MET cc_start: 0.9426 (ppp) cc_final: 0.9022 (ppp) REVERT: J 24 ASN cc_start: 0.9360 (m-40) cc_final: 0.9060 (m-40) REVERT: J 25 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8605 (tm-30) REVERT: J 44 ARG cc_start: 0.7573 (ttm170) cc_final: 0.7347 (ttm170) REVERT: J 67 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8426 (tm-30) REVERT: J 80 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7376 (ttp-170) REVERT: J 94 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8663 (tt) REVERT: J 116 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8250 (mt) REVERT: J 172 TYR cc_start: 0.8917 (m-80) cc_final: 0.8526 (m-10) REVERT: K 18 PHE cc_start: 0.9333 (t80) cc_final: 0.9119 (t80) REVERT: K 52 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8421 (pttm) REVERT: K 55 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8570 (tm-30) REVERT: K 58 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8333 (tp30) REVERT: K 164 ASP cc_start: 0.7900 (t70) cc_final: 0.7163 (p0) REVERT: L 108 ARG cc_start: 0.7296 (mmt90) cc_final: 0.6975 (mtt180) REVERT: M 102 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7895 (t80) REVERT: N 17 ARG cc_start: 0.8780 (mtm-85) cc_final: 0.8393 (mtt-85) REVERT: N 20 GLU cc_start: 0.8567 (pt0) cc_final: 0.8161 (pp20) REVERT: N 58 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8976 (tppt) REVERT: O 15 GLU cc_start: 0.8355 (tt0) cc_final: 0.7959 (tp30) REVERT: O 21 LYS cc_start: 0.9083 (mtmt) cc_final: 0.8510 (ptmt) REVERT: O 102 PHE cc_start: 0.7592 (m-80) cc_final: 0.7283 (t80) REVERT: O 104 CYS cc_start: 0.8146 (m) cc_final: 0.7761 (m) REVERT: P 96 MET cc_start: 0.4245 (mtp) cc_final: 0.4038 (ptp) REVERT: P 156 MET cc_start: -0.0976 (mtp) cc_final: -0.2352 (mmt) REVERT: P 208 MET cc_start: 0.5482 (mmm) cc_final: 0.5267 (mmm) REVERT: P 309 MET cc_start: 0.8004 (mtm) cc_final: 0.7179 (mpp) REVERT: P 426 ARG cc_start: 0.8714 (ptm-80) cc_final: 0.8415 (ptm-80) REVERT: P 451 ASN cc_start: 0.9050 (m-40) cc_final: 0.8704 (t0) REVERT: Q 115 MET cc_start: 0.7172 (mmt) cc_final: 0.6902 (mmt) REVERT: Q 161 MET cc_start: 0.8711 (tmm) cc_final: 0.8015 (tmm) REVERT: Q 188 MET cc_start: 0.7414 (ttm) cc_final: 0.6872 (ttm) REVERT: Q 197 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7364 (t80) REVERT: R 32 CYS cc_start: 0.8656 (m) cc_final: 0.8231 (m) REVERT: R 60 TYR cc_start: 0.7796 (m-80) cc_final: 0.7522 (m-80) REVERT: R 103 MET cc_start: 0.8478 (mtp) cc_final: 0.7372 (mmt) REVERT: R 161 MET cc_start: 0.8498 (tmm) cc_final: 0.7986 (tmm) REVERT: R 205 LYS cc_start: 0.8553 (tptt) cc_final: 0.8194 (mmtt) REVERT: R 256 THR cc_start: 0.8946 (p) cc_final: 0.8649 (t) REVERT: S 93 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8473 (ttp80) REVERT: S 188 MET cc_start: 0.7240 (tpp) cc_final: 0.6918 (ttm) REVERT: T 90 LEU cc_start: 0.9051 (tp) cc_final: 0.8662 (mt) REVERT: T 214 ASP cc_start: 0.8721 (m-30) cc_final: 0.7626 (t0) outliers start: 86 outliers final: 54 residues processed: 858 average time/residue: 0.6497 time to fit residues: 910.9115 Evaluate side-chains 843 residues out of total 5432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 773 time to evaluate : 5.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 210 GLU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 102 PHE Chi-restraints excluded: chain N residue 58 LYS Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain P residue 349 LEU Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain Q residue 197 TYR Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 170 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 388 optimal weight: 0.9980 chunk 520 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 450 optimal weight: 30.0000 chunk 72 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 489 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 502 optimal weight: 40.0000 chunk 61 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN E 393 ASN ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 ASN K 221 ASN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 HIS ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.186225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.148302 restraints weight = 66213.262| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.92 r_work: 0.3315 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 50486 Z= 0.244 Angle : 0.598 13.933 68109 Z= 0.304 Chirality : 0.043 0.414 7609 Planarity : 0.004 0.060 8813 Dihedral : 5.075 168.575 6801 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.51 % Allowed : 14.53 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.11), residues: 6176 helix: 2.06 (0.09), residues: 3196 sheet: -0.60 (0.19), residues: 714 loop : -0.42 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 450 HIS 0.010 0.001 HIS A 444 PHE 0.032 0.001 PHE S 200 TYR 0.038 0.001 TYR Q 232 ARG 0.014 0.001 ARG C 553 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15904.01 seconds wall clock time: 281 minutes 5.47 seconds (16865.47 seconds total)