Starting phenix.real_space_refine on Mon Feb 19 12:19:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjk_25928/02_2024/7tjk_25928_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjk_25928/02_2024/7tjk_25928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjk_25928/02_2024/7tjk_25928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjk_25928/02_2024/7tjk_25928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjk_25928/02_2024/7tjk_25928_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjk_25928/02_2024/7tjk_25928_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 93 5.49 5 Mg 4 5.21 5 S 107 5.16 5 C 15504 2.51 5 N 4101 2.21 5 O 4859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24668 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3889 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 475} Chain breaks: 4 Chain: "B" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2057 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 1 Chain: "C" Number of atoms: 4504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4504 Classifications: {'peptide': 544} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 528} Chain breaks: 5 Chain: "D" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3536 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 3 Chain: "E" Number of atoms: 3588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3588 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 21, 'TRANS': 415} Chain breaks: 3 Chain: "F" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2163 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 7, 'TRANS': 254} Chain breaks: 2 Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 832 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 846 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "I" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2995 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 14, 'TRANS': 361} Chain breaks: 7 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 13.94, per 1000 atoms: 0.57 Number of scatterers: 24668 At special positions: 0 Unit cell: (116.96, 138.46, 179.74, 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 107 16.00 P 93 15.00 Mg 4 11.99 O 4859 8.00 N 4101 7.00 C 15504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.53 Conformation dependent library (CDL) restraints added in 4.0 seconds 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5406 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 146 helices and 12 sheets defined 53.1% alpha, 7.7% beta 41 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 11.20 Creating SS restraints... Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 422 through 429 removed outlier: 4.106A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 485 through 501 Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.590A pdb=" N CYS A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 528 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TRP A 529 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 533 " --> pdb=" O ASN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 551 Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 577 through 587 removed outlier: 3.962A pdb=" N THR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 611 through 617 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 686 through 699 Processing helix chain 'A' and resid 703 through 725 Processing helix chain 'A' and resid 775 through 784 Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 799 through 814 Processing helix chain 'A' and resid 822 through 835 Processing helix chain 'A' and resid 840 through 851 removed outlier: 5.100A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.916A pdb=" N ASN A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 271 through 284 Processing helix chain 'B' and resid 287 through 309 removed outlier: 4.154A pdb=" N LYS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N MET B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 390 through 393 No H-bonds generated for 'chain 'B' and resid 390 through 393' Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.515A pdb=" N ASP B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 461 through 464 Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'B' and resid 489 through 492 removed outlier: 3.876A pdb=" N PHE B 492 " --> pdb=" O GLU B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 489 through 492' Processing helix chain 'C' and resid 17 through 19 No H-bonds generated for 'chain 'C' and resid 17 through 19' Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 51 through 92 removed outlier: 3.816A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 157 Processing helix chain 'C' and resid 186 through 189 No H-bonds generated for 'chain 'C' and resid 186 through 189' Processing helix chain 'C' and resid 191 through 195 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.609A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 313 through 331 Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.904A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 338 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 348 through 353 Processing helix chain 'C' and resid 358 through 370 Processing helix chain 'C' and resid 389 through 396 removed outlier: 3.736A pdb=" N PHE C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU C 396 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 415 Processing helix chain 'C' and resid 424 through 433 Processing helix chain 'C' and resid 436 through 442 removed outlier: 4.483A pdb=" N ARG C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 453 No H-bonds generated for 'chain 'C' and resid 450 through 453' Processing helix chain 'C' and resid 475 through 478 No H-bonds generated for 'chain 'C' and resid 475 through 478' Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.855A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 547 removed outlier: 3.833A pdb=" N THR C 547 " --> pdb=" O ALA C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 557 Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 575 through 594 removed outlier: 3.856A pdb=" N LEU C 581 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 60 Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.525A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 Processing helix chain 'D' and resid 141 through 157 removed outlier: 4.104A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 157 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 187 Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 229 through 240 Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 262 through 267 Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 302 through 314 Processing helix chain 'D' and resid 319 through 330 Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.640A pdb=" N SER D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 351 through 360 Processing helix chain 'D' and resid 362 through 372 removed outlier: 3.564A pdb=" N LEU D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 382 Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 408 through 423 Processing helix chain 'D' and resid 453 through 465 removed outlier: 4.628A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 489 removed outlier: 3.542A pdb=" N ASN D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 495 No H-bonds generated for 'chain 'D' and resid 493 through 495' Processing helix chain 'D' and resid 499 through 501 No H-bonds generated for 'chain 'D' and resid 499 through 501' Processing helix chain 'D' and resid 510 through 516 removed outlier: 3.630A pdb=" N ILE D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 527 Processing helix chain 'E' and resid 12 through 21 Processing helix chain 'E' and resid 26 through 28 No H-bonds generated for 'chain 'E' and resid 26 through 28' Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 64 through 67 No H-bonds generated for 'chain 'E' and resid 64 through 67' Processing helix chain 'E' and resid 70 through 88 removed outlier: 3.739A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 105 through 119 removed outlier: 4.169A pdb=" N GLN E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR E 119 " --> pdb=" O ILE E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.522A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASN E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLU E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 removed outlier: 4.154A pdb=" N TYR E 179 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N HIS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 210 removed outlier: 5.740A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 218 Processing helix chain 'E' and resid 230 through 251 removed outlier: 5.671A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 272 Proline residue: E 267 - end of helix removed outlier: 3.866A pdb=" N ARG E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 287 Processing helix chain 'E' and resid 289 through 292 Processing helix chain 'E' and resid 326 through 340 Processing helix chain 'E' and resid 343 through 349 removed outlier: 4.160A pdb=" N ALA E 347 " --> pdb=" O ARG E 344 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 349 " --> pdb=" O ASP E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 383 through 393 Processing helix chain 'E' and resid 418 through 429 Processing helix chain 'E' and resid 456 through 465 removed outlier: 4.072A pdb=" N GLU E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 14 Processing helix chain 'F' and resid 27 through 46 removed outlier: 4.194A pdb=" N ASN F 45 " --> pdb=" O ASN F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 71 removed outlier: 3.890A pdb=" N VAL F 55 " --> pdb=" O GLN F 51 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N CYS F 58 " --> pdb=" O GLU F 54 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 88 through 102 Processing helix chain 'F' and resid 106 through 109 No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 282 through 291 removed outlier: 3.601A pdb=" N ASP F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 308 Processing helix chain 'F' and resid 316 through 331 removed outlier: 3.911A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 340 through 351 removed outlier: 4.152A pdb=" N ILE F 346 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL F 347 " --> pdb=" O HIS F 344 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET F 350 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 372 removed outlier: 4.313A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 386 Processing helix chain 'F' and resid 394 through 401 removed outlier: 4.042A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 426 Processing helix chain 'I' and resid 54 through 61 Processing helix chain 'I' and resid 82 through 97 Processing helix chain 'I' and resid 114 through 124 Processing helix chain 'I' and resid 178 through 187 removed outlier: 3.705A pdb=" N ILE I 181 " --> pdb=" O PRO I 178 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE I 182 " --> pdb=" O SER I 179 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP I 187 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 209 Processing helix chain 'I' and resid 225 through 228 Processing helix chain 'I' and resid 235 through 250 removed outlier: 4.604A pdb=" N THR I 241 " --> pdb=" O GLN I 237 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE I 242 " --> pdb=" O SER I 238 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU I 244 " --> pdb=" O ARG I 240 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU I 248 " --> pdb=" O GLU I 244 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA I 249 " --> pdb=" O LEU I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 303 Processing helix chain 'I' and resid 314 through 323 Processing helix chain 'I' and resid 331 through 348 Processing helix chain 'I' and resid 387 through 396 Processing helix chain 'I' and resid 403 through 408 Processing helix chain 'I' and resid 412 through 427 removed outlier: 3.800A pdb=" N LEU I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 445 removed outlier: 3.811A pdb=" N LYS I 442 " --> pdb=" O ASP I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 468 Processing helix chain 'I' and resid 495 through 503 removed outlier: 3.580A pdb=" N TYR I 499 " --> pdb=" O MET I 495 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP I 500 " --> pdb=" O ARG I 496 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 511 No H-bonds generated for 'chain 'I' and resid 509 through 511' Processing sheet with id= A, first strand: chain 'A' and resid 621 through 624 removed outlier: 8.594A pdb=" N ILE A 622 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 476 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE A 624 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA A 478 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL A 598 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 565 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 657 through 659 Processing sheet with id= C, first strand: chain 'A' and resid 879 through 881 Processing sheet with id= D, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.299A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU B 420 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL B 453 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL B 423 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 361 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N HIS B 425 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU B 363 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 263 through 267 removed outlier: 6.728A pdb=" N THR C 104 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU C 266 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE C 106 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU C 199 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N SER C 235 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N MET C 201 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE C 237 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE C 203 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASN C 239 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE C 205 " --> pdb=" O ASN C 239 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 534 through 536 Processing sheet with id= G, first strand: chain 'D' and resid 272 through 274 removed outlier: 8.085A pdb=" N ILE D 273 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE D 99 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL D 212 " --> pdb=" O CYS D 246 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE D 248 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE D 214 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N CYS D 250 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE D 216 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 469 through 471 Processing sheet with id= I, first strand: chain 'E' and resid 185 through 189 removed outlier: 9.156A pdb=" N LEU E 33 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE E 166 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU E 35 " --> pdb=" O PHE E 166 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR E 168 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY E 37 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N MET E 170 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR E 169 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU E 132 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS E 58 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE E 131 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL E 60 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASP E 133 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 62 " --> pdb=" O ASP E 133 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 433 through 435 Processing sheet with id= K, first strand: chain 'I' and resid 284 through 288 removed outlier: 3.566A pdb=" N GLY I 108 " --> pdb=" O ALA I 262 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE I 218 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE I 259 " --> pdb=" O PHE I 218 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL I 220 " --> pdb=" O ILE I 259 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N MET I 261 " --> pdb=" O VAL I 220 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU I 222 " --> pdb=" O MET I 261 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASN I 263 " --> pdb=" O LEU I 222 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR I 217 " --> pdb=" O SER I 164 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 471 through 477 926 hydrogen bonds defined for protein. 2685 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 9.56 Time building geometry restraints manager: 11.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3832 1.31 - 1.44: 7010 1.44 - 1.56: 13980 1.56 - 1.69: 183 1.69 - 1.82: 176 Bond restraints: 25181 Sorted by residual: bond pdb=" N ILE I 170 " pdb=" CA ILE I 170 " ideal model delta sigma weight residual 1.459 1.518 -0.059 1.15e-02 7.56e+03 2.65e+01 bond pdb=" N ASN I 171 " pdb=" CA ASN I 171 " ideal model delta sigma weight residual 1.456 1.518 -0.063 1.22e-02 6.72e+03 2.64e+01 bond pdb=" C LYS B 419 " pdb=" O LYS B 419 " ideal model delta sigma weight residual 1.236 1.183 0.052 1.31e-02 5.83e+03 1.60e+01 bond pdb=" C ASN I 171 " pdb=" O ASN I 171 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.22e-02 6.72e+03 1.26e+01 bond pdb=" C MET A 779 " pdb=" O MET A 779 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.29e-02 6.01e+03 1.21e+01 ... (remaining 25176 not shown) Histogram of bond angle deviations from ideal: 97.66 - 106.42: 1049 106.42 - 115.17: 15209 115.17 - 123.92: 17242 123.92 - 132.68: 836 132.68 - 141.43: 38 Bond angle restraints: 34374 Sorted by residual: angle pdb=" PB ATP I1001 " pdb=" O3B ATP I1001 " pdb=" PG ATP I1001 " ideal model delta sigma weight residual 139.87 131.07 8.80 1.00e+00 1.00e+00 7.74e+01 angle pdb=" PA ATP I1001 " pdb=" O3A ATP I1001 " pdb=" PB ATP I1001 " ideal model delta sigma weight residual 136.83 129.57 7.26 1.00e+00 1.00e+00 5.28e+01 angle pdb=" N GLU D 151 " pdb=" CA GLU D 151 " pdb=" CB GLU D 151 " ideal model delta sigma weight residual 110.16 119.19 -9.03 1.48e+00 4.57e-01 3.72e+01 angle pdb=" N ASN I 171 " pdb=" CA ASN I 171 " pdb=" CB ASN I 171 " ideal model delta sigma weight residual 109.97 118.11 -8.14 1.47e+00 4.63e-01 3.07e+01 angle pdb=" C ILE F 81 " pdb=" N ASP F 82 " pdb=" CA ASP F 82 " ideal model delta sigma weight residual 120.38 127.29 -6.91 1.46e+00 4.69e-01 2.24e+01 ... (remaining 34369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13139 17.97 - 35.93: 1383 35.93 - 53.90: 499 53.90 - 71.87: 121 71.87 - 89.84: 29 Dihedral angle restraints: 15171 sinusoidal: 6901 harmonic: 8270 Sorted by residual: dihedral pdb=" CA SER A 854 " pdb=" C SER A 854 " pdb=" N ASP A 855 " pdb=" CA ASP A 855 " ideal model delta harmonic sigma weight residual 180.00 153.55 26.45 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA PHE B 475 " pdb=" C PHE B 475 " pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta harmonic sigma weight residual 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA VAL E 8 " pdb=" C VAL E 8 " pdb=" N ALA E 9 " pdb=" CA ALA E 9 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 15168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3159 0.061 - 0.122: 666 0.122 - 0.183: 78 0.183 - 0.245: 9 0.245 - 0.306: 2 Chirality restraints: 3914 Sorted by residual: chirality pdb=" CB VAL B 384 " pdb=" CA VAL B 384 " pdb=" CG1 VAL B 384 " pdb=" CG2 VAL B 384 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ARG I 240 " pdb=" N ARG I 240 " pdb=" C ARG I 240 " pdb=" CB ARG I 240 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA TRP C 494 " pdb=" N TRP C 494 " pdb=" C TRP C 494 " pdb=" CB TRP C 494 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3911 not shown) Planarity restraints: 4013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 26 " 0.081 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO C 27 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO C 27 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO C 27 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 50 " -0.021 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C LYS F 50 " 0.075 2.00e-02 2.50e+03 pdb=" O LYS F 50 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN F 51 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 418 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ILE B 418 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE B 418 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS B 419 " 0.020 2.00e-02 2.50e+03 ... (remaining 4010 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 131 2.49 - 3.09: 15773 3.09 - 3.69: 39042 3.69 - 4.30: 59373 4.30 - 4.90: 92395 Nonbonded interactions: 206714 Sorted by model distance: nonbonded pdb=" OD1 ASP E 136 " pdb=" O HOH E1101 " model vdw 1.886 2.440 nonbonded pdb=" O2B ATP I1001 " pdb="MG MG I1002 " model vdw 2.053 2.170 nonbonded pdb=" OG1 THR D 109 " pdb="MG MG D1002 " model vdw 2.066 2.170 nonbonded pdb=" OG1 THR I 115 " pdb="MG MG I1002 " model vdw 2.082 2.170 nonbonded pdb=" O2G ATP D1001 " pdb="MG MG D1002 " model vdw 2.108 2.170 ... (remaining 206709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.520 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 74.590 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 : 0.005 0.085 25181 Z= 0.297 Angle : 0.885 21.133 34374 Z= 0.509 Chirality : 0.050 0.306 3914 Planarity : 0.007 0.122 4013 Dihedral : 17.378 89.836 9765 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.39 % Allowed : 0.47 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 2721 helix: -1.13 (0.11), residues: 1523 sheet: 0.39 (0.31), residues: 253 loop : -1.05 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 450 HIS 0.012 0.002 HIS C 65 PHE 0.042 0.002 PHE F 329 TYR 0.026 0.002 TYR F 80 ARG 0.005 0.001 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 519 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8163 (mptp) REVERT: A 544 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7545 (mt-10) REVERT: C 343 VAL cc_start: 0.8379 (m) cc_final: 0.8042 (p) REVERT: C 395 PHE cc_start: 0.6935 (m-80) cc_final: 0.6231 (m-80) REVERT: C 408 PHE cc_start: 0.8881 (t80) cc_final: 0.8631 (t80) REVERT: D 83 ASP cc_start: 0.7777 (t0) cc_final: 0.7537 (t70) REVERT: F 67 GLN cc_start: 0.8279 (tt0) cc_final: 0.7872 (tt0) REVERT: F 100 GLN cc_start: 0.8607 (mt0) cc_final: 0.8404 (mt0) REVERT: F 332 PHE cc_start: 0.7911 (m-10) cc_final: 0.7455 (m-10) REVERT: F 417 GLN cc_start: 0.8649 (tt0) cc_final: 0.7896 (mm-40) REVERT: I 200 LYS cc_start: 0.8458 (ptpp) cc_final: 0.8013 (pptt) REVERT: I 247 LEU cc_start: 0.8453 (tt) cc_final: 0.8174 (mt) REVERT: I 409 LYS cc_start: 0.8950 (mttt) cc_final: 0.8713 (mtpp) REVERT: I 426 LYS cc_start: 0.8287 (mttt) cc_final: 0.7995 (mtmm) outliers start: 10 outliers final: 5 residues processed: 525 average time/residue: 1.6564 time to fit residues: 974.5115 Evaluate side-chains 282 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 277 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 238 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 134 optimal weight: 0.3980 chunk 165 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 810 ASN B 399 HIS C 38 HIS C 477 GLN D 158 HIS ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN F 410 ASN I 151 ASN I 203 GLN I 232 ASN I 327 ASN I 454 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 25181 Z= 0.382 Angle : 0.627 15.241 34374 Z= 0.333 Chirality : 0.044 0.197 3914 Planarity : 0.004 0.059 4013 Dihedral : 17.963 86.517 4080 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.50 % Allowed : 11.59 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 2721 helix: 0.21 (0.13), residues: 1542 sheet: 0.31 (0.30), residues: 253 loop : -0.71 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 456 HIS 0.007 0.001 HIS F 59 PHE 0.022 0.002 PHE D 363 TYR 0.026 0.002 TYR C 483 ARG 0.012 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 287 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8333 (mptp) REVERT: A 678 ARG cc_start: 0.7616 (mtp180) cc_final: 0.7273 (ttp80) REVERT: B 268 ASP cc_start: 0.8129 (t70) cc_final: 0.7843 (m-30) REVERT: B 377 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8216 (mppt) REVERT: C 80 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: C 147 MET cc_start: 0.8950 (mmp) cc_final: 0.8666 (mmp) REVERT: C 246 ASN cc_start: 0.8414 (m110) cc_final: 0.8212 (t0) REVERT: C 343 VAL cc_start: 0.8430 (m) cc_final: 0.8180 (p) REVERT: C 391 PHE cc_start: 0.7705 (t80) cc_final: 0.7329 (t80) REVERT: C 395 PHE cc_start: 0.7346 (m-80) cc_final: 0.7056 (m-80) REVERT: C 408 PHE cc_start: 0.8953 (t80) cc_final: 0.8593 (t80) REVERT: D 295 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6966 (mpt-90) REVERT: D 467 ASP cc_start: 0.7944 (t0) cc_final: 0.7743 (t0) REVERT: E 170 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7837 (mmm) REVERT: E 188 MET cc_start: 0.8669 (mpt) cc_final: 0.8227 (mpt) REVERT: E 275 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.5851 (mmtm) REVERT: E 367 LYS cc_start: 0.8446 (pptt) cc_final: 0.8048 (pttp) REVERT: E 462 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.6589 (mp) REVERT: F 5 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8414 (tp40) REVERT: F 67 GLN cc_start: 0.8435 (tt0) cc_final: 0.7951 (tt0) REVERT: F 71 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: F 100 GLN cc_start: 0.8724 (mt0) cc_final: 0.8479 (mt0) REVERT: F 354 MET cc_start: 0.5947 (mmp) cc_final: 0.5716 (tpt) REVERT: F 417 GLN cc_start: 0.8768 (tt0) cc_final: 0.7954 (mm-40) REVERT: I 57 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7986 (mtm180) REVERT: I 200 LYS cc_start: 0.8391 (ptpp) cc_final: 0.8133 (pptt) REVERT: I 247 LEU cc_start: 0.8655 (tt) cc_final: 0.8357 (mt) outliers start: 64 outliers final: 23 residues processed: 324 average time/residue: 1.5103 time to fit residues: 558.5011 Evaluate side-chains 270 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 496 ARG Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 142 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 213 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 257 optimal weight: 0.0170 chunk 278 optimal weight: 4.9990 chunk 229 optimal weight: 0.4980 chunk 255 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 overall best weight: 1.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 774 HIS D 240 HIS E 2 ASN F 7 GLN F 45 ASN F 67 GLN F 318 GLN F 410 ASN I 99 HIS I 327 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25181 Z= 0.212 Angle : 0.522 15.075 34374 Z= 0.277 Chirality : 0.040 0.174 3914 Planarity : 0.003 0.052 4013 Dihedral : 17.689 88.209 4073 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.15 % Allowed : 13.62 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2721 helix: 0.84 (0.13), residues: 1544 sheet: 0.29 (0.30), residues: 261 loop : -0.47 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 539 HIS 0.008 0.001 HIS F 8 PHE 0.015 0.001 PHE C 455 TYR 0.019 0.001 TYR C 483 ARG 0.011 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 272 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8382 (mptp) REVERT: A 678 ARG cc_start: 0.7636 (mtp180) cc_final: 0.7254 (ttp80) REVERT: A 681 ARG cc_start: 0.8195 (tmm-80) cc_final: 0.7976 (tmm-80) REVERT: B 268 ASP cc_start: 0.8096 (t70) cc_final: 0.7772 (m-30) REVERT: B 377 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8202 (mppt) REVERT: C 80 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: C 343 VAL cc_start: 0.8438 (m) cc_final: 0.8158 (p) REVERT: C 346 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7886 (mp) REVERT: C 391 PHE cc_start: 0.7680 (t80) cc_final: 0.7424 (t80) REVERT: C 408 PHE cc_start: 0.8850 (t80) cc_final: 0.8465 (t80) REVERT: C 411 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7909 (ptt180) REVERT: C 412 PHE cc_start: 0.8511 (t80) cc_final: 0.8171 (t80) REVERT: C 435 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8078 (mppt) REVERT: D 261 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: D 295 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6961 (mpt180) REVERT: D 467 ASP cc_start: 0.7921 (t0) cc_final: 0.7689 (t0) REVERT: E 188 MET cc_start: 0.8751 (mpt) cc_final: 0.8296 (mpt) REVERT: E 275 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.5855 (mmtm) REVERT: E 367 LYS cc_start: 0.8469 (pptt) cc_final: 0.8106 (pttp) REVERT: E 462 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6748 (mp) REVERT: F 5 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8354 (tp40) REVERT: F 8 HIS cc_start: 0.8527 (t-170) cc_final: 0.8325 (t-170) REVERT: F 67 GLN cc_start: 0.8406 (tt0) cc_final: 0.8003 (tt0) REVERT: F 71 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: F 100 GLN cc_start: 0.8620 (mt0) cc_final: 0.8384 (mt0) REVERT: F 318 GLN cc_start: 0.6388 (mt0) cc_final: 0.5831 (mt0) REVERT: F 321 CYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7414 (p) REVERT: F 410 ASN cc_start: 0.7281 (t0) cc_final: 0.7078 (p0) REVERT: F 417 GLN cc_start: 0.8779 (tt0) cc_final: 0.7981 (mm-40) REVERT: I 200 LYS cc_start: 0.8384 (ptpp) cc_final: 0.8098 (pptt) REVERT: I 247 LEU cc_start: 0.8680 (tt) cc_final: 0.8466 (mt) outliers start: 55 outliers final: 24 residues processed: 305 average time/residue: 1.5485 time to fit residues: 538.1146 Evaluate side-chains 274 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 241 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 254 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 258 optimal weight: 10.0000 chunk 273 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 774 HIS ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 241 ASN C 430 ASN D 152 GLN E 245 GLN F 7 GLN F 45 ASN I 327 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25181 Z= 0.267 Angle : 0.535 14.902 34374 Z= 0.285 Chirality : 0.041 0.164 3914 Planarity : 0.003 0.050 4013 Dihedral : 17.686 89.143 4071 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.77 % Allowed : 13.90 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2721 helix: 1.15 (0.14), residues: 1534 sheet: 0.30 (0.30), residues: 252 loop : -0.44 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 539 HIS 0.007 0.001 HIS F 8 PHE 0.025 0.001 PHE C 395 TYR 0.021 0.001 TYR C 483 ARG 0.013 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 262 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7254 (mp0) cc_final: 0.6858 (mp0) REVERT: A 425 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8383 (mptp) REVERT: A 678 ARG cc_start: 0.7606 (mtp180) cc_final: 0.7314 (ttp80) REVERT: B 268 ASP cc_start: 0.8125 (t70) cc_final: 0.7811 (m-30) REVERT: B 377 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8175 (mppt) REVERT: C 80 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: C 343 VAL cc_start: 0.8442 (m) cc_final: 0.8180 (p) REVERT: C 395 PHE cc_start: 0.7107 (m-80) cc_final: 0.6569 (m-80) REVERT: C 408 PHE cc_start: 0.8881 (t80) cc_final: 0.8495 (t80) REVERT: C 585 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6556 (tpt) REVERT: D 261 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: D 295 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6944 (mpt180) REVERT: D 467 ASP cc_start: 0.7933 (t0) cc_final: 0.7704 (t0) REVERT: E 275 LYS cc_start: 0.6404 (OUTLIER) cc_final: 0.5934 (mmmm) REVERT: E 367 LYS cc_start: 0.8508 (pptt) cc_final: 0.8108 (pttp) REVERT: E 449 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7215 (mtp85) REVERT: E 462 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.6786 (mp) REVERT: F 5 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8336 (tp40) REVERT: F 8 HIS cc_start: 0.8532 (t70) cc_final: 0.7743 (t-170) REVERT: F 67 GLN cc_start: 0.8471 (tt0) cc_final: 0.8071 (tt0) REVERT: F 71 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: F 279 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7627 (tppt) REVERT: F 318 GLN cc_start: 0.6383 (mt0) cc_final: 0.5852 (mt0) REVERT: F 321 CYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7326 (p) REVERT: F 410 ASN cc_start: 0.7272 (t0) cc_final: 0.7052 (p0) REVERT: F 417 GLN cc_start: 0.8811 (tt0) cc_final: 0.8021 (mm-40) REVERT: I 57 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8015 (mtm180) REVERT: I 200 LYS cc_start: 0.8386 (ptpp) cc_final: 0.8104 (pptt) outliers start: 71 outliers final: 31 residues processed: 306 average time/residue: 1.4691 time to fit residues: 516.2645 Evaluate side-chains 275 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 233 time to evaluate : 5.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 472 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 227 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN D 58 GLN E 91 ASN E 428 HIS F 7 GLN F 59 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 25181 Z= 0.417 Angle : 0.598 14.272 34374 Z= 0.316 Chirality : 0.044 0.165 3914 Planarity : 0.004 0.057 4013 Dihedral : 17.847 89.592 4071 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.20 % Allowed : 14.01 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.16), residues: 2721 helix: 1.09 (0.14), residues: 1530 sheet: 0.24 (0.30), residues: 247 loop : -0.43 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 539 HIS 0.008 0.001 HIS F 8 PHE 0.019 0.002 PHE D 363 TYR 0.025 0.002 TYR C 483 ARG 0.014 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 239 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7167 (mp0) cc_final: 0.6667 (mp0) REVERT: A 678 ARG cc_start: 0.7644 (mtp180) cc_final: 0.7373 (ttp80) REVERT: A 725 HIS cc_start: 0.8504 (m-70) cc_final: 0.8271 (m-70) REVERT: B 268 ASP cc_start: 0.7938 (t70) cc_final: 0.7649 (m-30) REVERT: B 377 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8192 (mppt) REVERT: C 80 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: C 343 VAL cc_start: 0.8419 (m) cc_final: 0.8104 (p) REVERT: C 408 PHE cc_start: 0.8805 (t80) cc_final: 0.8370 (t80) REVERT: C 585 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6653 (tpt) REVERT: D 261 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: D 295 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6851 (mpt180) REVERT: D 467 ASP cc_start: 0.7977 (t0) cc_final: 0.7742 (t0) REVERT: E 170 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7918 (mtt) REVERT: E 275 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.5734 (mmtm) REVERT: E 367 LYS cc_start: 0.8566 (pptt) cc_final: 0.8159 (pttp) REVERT: E 449 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7247 (mtp85) REVERT: E 462 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.6989 (mp) REVERT: F 71 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: F 279 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7614 (tppt) REVERT: F 287 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7911 (mmp80) REVERT: F 410 ASN cc_start: 0.7307 (t0) cc_final: 0.7040 (p0) REVERT: I 57 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8087 (mtm180) REVERT: I 200 LYS cc_start: 0.8476 (ptpp) cc_final: 0.8111 (ptmt) outliers start: 82 outliers final: 37 residues processed: 294 average time/residue: 1.4838 time to fit residues: 497.8214 Evaluate side-chains 268 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 219 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain F residue 415 ASP Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 92 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 273 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN D 58 GLN D 240 HIS F 45 ASN I 151 ASN I 327 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25181 Z= 0.211 Angle : 0.524 14.687 34374 Z= 0.278 Chirality : 0.040 0.204 3914 Planarity : 0.003 0.059 4013 Dihedral : 17.691 87.197 4071 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.58 % Allowed : 15.42 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.16), residues: 2721 helix: 1.34 (0.14), residues: 1517 sheet: 0.28 (0.31), residues: 247 loop : -0.40 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 154 HIS 0.007 0.001 HIS F 8 PHE 0.017 0.001 PHE C 391 TYR 0.018 0.001 TYR C 483 ARG 0.015 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 240 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7214 (mp0) cc_final: 0.6728 (mp0) REVERT: A 678 ARG cc_start: 0.7633 (mtp180) cc_final: 0.7355 (ttp80) REVERT: B 268 ASP cc_start: 0.7857 (t70) cc_final: 0.7577 (m-30) REVERT: B 377 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8174 (mppt) REVERT: C 80 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: C 343 VAL cc_start: 0.8363 (m) cc_final: 0.8025 (p) REVERT: C 408 PHE cc_start: 0.8806 (t80) cc_final: 0.8323 (t80) REVERT: C 454 HIS cc_start: 0.7307 (OUTLIER) cc_final: 0.6909 (p-80) REVERT: C 550 LYS cc_start: 0.8579 (ptmm) cc_final: 0.8232 (tttt) REVERT: C 585 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6579 (tpt) REVERT: D 261 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: D 295 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6815 (mpt180) REVERT: D 467 ASP cc_start: 0.7936 (t0) cc_final: 0.7701 (t0) REVERT: E 367 LYS cc_start: 0.8569 (pptt) cc_final: 0.8156 (pttp) REVERT: E 449 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7204 (mtp85) REVERT: E 462 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.6856 (mp) REVERT: F 71 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: F 279 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7654 (tppt) REVERT: F 287 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7966 (mmp80) REVERT: F 321 CYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7350 (p) REVERT: F 410 ASN cc_start: 0.7305 (t0) cc_final: 0.7039 (p0) REVERT: I 200 LYS cc_start: 0.8475 (ptpp) cc_final: 0.8168 (ptmt) outliers start: 66 outliers final: 35 residues processed: 285 average time/residue: 1.4876 time to fit residues: 485.7853 Evaluate side-chains 274 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 228 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 263 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 230 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 272 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 600 ASN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN I 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25181 Z= 0.233 Angle : 0.532 14.715 34374 Z= 0.281 Chirality : 0.040 0.198 3914 Planarity : 0.003 0.067 4013 Dihedral : 17.638 88.627 4071 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.62 % Allowed : 15.85 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.16), residues: 2721 helix: 1.39 (0.14), residues: 1527 sheet: 0.30 (0.31), residues: 247 loop : -0.39 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 154 HIS 0.009 0.001 HIS F 8 PHE 0.024 0.001 PHE C 391 TYR 0.017 0.001 TYR C 483 ARG 0.017 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 236 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7232 (mp0) cc_final: 0.6750 (mp0) REVERT: A 678 ARG cc_start: 0.7654 (mtp180) cc_final: 0.7390 (ttp80) REVERT: B 377 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8170 (mppt) REVERT: C 80 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: C 343 VAL cc_start: 0.8421 (m) cc_final: 0.8093 (p) REVERT: C 454 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6903 (p-80) REVERT: C 495 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: C 550 LYS cc_start: 0.8581 (ptmm) cc_final: 0.8259 (tttt) REVERT: C 585 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6524 (tpt) REVERT: D 261 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: D 295 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6824 (mpt180) REVERT: D 467 ASP cc_start: 0.7942 (t0) cc_final: 0.7709 (t0) REVERT: E 170 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7886 (mtt) REVERT: E 357 ILE cc_start: 0.7861 (mm) cc_final: 0.7525 (mm) REVERT: E 367 LYS cc_start: 0.8640 (pptt) cc_final: 0.8211 (tmmm) REVERT: E 449 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7203 (mtp85) REVERT: E 462 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.6996 (mp) REVERT: F 71 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: F 279 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7647 (tppt) REVERT: F 287 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8002 (mmp80) REVERT: F 321 CYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7285 (p) REVERT: F 410 ASN cc_start: 0.7366 (t0) cc_final: 0.7073 (p0) REVERT: I 200 LYS cc_start: 0.8438 (ptpp) cc_final: 0.8139 (ptmt) outliers start: 67 outliers final: 41 residues processed: 279 average time/residue: 1.4451 time to fit residues: 461.7020 Evaluate side-chains 278 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 224 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 168 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 185 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 600 ASN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 ASN C 403 ASN D 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25181 Z= 0.384 Angle : 0.599 14.267 34374 Z= 0.314 Chirality : 0.044 0.191 3914 Planarity : 0.004 0.074 4013 Dihedral : 17.841 88.049 4071 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.50 % Allowed : 16.24 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.16), residues: 2721 helix: 1.21 (0.14), residues: 1538 sheet: 0.27 (0.31), residues: 247 loop : -0.39 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 154 HIS 0.008 0.001 HIS F 8 PHE 0.031 0.002 PHE C 391 TYR 0.025 0.002 TYR C 483 ARG 0.017 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 237 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 ARG cc_start: 0.7658 (mtp180) cc_final: 0.7432 (ttp80) REVERT: B 377 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8190 (mppt) REVERT: C 48 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8513 (tmtt) REVERT: C 80 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: C 343 VAL cc_start: 0.8438 (m) cc_final: 0.8086 (p) REVERT: C 454 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.6845 (p-80) REVERT: C 550 LYS cc_start: 0.8568 (ptmm) cc_final: 0.8225 (tttt) REVERT: C 585 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6711 (tpt) REVERT: D 261 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: D 295 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6839 (mpt180) REVERT: D 467 ASP cc_start: 0.7979 (t0) cc_final: 0.7736 (t0) REVERT: E 170 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7961 (mtt) REVERT: E 357 ILE cc_start: 0.7957 (mm) cc_final: 0.7596 (mm) REVERT: E 367 LYS cc_start: 0.8706 (pptt) cc_final: 0.8280 (tmmm) REVERT: E 449 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7273 (mtp85) REVERT: E 462 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7267 (mp) REVERT: F 71 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: F 80 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6302 (m-80) REVERT: F 279 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7681 (tppt) REVERT: F 280 MET cc_start: 0.6559 (mtt) cc_final: 0.6083 (mtp) REVERT: F 287 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8086 (mmp80) REVERT: F 410 ASN cc_start: 0.7353 (t0) cc_final: 0.7065 (p0) REVERT: I 57 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8125 (mtm180) REVERT: I 200 LYS cc_start: 0.8454 (ptpp) cc_final: 0.8104 (ptmt) outliers start: 64 outliers final: 37 residues processed: 281 average time/residue: 1.5559 time to fit residues: 498.4684 Evaluate side-chains 272 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 222 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 248 optimal weight: 5.9990 chunk 261 optimal weight: 0.0270 chunk 238 optimal weight: 6.9990 chunk 254 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 229 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 overall best weight: 1.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN C 430 ASN D 58 GLN D 240 HIS F 51 GLN I 151 ASN I 327 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25181 Z= 0.210 Angle : 0.540 14.510 34374 Z= 0.283 Chirality : 0.040 0.196 3914 Planarity : 0.003 0.071 4013 Dihedral : 17.640 87.551 4071 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.07 % Allowed : 17.10 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.16), residues: 2721 helix: 1.44 (0.14), residues: 1527 sheet: 0.31 (0.31), residues: 247 loop : -0.34 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 154 HIS 0.004 0.001 HIS C 69 PHE 0.038 0.001 PHE C 391 TYR 0.017 0.001 TYR C 483 ARG 0.017 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 241 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7323 (mp0) cc_final: 0.6988 (mp0) REVERT: A 678 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7414 (ttp80) REVERT: A 715 GLU cc_start: 0.7960 (tp30) cc_final: 0.7759 (tp30) REVERT: B 377 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8165 (mppt) REVERT: C 80 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: C 147 MET cc_start: 0.8911 (mmp) cc_final: 0.8655 (mmp) REVERT: C 343 VAL cc_start: 0.8466 (m) cc_final: 0.8178 (p) REVERT: C 454 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.6824 (p-80) REVERT: C 495 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: C 550 LYS cc_start: 0.8605 (ptmm) cc_final: 0.8284 (tttt) REVERT: C 585 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6551 (tpt) REVERT: D 261 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: D 295 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6841 (mpt180) REVERT: D 467 ASP cc_start: 0.7947 (t0) cc_final: 0.7711 (t0) REVERT: E 170 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7888 (mtt) REVERT: E 357 ILE cc_start: 0.7936 (mm) cc_final: 0.7581 (mm) REVERT: E 367 LYS cc_start: 0.8677 (pptt) cc_final: 0.8245 (tmmm) REVERT: E 462 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7236 (mp) REVERT: F 71 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: F 80 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.6133 (m-80) REVERT: F 279 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7689 (tppt) REVERT: F 280 MET cc_start: 0.6415 (mtt) cc_final: 0.5875 (mtp) REVERT: F 287 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8113 (mmp80) REVERT: F 321 CYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7376 (p) REVERT: F 410 ASN cc_start: 0.7369 (t0) cc_final: 0.7087 (p0) REVERT: I 57 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8070 (mtm180) REVERT: I 200 LYS cc_start: 0.8433 (ptpp) cc_final: 0.8062 (ptmt) REVERT: I 206 GLN cc_start: 0.8926 (tt0) cc_final: 0.8560 (pt0) outliers start: 53 outliers final: 34 residues processed: 278 average time/residue: 1.5170 time to fit residues: 480.3613 Evaluate side-chains 273 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 225 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 166 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 600 ASN D 240 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25181 Z= 0.274 Angle : 0.571 14.442 34374 Z= 0.298 Chirality : 0.041 0.171 3914 Planarity : 0.004 0.082 4013 Dihedral : 17.677 88.981 4071 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.11 % Allowed : 17.72 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.16), residues: 2721 helix: 1.39 (0.14), residues: 1540 sheet: 0.30 (0.31), residues: 247 loop : -0.36 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 154 HIS 0.010 0.001 HIS F 8 PHE 0.028 0.001 PHE C 395 TYR 0.020 0.001 TYR C 483 ARG 0.019 0.000 ARG D 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 231 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7320 (mp0) cc_final: 0.7005 (mp0) REVERT: A 678 ARG cc_start: 0.7638 (mtp180) cc_final: 0.7430 (ttp80) REVERT: B 377 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8168 (mppt) REVERT: C 80 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: C 147 MET cc_start: 0.8925 (mmp) cc_final: 0.8663 (mmp) REVERT: C 343 VAL cc_start: 0.8467 (m) cc_final: 0.8179 (p) REVERT: C 442 ARG cc_start: 0.7411 (ppt-90) cc_final: 0.6975 (ptt-90) REVERT: C 454 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.6840 (p-80) REVERT: C 550 LYS cc_start: 0.8606 (ptmm) cc_final: 0.8285 (tttt) REVERT: C 585 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6564 (tpt) REVERT: D 258 GLU cc_start: 0.8063 (mp0) cc_final: 0.7780 (mt-10) REVERT: D 261 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: D 295 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6837 (mpt180) REVERT: D 467 ASP cc_start: 0.7956 (t0) cc_final: 0.7716 (t0) REVERT: E 170 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7903 (mtt) REVERT: E 357 ILE cc_start: 0.7960 (mm) cc_final: 0.7592 (mm) REVERT: E 367 LYS cc_start: 0.8689 (pptt) cc_final: 0.8264 (tmmm) REVERT: E 462 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7261 (mp) REVERT: F 8 HIS cc_start: 0.8450 (t-170) cc_final: 0.7916 (t-170) REVERT: F 12 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8398 (mt-10) REVERT: F 71 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: F 80 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6220 (m-80) REVERT: F 279 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7676 (tppt) REVERT: F 280 MET cc_start: 0.6479 (mtt) cc_final: 0.5956 (mtp) REVERT: F 287 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8121 (mmp80) REVERT: F 321 CYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7304 (p) REVERT: F 410 ASN cc_start: 0.7298 (t0) cc_final: 0.7042 (p0) REVERT: I 57 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8070 (mtm180) REVERT: I 200 LYS cc_start: 0.8434 (ptpp) cc_final: 0.8079 (ptmt) REVERT: I 206 GLN cc_start: 0.8930 (tt0) cc_final: 0.8569 (pt0) outliers start: 54 outliers final: 37 residues processed: 271 average time/residue: 1.5507 time to fit residues: 484.9455 Evaluate side-chains 270 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 221 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 178 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN D 240 HIS I 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.108238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073694 restraints weight = 43908.805| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.21 r_work: 0.2851 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25181 Z= 0.301 Angle : 0.578 14.344 34374 Z= 0.302 Chirality : 0.042 0.207 3914 Planarity : 0.004 0.082 4013 Dihedral : 17.725 88.907 4071 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.11 % Allowed : 17.68 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.16), residues: 2721 helix: 1.36 (0.14), residues: 1536 sheet: 0.28 (0.31), residues: 247 loop : -0.36 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 154 HIS 0.010 0.001 HIS F 8 PHE 0.026 0.001 PHE C 391 TYR 0.021 0.001 TYR C 483 ARG 0.019 0.000 ARG D 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8931.16 seconds wall clock time: 159 minutes 59.47 seconds (9599.47 seconds total)