Starting phenix.real_space_refine on Mon Feb 19 06:30:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjh_25925/02_2024/7tjh_25925_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjh_25925/02_2024/7tjh_25925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjh_25925/02_2024/7tjh_25925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjh_25925/02_2024/7tjh_25925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjh_25925/02_2024/7tjh_25925_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjh_25925/02_2024/7tjh_25925_updated.pdb" } resolution = 2.5 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 97 5.16 5 C 14998 2.51 5 N 3971 2.21 5 O 4736 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 "C GLU 592": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23899 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3871 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 473} Chain breaks: 4 Chain: "B" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2080 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 1 Chain: "C" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4517 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 530} Chain breaks: 5 Chain: "D" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3544 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 421} Chain breaks: 3 Chain: "E" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3604 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 21, 'TRANS': 417} Chain breaks: 3 Chain: "F" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1314 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} 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: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3015 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 14, 'TRANS': 364} Chain breaks: 5 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} 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: 12.19, per 1000 atoms: 0.51 Number of scatterers: 23899 At special positions: 0 Unit cell: (116.1, 142.76, 178.88, 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 97 16.00 P 93 15.00 Mg 4 11.99 O 4736 8.00 N 3971 7.00 C 14998 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: 9.38 Conformation dependent library (CDL) restraints added in 3.6 seconds 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 12 sheets defined 52.7% alpha, 7.9% beta 41 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 10.79 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 407 through 410 removed outlier: 3.772A pdb=" N LEU A 410 " --> pdb=" O GLU A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'A' and resid 424 through 429 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: 3.627A pdb=" N CYS A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 528 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP A 529 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER A 533 " --> pdb=" O ASN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 552 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: 4.040A pdb=" N THR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 No H-bonds generated for 'chain 'A' and resid 604 through 607' 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 790 through 796 removed outlier: 3.576A pdb=" N ARG A 796 " --> pdb=" O THR A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 815 Processing helix chain 'A' and resid 822 through 835 Processing helix chain 'A' and resid 840 through 851 removed outlier: 5.269A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 4.652A 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: 3.755A 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 271 through 284 Processing helix chain 'B' and resid 287 through 309 removed outlier: 4.098A pdb=" N LYS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 4.338A 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 399 through 411 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 487 through 492 removed outlier: 3.878A pdb=" N THR B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 492' 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: 4.043A 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: 3.957A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 253 through 261 removed outlier: 3.927A pdb=" N ARG C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.949A pdb=" N LYS C 275 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR C 276 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 277 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN C 278 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 281 " --> pdb=" O ASN C 278 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 287 " --> pdb=" O PHE C 284 " (cutoff:3.500A) 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: 4.047A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 345 Processing helix chain 'C' and resid 348 through 354 Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'C' and resid 386 through 396 removed outlier: 4.019A 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: 5.103A pdb=" N ARG C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 511 through 516 removed outlier: 3.647A pdb=" N LYS C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 529 Processing helix chain 'C' and resid 537 through 545 Processing helix chain 'C' and resid 550 through 557 Processing helix chain 'C' and resid 564 through 571 Processing helix chain 'C' and resid 575 through 594 Processing helix chain 'D' and resid 47 through 61 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 73 through 89 removed outlier: 5.128A pdb=" N ASP D 77 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS D 78 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN D 80 " --> pdb=" O ASP D 77 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE D 86 " --> 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 Processing helix chain 'D' and resid 177 through 188 Processing helix chain 'D' and resid 219 through 222 Processing helix chain 'D' and resid 229 through 239 Processing helix chain 'D' and resid 256 through 259 No H-bonds generated for 'chain 'D' and resid 256 through 259' 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: 3.549A 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 371 Processing helix chain 'D' and resid 376 through 382 removed outlier: 3.638A pdb=" N GLN D 381 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER D 382 " --> pdb=" O GLY D 378 " (cutoff:3.500A) 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: 3.620A pdb=" N LYS D 457 " --> pdb=" O LYS D 453 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 489 removed outlier: 3.527A 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 Processing helix chain 'D' and resid 524 through 526 No H-bonds generated for 'chain 'D' and resid 524 through 526' 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 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 70 through 88 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: 4.142A pdb=" N GLN E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 4.588A 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 150 removed outlier: 3.669A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 154 No H-bonds generated for 'chain 'E' and resid 152 through 154' Processing helix chain 'E' and resid 173 through 182 removed outlier: 4.181A pdb=" N TYR E 179 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THR E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N HIS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 210 removed outlier: 5.678A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 221 removed outlier: 3.880A pdb=" N ILE E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 251 removed outlier: 5.908A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.546A 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: 3.799A 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 350 removed outlier: 3.626A pdb=" N ASP E 346 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA E 347 " --> pdb=" O ARG E 344 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE E 350 " --> pdb=" O ALA E 347 " (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 Processing helix chain 'E' and resid 471 through 473 No H-bonds generated for 'chain 'E' and resid 471 through 473' Processing helix chain 'F' and resid 282 through 290 removed outlier: 3.910A pdb=" N ILE F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 308 Processing helix chain 'F' and resid 316 through 331 removed outlier: 3.644A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 removed outlier: 3.705A pdb=" N LYS F 338 " --> pdb=" O GLU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 353 Processing helix chain 'F' and resid 359 through 373 removed outlier: 4.002A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 3.993A 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 402 removed outlier: 5.066A 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 98 removed outlier: 4.543A pdb=" N SER I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 125 Processing helix chain 'I' and resid 178 through 187 removed outlier: 3.788A pdb=" N ILE I 181 " --> pdb=" O PRO I 178 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE I 182 " --> pdb=" O SER I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 208 Processing helix chain 'I' and resid 226 through 228 No H-bonds generated for 'chain 'I' and resid 226 through 228' Processing helix chain 'I' and resid 240 through 248 Processing helix chain 'I' and resid 293 through 306 removed outlier: 4.612A pdb=" N SER I 306 " --> pdb=" O GLN I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 325 Processing helix chain 'I' and resid 331 through 348 removed outlier: 3.568A pdb=" N GLU I 348 " --> pdb=" O ILE I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 396 removed outlier: 3.893A pdb=" N ALA I 391 " --> pdb=" O LEU I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 409 removed outlier: 3.510A pdb=" N LYS I 409 " --> pdb=" O THR I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 428 Processing helix chain 'I' and resid 433 through 445 Processing helix chain 'I' and resid 455 through 468 Processing helix chain 'I' and resid 495 through 503 Processing sheet with id= A, first strand: chain 'A' and resid 622 through 624 removed outlier: 6.552A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL A 598 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.546A 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 removed outlier: 3.697A pdb=" N SER A 646 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 819 through 821 Processing sheet with id= D, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.225A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 420 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL B 453 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL B 423 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 361 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N HIS B 425 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.258A 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: 6.609A pdb=" N THR C 104 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU C 266 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE C 106 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 199 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N SER C 235 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET C 201 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE C 237 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE C 203 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ASN C 239 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 7.554A 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: 7.989A pdb=" N ILE D 273 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.390A 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: 7.708A pdb=" N PHE D 248 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE D 214 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N CYS D 250 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 6.767A 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: 9.024A pdb=" N LEU E 33 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE E 166 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU E 35 " --> pdb=" O PHE E 166 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR E 168 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY E 37 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N MET E 170 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N THR E 169 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU E 132 " --> pdb=" O THR E 169 " (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: 6.105A pdb=" N PHE I 218 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE I 259 " --> pdb=" O PHE I 218 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL I 220 " --> pdb=" O ILE I 259 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N MET I 261 " --> pdb=" O VAL I 220 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU I 222 " --> pdb=" O MET I 261 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 471 through 477 915 hydrogen bonds defined for protein. 2577 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 9.08 Time building geometry restraints manager: 10.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3887 1.32 - 1.45: 6741 1.45 - 1.58: 13410 1.58 - 1.70: 179 1.70 - 1.83: 160 Bond restraints: 24377 Sorted by residual: bond pdb=" C LYS I 509 " pdb=" N PRO I 510 " ideal model delta sigma weight residual 1.337 1.379 -0.042 9.80e-03 1.04e+04 1.88e+01 bond pdb=" CA SER F 352 " pdb=" CB SER F 352 " ideal model delta sigma weight residual 1.532 1.486 0.046 1.28e-02 6.10e+03 1.28e+01 bond pdb=" C LEU A 593 " pdb=" O LEU A 593 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.14e-02 7.69e+03 1.24e+01 bond pdb=" C LYS E 43 " pdb=" O LYS E 43 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" N MET I 225 " pdb=" CA MET I 225 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.30e-02 5.92e+03 9.62e+00 ... (remaining 24372 not shown) Histogram of bond angle deviations from ideal: 97.56 - 106.04: 885 106.04 - 114.52: 14374 114.52 - 123.01: 16276 123.01 - 131.49: 1683 131.49 - 139.97: 76 Bond angle restraints: 33294 Sorted by residual: angle pdb=" O GLU I 224 " pdb=" C GLU I 224 " pdb=" N MET I 225 " ideal model delta sigma weight residual 122.67 109.86 12.81 1.13e+00 7.83e-01 1.29e+02 angle pdb=" N ARG F 312 " pdb=" CA ARG F 312 " pdb=" C ARG F 312 " ideal model delta sigma weight residual 113.38 103.12 10.26 1.17e+00 7.31e-01 7.69e+01 angle pdb=" CA GLU I 224 " pdb=" C GLU I 224 " pdb=" N MET I 225 " ideal model delta sigma weight residual 115.83 125.76 -9.93 1.18e+00 7.18e-01 7.08e+01 angle pdb=" N LEU E 432 " pdb=" CA LEU E 432 " pdb=" C LEU E 432 " ideal model delta sigma weight residual 113.23 104.50 8.73 1.24e+00 6.50e-01 4.95e+01 angle pdb=" N GLN C 496 " pdb=" CA GLN C 496 " pdb=" C GLN C 496 " ideal model delta sigma weight residual 113.38 106.86 6.52 1.23e+00 6.61e-01 2.81e+01 ... (remaining 33289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.73: 12251 18.73 - 37.47: 1615 37.47 - 56.20: 659 56.20 - 74.93: 115 74.93 - 93.67: 37 Dihedral angle restraints: 14677 sinusoidal: 6699 harmonic: 7978 Sorted by residual: dihedral pdb=" CA MET I 502 " pdb=" C MET I 502 " pdb=" N THR I 503 " pdb=" CA THR I 503 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA LYS I 509 " pdb=" C LYS I 509 " pdb=" N PRO I 510 " pdb=" CA PRO I 510 " ideal model delta harmonic sigma weight residual -180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+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 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 14674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3046 0.062 - 0.124: 646 0.124 - 0.186: 87 0.186 - 0.248: 9 0.248 - 0.310: 6 Chirality restraints: 3794 Sorted by residual: chirality pdb=" CA ALA A 591 " pdb=" N ALA A 591 " pdb=" C ALA A 591 " pdb=" CB ALA A 591 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA ASP I 223 " pdb=" N ASP I 223 " pdb=" C ASP I 223 " pdb=" CB ASP I 223 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA ARG I 484 " pdb=" N ARG I 484 " pdb=" C ARG I 484 " pdb=" CB ARG I 484 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 3791 not shown) Planarity restraints: 3884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 224 " -0.028 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C GLU I 224 " 0.087 2.00e-02 2.50e+03 pdb=" O GLU I 224 " -0.030 2.00e-02 2.50e+03 pdb=" N MET I 225 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU I 251 " 0.076 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO I 252 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO I 252 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO I 252 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 157 " -0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO I 158 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO I 158 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO I 158 " -0.044 5.00e-02 4.00e+02 ... (remaining 3881 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 330 2.64 - 3.21: 20021 3.21 - 3.77: 40412 3.77 - 4.34: 55711 4.34 - 4.90: 85982 Nonbonded interactions: 202456 Sorted by model distance: nonbonded pdb="MG MG I1002 " pdb=" O HOH I1102 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR E 44 " pdb="MG MG E1002 " model vdw 2.094 2.170 nonbonded pdb=" OG1 THR I 115 " pdb="MG MG I1002 " model vdw 2.095 2.170 nonbonded pdb=" OG1 THR D 109 " pdb="MG MG D1002 " model vdw 2.100 2.170 nonbonded pdb="MG MG A1002 " pdb=" O HOH A1104 " model vdw 2.122 2.170 ... (remaining 202451 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.560 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 68.680 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.090 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:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 0.076 24377 Z= 0.317 Angle : 0.913 14.086 33294 Z= 0.516 Chirality : 0.053 0.310 3794 Planarity : 0.007 0.116 3884 Dihedral : 19.973 93.668 9465 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.06 % Allowed : 18.00 % Favored : 79.94 % 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: -1.38 (0.14), residues: 2633 helix: -0.94 (0.12), residues: 1460 sheet: 0.03 (0.30), residues: 270 loop : -0.85 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 456 HIS 0.010 0.001 HIS B 425 PHE 0.031 0.002 PHE I 186 TYR 0.026 0.002 TYR C 328 ARG 0.020 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 438 time to evaluate : 2.632 Fit side-chains revert: symmetry clash REVERT: A 879 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8893 (mp) REVERT: B 265 MET cc_start: 0.7696 (ptp) cc_final: 0.7381 (pmm) REVERT: B 287 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8463 (tppp) REVERT: C 344 ASP cc_start: 0.8401 (p0) cc_final: 0.8165 (p0) REVERT: C 412 PHE cc_start: 0.8992 (t80) cc_final: 0.8756 (t80) REVERT: C 555 ASN cc_start: 0.8768 (m-40) cc_final: 0.8428 (m-40) REVERT: F 287 ARG cc_start: 0.8428 (ttp-170) cc_final: 0.8151 (ttp80) REVERT: F 312 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.6872 (ptm160) REVERT: F 329 PHE cc_start: 0.8947 (m-80) cc_final: 0.8599 (m-80) REVERT: F 332 PHE cc_start: 0.8899 (m-10) cc_final: 0.8652 (m-80) REVERT: F 333 ASN cc_start: 0.8321 (p0) cc_final: 0.8056 (p0) REVERT: F 349 LYS cc_start: 0.7588 (ttmt) cc_final: 0.7137 (ttpp) REVERT: F 388 ASP cc_start: 0.7168 (t70) cc_final: 0.6896 (t0) REVERT: I 471 VAL cc_start: 0.8670 (t) cc_final: 0.8435 (t) REVERT: I 507 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.7141 (tp) outliers start: 51 outliers final: 18 residues processed: 476 average time/residue: 1.6731 time to fit residues: 890.6187 Evaluate side-chains 278 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 256 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 507 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 114 optimal weight: 0.0060 chunk 70 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 213 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 159 optimal weight: 0.1980 chunk 247 optimal weight: 0.7980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 856 ASN C 423 ASN C 454 HIS C 523 GLN D 79 GLN D 80 GLN D 120 GLN E 233 GLN I 150 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24377 Z= 0.169 Angle : 0.534 10.060 33294 Z= 0.286 Chirality : 0.039 0.152 3794 Planarity : 0.004 0.086 3884 Dihedral : 17.684 82.805 4005 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.40 % Allowed : 20.06 % Favored : 76.54 % 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: -0.12 (0.16), residues: 2633 helix: 0.30 (0.13), residues: 1474 sheet: 0.31 (0.31), residues: 267 loop : -0.64 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 58 HIS 0.006 0.001 HIS A 720 PHE 0.025 0.001 PHE C 462 TYR 0.019 0.001 TYR C 528 ARG 0.008 0.001 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 277 time to evaluate : 2.651 Fit side-chains REVERT: A 495 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: A 884 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7745 (tpt) REVERT: B 265 MET cc_start: 0.7782 (ptp) cc_final: 0.7473 (pmm) REVERT: B 287 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8388 (tppp) REVERT: C 56 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8816 (ptpp) REVERT: C 198 ASP cc_start: 0.7978 (m-30) cc_final: 0.7713 (m-30) REVERT: C 347 ASN cc_start: 0.7534 (t0) cc_final: 0.7222 (t0) REVERT: C 462 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7378 (p90) REVERT: C 555 ASN cc_start: 0.8784 (m-40) cc_final: 0.8491 (m-40) REVERT: D 239 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7625 (mm-30) REVERT: E 170 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.7995 (mmm) REVERT: E 210 MET cc_start: 0.8010 (ptp) cc_final: 0.7706 (ptp) REVERT: E 368 LYS cc_start: 0.8075 (mttt) cc_final: 0.7827 (mtpp) REVERT: E 439 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7780 (pttt) REVERT: E 469 ASN cc_start: 0.7719 (p0) cc_final: 0.7462 (p0) REVERT: F 284 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7591 (tm-30) REVERT: F 287 ARG cc_start: 0.8405 (ttp-170) cc_final: 0.8134 (ttp80) REVERT: F 296 ARG cc_start: 0.7694 (mmp-170) cc_final: 0.7450 (mmp-170) REVERT: F 329 PHE cc_start: 0.8788 (m-80) cc_final: 0.8519 (m-80) REVERT: F 332 PHE cc_start: 0.8819 (m-10) cc_final: 0.8538 (m-80) REVERT: F 333 ASN cc_start: 0.8391 (p0) cc_final: 0.8131 (p0) REVERT: F 358 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8319 (mmtt) REVERT: F 364 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7529 (pt0) REVERT: F 388 ASP cc_start: 0.7418 (t70) cc_final: 0.6993 (t0) REVERT: I 120 MET cc_start: 0.9083 (tpp) cc_final: 0.8707 (tpt) REVERT: I 460 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7415 (tt0) REVERT: I 484 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7011 (mtt-85) outliers start: 84 outliers final: 17 residues processed: 343 average time/residue: 1.5503 time to fit residues: 602.7063 Evaluate side-chains 262 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 237 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 484 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 221 optimal weight: 20.0000 chunk 246 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 199 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 634 ASN B 399 HIS ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 454 HIS C 523 GLN C 532 ASN D 158 HIS E 248 HIS E 377 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24377 Z= 0.394 Angle : 0.616 8.715 33294 Z= 0.328 Chirality : 0.045 0.156 3794 Planarity : 0.004 0.073 3884 Dihedral : 18.136 88.073 3980 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.92 % Allowed : 18.81 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2633 helix: 0.72 (0.13), residues: 1472 sheet: 0.40 (0.31), residues: 259 loop : -0.53 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 526 HIS 0.007 0.001 HIS C 69 PHE 0.024 0.002 PHE C 462 TYR 0.026 0.002 TYR C 483 ARG 0.007 0.001 ARG D 425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 252 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: A 884 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8052 (tpt) REVERT: B 265 MET cc_start: 0.7942 (ptp) cc_final: 0.7543 (pmm) REVERT: B 287 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8499 (tppp) REVERT: C 56 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8727 (ptpp) REVERT: C 121 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8069 (pt0) REVERT: C 198 ASP cc_start: 0.8026 (m-30) cc_final: 0.7786 (m-30) REVERT: C 347 ASN cc_start: 0.7776 (t0) cc_final: 0.7439 (t0) REVERT: C 361 MET cc_start: 0.6104 (mmm) cc_final: 0.5769 (mmm) REVERT: C 411 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8104 (ptp90) REVERT: C 555 ASN cc_start: 0.8807 (m-40) cc_final: 0.8507 (m-40) REVERT: E 276 GLU cc_start: 0.8180 (mp0) cc_final: 0.7920 (mp0) REVERT: E 469 ASN cc_start: 0.7980 (p0) cc_final: 0.7555 (p0) REVERT: F 287 ARG cc_start: 0.8386 (ttp-170) cc_final: 0.7964 (tmt-80) REVERT: F 329 PHE cc_start: 0.8836 (m-80) cc_final: 0.8468 (m-80) REVERT: F 333 ASN cc_start: 0.8430 (p0) cc_final: 0.8160 (p0) REVERT: F 358 LYS cc_start: 0.8472 (mmtt) cc_final: 0.7779 (mmmm) REVERT: F 376 GLU cc_start: 0.8205 (mp0) cc_final: 0.7957 (mp0) REVERT: F 377 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8087 (tppt) REVERT: F 388 ASP cc_start: 0.7585 (t70) cc_final: 0.7141 (t0) REVERT: I 57 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8728 (mtm180) REVERT: I 446 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7846 (pttt) REVERT: I 460 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7601 (tt0) REVERT: I 484 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7135 (mtt-85) REVERT: I 502 MET cc_start: 0.8031 (mmt) cc_final: 0.7778 (mmm) outliers start: 97 outliers final: 35 residues processed: 325 average time/residue: 1.5820 time to fit residues: 578.7494 Evaluate side-chains 279 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 446 LYS Chi-restraints excluded: chain I residue 447 THR Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 523 GLN C 593 ASN D 120 GLN E 377 GLN F 318 GLN F 407 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24377 Z= 0.177 Angle : 0.518 8.124 33294 Z= 0.278 Chirality : 0.040 0.137 3794 Planarity : 0.003 0.063 3884 Dihedral : 17.755 86.967 3980 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.87 % Allowed : 19.70 % Favored : 77.43 % 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: 0.75 (0.16), residues: 2633 helix: 1.11 (0.14), residues: 1473 sheet: 0.42 (0.31), residues: 259 loop : -0.38 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 58 HIS 0.005 0.001 HIS C 69 PHE 0.024 0.001 PHE C 408 TYR 0.022 0.001 TYR A 721 ARG 0.007 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 255 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: A 678 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7267 (ttp80) REVERT: A 681 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7700 (ttm170) REVERT: A 884 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.8012 (tpt) REVERT: B 265 MET cc_start: 0.7925 (ptp) cc_final: 0.7528 (pmm) REVERT: B 287 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8437 (tppp) REVERT: C 121 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: C 198 ASP cc_start: 0.8007 (m-30) cc_final: 0.7754 (m-30) REVERT: C 347 ASN cc_start: 0.7858 (t0) cc_final: 0.7530 (t0) REVERT: C 361 MET cc_start: 0.6076 (mmm) cc_final: 0.5765 (mmm) REVERT: C 555 ASN cc_start: 0.8751 (m-40) cc_final: 0.8474 (m-40) REVERT: D 239 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7490 (mm-30) REVERT: E 276 GLU cc_start: 0.8194 (mp0) cc_final: 0.7940 (pm20) REVERT: E 438 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7549 (m-40) REVERT: E 439 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7849 (pttt) REVERT: E 469 ASN cc_start: 0.7878 (p0) cc_final: 0.7423 (p0) REVERT: F 287 ARG cc_start: 0.8374 (ttp-170) cc_final: 0.8004 (tmt-80) REVERT: F 296 ARG cc_start: 0.7673 (mmp-170) cc_final: 0.7363 (mmp-170) REVERT: F 329 PHE cc_start: 0.8841 (m-80) cc_final: 0.8554 (m-80) REVERT: F 333 ASN cc_start: 0.8413 (p0) cc_final: 0.8200 (p0) REVERT: F 358 LYS cc_start: 0.8500 (mmtt) cc_final: 0.7864 (mmmm) REVERT: F 364 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7605 (pt0) REVERT: F 376 GLU cc_start: 0.8303 (mp0) cc_final: 0.7959 (mp0) REVERT: F 385 ARG cc_start: 0.8305 (ptm-80) cc_final: 0.8029 (ptm160) REVERT: F 388 ASP cc_start: 0.7459 (t70) cc_final: 0.7060 (t0) REVERT: I 120 MET cc_start: 0.8687 (tpt) cc_final: 0.8187 (tpt) REVERT: I 446 LYS cc_start: 0.8244 (tmmm) cc_final: 0.7930 (pttt) REVERT: I 460 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: I 488 LYS cc_start: 0.7969 (mtpm) cc_final: 0.7530 (mtmt) REVERT: I 504 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7819 (ptpp) outliers start: 71 outliers final: 30 residues processed: 306 average time/residue: 1.6412 time to fit residues: 570.0616 Evaluate side-chains 272 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 460 GLU Chi-restraints excluded: chain I residue 504 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 0.9990 chunk 149 optimal weight: 0.0670 chunk 3 optimal weight: 5.9990 chunk 196 optimal weight: 0.1980 chunk 108 optimal weight: 0.6980 chunk 225 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 454 HIS C 523 GLN C 563 ASN ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 377 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24377 Z= 0.142 Angle : 0.494 9.191 33294 Z= 0.265 Chirality : 0.038 0.160 3794 Planarity : 0.003 0.056 3884 Dihedral : 17.422 83.477 3979 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.51 % Allowed : 20.31 % Favored : 77.18 % 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: 1.03 (0.17), residues: 2633 helix: 1.37 (0.14), residues: 1471 sheet: 0.40 (0.31), residues: 259 loop : -0.26 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 58 HIS 0.005 0.000 HIS C 69 PHE 0.029 0.001 PHE C 408 TYR 0.022 0.001 TYR A 721 ARG 0.015 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 242 time to evaluate : 2.674 Fit side-chains revert: symmetry clash REVERT: A 391 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7959 (mp) REVERT: A 678 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7257 (ttp80) REVERT: B 265 MET cc_start: 0.7968 (ptp) cc_final: 0.7585 (OUTLIER) REVERT: B 287 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8431 (tppp) REVERT: C 121 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7670 (pt0) REVERT: C 198 ASP cc_start: 0.8019 (m-30) cc_final: 0.7774 (m-30) REVERT: C 347 ASN cc_start: 0.7905 (t0) cc_final: 0.7580 (t0) REVERT: C 361 MET cc_start: 0.6194 (mmm) cc_final: 0.5868 (mmm) REVERT: C 555 ASN cc_start: 0.8727 (m-40) cc_final: 0.8477 (m-40) REVERT: D 239 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7462 (mm-30) REVERT: E 276 GLU cc_start: 0.8192 (mp0) cc_final: 0.7984 (pm20) REVERT: E 368 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7807 (mtpp) REVERT: E 469 ASN cc_start: 0.7880 (p0) cc_final: 0.7460 (p0) REVERT: F 287 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.8020 (tmt-80) REVERT: F 296 ARG cc_start: 0.7688 (mmp-170) cc_final: 0.7343 (mmp-170) REVERT: F 329 PHE cc_start: 0.8819 (m-10) cc_final: 0.8487 (m-80) REVERT: F 333 ASN cc_start: 0.8460 (p0) cc_final: 0.8249 (p0) REVERT: F 358 LYS cc_start: 0.8522 (mmtt) cc_final: 0.7882 (mmmm) REVERT: F 364 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7600 (pt0) REVERT: F 376 GLU cc_start: 0.8336 (mp0) cc_final: 0.7906 (mp0) REVERT: F 388 ASP cc_start: 0.7398 (t70) cc_final: 0.7019 (t0) REVERT: I 57 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8721 (mtm110) REVERT: I 453 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7120 (pp) REVERT: I 460 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: I 488 LYS cc_start: 0.7942 (mtpm) cc_final: 0.7631 (mtmt) outliers start: 62 outliers final: 28 residues processed: 288 average time/residue: 1.6148 time to fit residues: 523.8275 Evaluate side-chains 260 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 227 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 460 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 219 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 87 optimal weight: 0.2980 chunk 138 optimal weight: 10.0000 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN D 240 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 377 GLN F 383 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24377 Z= 0.208 Angle : 0.522 10.394 33294 Z= 0.278 Chirality : 0.040 0.155 3794 Planarity : 0.004 0.061 3884 Dihedral : 17.488 84.650 3979 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.83 % Allowed : 19.82 % Favored : 77.35 % 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: 1.11 (0.17), residues: 2633 helix: 1.43 (0.14), residues: 1473 sheet: 0.44 (0.31), residues: 259 loop : -0.20 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 58 HIS 0.006 0.001 HIS C 69 PHE 0.034 0.001 PHE C 462 TYR 0.021 0.001 TYR A 721 ARG 0.014 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 236 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7957 (mp) REVERT: A 468 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: A 690 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8167 (tp30) REVERT: B 287 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8464 (tppp) REVERT: C 121 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7729 (pt0) REVERT: C 198 ASP cc_start: 0.8008 (m-30) cc_final: 0.7757 (m-30) REVERT: C 347 ASN cc_start: 0.7949 (t0) cc_final: 0.7654 (t0) REVERT: C 361 MET cc_start: 0.6350 (mmm) cc_final: 0.6069 (mmm) REVERT: C 412 PHE cc_start: 0.8945 (t80) cc_final: 0.8675 (t80) REVERT: C 555 ASN cc_start: 0.8727 (m-40) cc_final: 0.8486 (m-40) REVERT: D 239 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7480 (mm-30) REVERT: E 276 GLU cc_start: 0.8216 (mp0) cc_final: 0.8007 (pm20) REVERT: E 368 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7648 (mtpp) REVERT: E 469 ASN cc_start: 0.7922 (p0) cc_final: 0.7500 (p0) REVERT: F 287 ARG cc_start: 0.8406 (ttp-170) cc_final: 0.8006 (tmt-80) REVERT: F 293 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8450 (mp0) REVERT: F 296 ARG cc_start: 0.7681 (mmp-170) cc_final: 0.7158 (mmp-170) REVERT: F 329 PHE cc_start: 0.8814 (m-10) cc_final: 0.8542 (m-80) REVERT: F 333 ASN cc_start: 0.8485 (p0) cc_final: 0.8243 (p0) REVERT: F 358 LYS cc_start: 0.8461 (mmtt) cc_final: 0.7888 (mmmm) REVERT: F 364 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7587 (pt0) REVERT: F 376 GLU cc_start: 0.8349 (mp0) cc_final: 0.7842 (mp0) REVERT: F 377 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8064 (tppt) REVERT: F 385 ARG cc_start: 0.8322 (ptm-80) cc_final: 0.8057 (ptm160) REVERT: F 388 ASP cc_start: 0.7462 (t70) cc_final: 0.7057 (t0) REVERT: I 57 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8749 (mtm180) REVERT: I 318 LYS cc_start: 0.9212 (mttt) cc_final: 0.8937 (mtpp) REVERT: I 453 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7192 (pp) REVERT: I 460 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: I 488 LYS cc_start: 0.7924 (mtpm) cc_final: 0.7626 (mtmt) outliers start: 70 outliers final: 34 residues processed: 288 average time/residue: 1.5570 time to fit residues: 506.8475 Evaluate side-chains 263 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 220 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 460 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 263 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 377 GLN F 383 GLN F 407 GLN I 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24377 Z= 0.298 Angle : 0.564 9.283 33294 Z= 0.300 Chirality : 0.042 0.153 3794 Planarity : 0.004 0.063 3884 Dihedral : 17.766 87.016 3979 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.87 % Allowed : 20.23 % Favored : 76.90 % 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: 2633 helix: 1.35 (0.14), residues: 1477 sheet: 0.45 (0.31), residues: 253 loop : -0.22 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 539 HIS 0.006 0.001 HIS C 69 PHE 0.032 0.001 PHE C 408 TYR 0.022 0.002 TYR C 528 ARG 0.016 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 226 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7960 (mp) REVERT: A 417 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7713 (mm-40) REVERT: A 468 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: A 683 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7737 (ttm-80) REVERT: A 690 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8129 (tp30) REVERT: B 287 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8487 (tppp) REVERT: C 121 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7890 (pt0) REVERT: C 198 ASP cc_start: 0.8036 (m-30) cc_final: 0.7782 (m-30) REVERT: C 347 ASN cc_start: 0.7948 (t0) cc_final: 0.7652 (t0) REVERT: C 361 MET cc_start: 0.6467 (mmm) cc_final: 0.6251 (mmm) REVERT: C 555 ASN cc_start: 0.8740 (m-40) cc_final: 0.8506 (m-40) REVERT: C 598 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8660 (ptpp) REVERT: D 239 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7491 (mm-30) REVERT: E 368 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7897 (mtpp) REVERT: E 469 ASN cc_start: 0.7919 (p0) cc_final: 0.7514 (p0) REVERT: F 287 ARG cc_start: 0.8394 (ttp-170) cc_final: 0.7997 (tmt-80) REVERT: F 329 PHE cc_start: 0.8845 (m-10) cc_final: 0.8597 (m-80) REVERT: F 333 ASN cc_start: 0.8513 (p0) cc_final: 0.8288 (p0) REVERT: F 358 LYS cc_start: 0.8454 (mmtt) cc_final: 0.7852 (mmmm) REVERT: F 364 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7612 (pt0) REVERT: F 376 GLU cc_start: 0.8432 (mp0) cc_final: 0.7774 (mp0) REVERT: F 377 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8081 (tppt) REVERT: F 385 ARG cc_start: 0.8339 (ptm-80) cc_final: 0.8092 (ptm160) REVERT: F 388 ASP cc_start: 0.7553 (t70) cc_final: 0.7147 (t0) REVERT: I 57 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8756 (mtm180) REVERT: I 453 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7309 (pp) REVERT: I 460 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7622 (tt0) outliers start: 71 outliers final: 37 residues processed: 282 average time/residue: 1.6112 time to fit residues: 513.7976 Evaluate side-chains 267 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 219 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 447 THR Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 460 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 179 optimal weight: 0.0870 chunk 130 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 206 optimal weight: 7.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 523 GLN ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 377 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24377 Z= 0.146 Angle : 0.520 11.049 33294 Z= 0.274 Chirality : 0.039 0.188 3794 Planarity : 0.003 0.059 3884 Dihedral : 17.345 86.465 3979 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.90 % Allowed : 21.28 % Favored : 76.82 % 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: 1.25 (0.17), residues: 2633 helix: 1.53 (0.14), residues: 1469 sheet: 0.47 (0.31), residues: 253 loop : -0.11 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 539 HIS 0.005 0.000 HIS C 69 PHE 0.038 0.001 PHE C 408 TYR 0.020 0.001 TYR A 721 ARG 0.014 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 237 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: A 683 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7765 (ttm-80) REVERT: B 287 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8441 (tppp) REVERT: C 121 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7703 (pt0) REVERT: C 198 ASP cc_start: 0.8001 (m-30) cc_final: 0.7748 (m-30) REVERT: C 347 ASN cc_start: 0.7989 (t0) cc_final: 0.7672 (t0) REVERT: C 361 MET cc_start: 0.6590 (mmm) cc_final: 0.6348 (mmm) REVERT: C 555 ASN cc_start: 0.8695 (m-40) cc_final: 0.8454 (m-40) REVERT: D 239 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7445 (mm-30) REVERT: E 469 ASN cc_start: 0.7935 (p0) cc_final: 0.7515 (p0) REVERT: F 287 ARG cc_start: 0.8400 (ttp-170) cc_final: 0.7996 (tmt-80) REVERT: F 293 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8383 (mp0) REVERT: F 296 ARG cc_start: 0.7680 (mmp-170) cc_final: 0.7271 (mmp-170) REVERT: F 329 PHE cc_start: 0.8847 (m-10) cc_final: 0.8578 (m-80) REVERT: F 333 ASN cc_start: 0.8516 (p0) cc_final: 0.8251 (p0) REVERT: F 358 LYS cc_start: 0.8477 (mmtt) cc_final: 0.7900 (mmmm) REVERT: F 364 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7570 (pt0) REVERT: F 376 GLU cc_start: 0.8429 (mp0) cc_final: 0.7679 (mp0) REVERT: F 385 ARG cc_start: 0.8318 (ptm-80) cc_final: 0.8106 (ptm160) REVERT: F 388 ASP cc_start: 0.7431 (t70) cc_final: 0.6988 (t0) REVERT: I 57 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8735 (mtm110) REVERT: I 315 MET cc_start: 0.8103 (mpp) cc_final: 0.7616 (mpp) REVERT: I 453 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7161 (pp) REVERT: I 460 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7553 (tt0) outliers start: 47 outliers final: 26 residues processed: 273 average time/residue: 1.7100 time to fit residues: 524.5503 Evaluate side-chains 256 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 460 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 9.9990 chunk 252 optimal weight: 0.2980 chunk 229 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 312 HIS ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN D 240 HIS D 493 GLN E 2 ASN E 377 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 24377 Z= 0.465 Angle : 0.634 12.031 33294 Z= 0.334 Chirality : 0.046 0.194 3794 Planarity : 0.004 0.060 3884 Dihedral : 17.967 89.024 3979 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.06 % Allowed : 21.32 % Favored : 76.62 % 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: 0.93 (0.16), residues: 2633 helix: 1.26 (0.14), residues: 1468 sheet: 0.35 (0.31), residues: 254 loop : -0.24 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 317 HIS 0.007 0.001 HIS C 62 PHE 0.032 0.002 PHE C 462 TYR 0.026 0.002 TYR C 483 ARG 0.014 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 227 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: A 678 ARG cc_start: 0.8025 (mtp180) cc_final: 0.7453 (ttp80) REVERT: B 287 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8489 (tppp) REVERT: C 121 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: C 198 ASP cc_start: 0.8032 (m-30) cc_final: 0.7768 (m-30) REVERT: C 347 ASN cc_start: 0.7942 (t0) cc_final: 0.7649 (t0) REVERT: C 462 PHE cc_start: 0.7982 (p90) cc_final: 0.7255 (p90) REVERT: C 555 ASN cc_start: 0.8753 (m-40) cc_final: 0.8512 (m-40) REVERT: D 239 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7510 (mm-30) REVERT: E 368 LYS cc_start: 0.8247 (mtpp) cc_final: 0.7794 (mtpp) REVERT: E 469 ASN cc_start: 0.7851 (p0) cc_final: 0.7446 (p0) REVERT: F 287 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.8001 (tmt-80) REVERT: F 329 PHE cc_start: 0.8921 (m-10) cc_final: 0.8678 (m-80) REVERT: F 333 ASN cc_start: 0.8506 (p0) cc_final: 0.8259 (p0) REVERT: F 358 LYS cc_start: 0.8396 (mmtt) cc_final: 0.7772 (mmmm) REVERT: F 376 GLU cc_start: 0.8458 (mp0) cc_final: 0.7773 (mp0) REVERT: F 388 ASP cc_start: 0.7601 (t70) cc_final: 0.7173 (t0) REVERT: I 57 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8782 (mtm180) REVERT: I 315 MET cc_start: 0.8140 (mpp) cc_final: 0.7647 (mpp) REVERT: I 404 ARG cc_start: 0.8284 (mpp-170) cc_final: 0.7414 (mtp85) REVERT: I 453 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7390 (pp) REVERT: I 460 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7639 (tt0) outliers start: 51 outliers final: 29 residues processed: 271 average time/residue: 1.5771 time to fit residues: 483.4893 Evaluate side-chains 256 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 221 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 460 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 271 optimal weight: 0.6980 chunk 250 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 167 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN D 240 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 377 GLN F 407 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24377 Z= 0.183 Angle : 0.558 11.702 33294 Z= 0.294 Chirality : 0.040 0.170 3794 Planarity : 0.004 0.078 3884 Dihedral : 17.655 88.338 3979 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.58 % Allowed : 21.72 % Favored : 76.70 % 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: 1.16 (0.17), residues: 2633 helix: 1.43 (0.14), residues: 1474 sheet: 0.38 (0.31), residues: 255 loop : -0.10 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 539 HIS 0.006 0.001 HIS C 69 PHE 0.031 0.001 PHE C 462 TYR 0.021 0.001 TYR A 721 ARG 0.020 0.001 ARG A 607 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 226 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8991 (mmtp) cc_final: 0.8785 (mppt) REVERT: A 417 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7699 (mm-40) REVERT: A 468 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: A 641 LYS cc_start: 0.9026 (tppt) cc_final: 0.8787 (ttmp) REVERT: B 287 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8456 (tppp) REVERT: C 121 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7866 (pt0) REVERT: C 198 ASP cc_start: 0.8012 (m-30) cc_final: 0.7756 (m-30) REVERT: C 347 ASN cc_start: 0.7987 (t0) cc_final: 0.7683 (t0) REVERT: C 462 PHE cc_start: 0.7930 (p90) cc_final: 0.7417 (p90) REVERT: C 555 ASN cc_start: 0.8719 (m-40) cc_final: 0.8477 (m-40) REVERT: D 239 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7480 (mm-30) REVERT: E 123 GLN cc_start: 0.8423 (mp10) cc_final: 0.7954 (mm-40) REVERT: E 368 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7813 (mtpp) REVERT: E 437 MET cc_start: 0.7469 (tpp) cc_final: 0.7253 (ptm) REVERT: E 469 ASN cc_start: 0.7843 (p0) cc_final: 0.7424 (p0) REVERT: F 284 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7380 (tm-30) REVERT: F 287 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.8105 (ttp80) REVERT: F 329 PHE cc_start: 0.8872 (m-10) cc_final: 0.8622 (m-80) REVERT: F 333 ASN cc_start: 0.8504 (p0) cc_final: 0.8281 (p0) REVERT: F 358 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7820 (mmmm) REVERT: F 364 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7612 (pt0) REVERT: F 376 GLU cc_start: 0.8444 (mp0) cc_final: 0.7877 (mp0) REVERT: F 385 ARG cc_start: 0.8335 (ptm-80) cc_final: 0.7983 (ptm160) REVERT: F 388 ASP cc_start: 0.7457 (t70) cc_final: 0.7061 (t0) REVERT: I 57 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8776 (mtm110) REVERT: I 315 MET cc_start: 0.8124 (mpp) cc_final: 0.7638 (mpp) REVERT: I 453 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7326 (pp) REVERT: I 460 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7575 (tt0) outliers start: 39 outliers final: 26 residues processed: 256 average time/residue: 1.6004 time to fit residues: 462.5685 Evaluate side-chains 251 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 218 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 460 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 222 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN C 454 HIS C 523 GLN D 240 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 377 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.104232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.071298 restraints weight = 39616.501| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.14 r_work: 0.2779 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24377 Z= 0.177 Angle : 0.539 9.513 33294 Z= 0.287 Chirality : 0.039 0.158 3794 Planarity : 0.004 0.084 3884 Dihedral : 17.488 85.067 3979 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.66 % Allowed : 21.84 % Favored : 76.50 % 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: 1.26 (0.17), residues: 2633 helix: 1.51 (0.14), residues: 1471 sheet: 0.51 (0.31), residues: 253 loop : -0.07 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 58 HIS 0.006 0.001 HIS C 69 PHE 0.038 0.001 PHE C 412 TYR 0.020 0.001 TYR A 721 ARG 0.019 0.001 ARG A 607 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9552.31 seconds wall clock time: 171 minutes 12.48 seconds (10272.48 seconds total)