Starting phenix.real_space_refine on Fri Jun 20 14:01:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjh_25925/06_2025/7tjh_25925.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjh_25925/06_2025/7tjh_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/cci-nas-00/data/ceres_data/7tjh_25925/06_2025/7tjh_25925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjh_25925/06_2025/7tjh_25925.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjh_25925/06_2025/7tjh_25925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjh_25925/06_2025/7tjh_25925.cif" } 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. Time to flip 2 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.74, per 1000 atoms: 0.57 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.84 Conformation dependent library (CDL) restraints added in 2.7 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... Secondary structure from input PDB file: 150 helices and 14 sheets defined 61.9% alpha, 7.9% beta 41 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 8.36 Creating SS restraints... Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 406 through 409 removed outlier: 3.512A pdb=" N LYS A 409 " --> pdb=" O PHE A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 409' Processing helix chain 'A' and resid 423 through 430 Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 484 through 501 Processing helix chain 'A' and resid 522 through 534 removed outlier: 3.533A pdb=" N GLU A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 628 through 640 Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 702 through 726 Processing helix chain 'A' and resid 774 through 785 removed outlier: 4.038A pdb=" N THR A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 798 through 816 Processing helix chain 'A' and resid 822 through 836 Processing helix chain 'A' and resid 839 through 852 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 865 through 876 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.752A pdb=" N ASP A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 914 Processing helix chain 'B' and resid 241 through 250 removed outlier: 3.548A pdb=" N ARG B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 266 removed outlier: 3.903A pdb=" N MET B 265 " --> pdb=" O THR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.528A pdb=" N GLN B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 371 through 384 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 434 through 447 removed outlier: 4.066A pdb=" N ILE B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 486 through 491 removed outlier: 3.878A pdb=" N THR B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'C' and resid 50 through 93 removed outlier: 4.043A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 158 removed outlier: 3.813A pdb=" N GLU C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 196 Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 225 through 229 removed outlier: 4.064A pdb=" N LYS C 228 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 229' Processing helix chain 'C' and resid 243 through 250 removed outlier: 3.855A pdb=" N ILE C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C 250 " --> pdb=" O ASN C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.614A pdb=" N GLN C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 312 through 332 Processing helix chain 'C' and resid 333 through 339 removed outlier: 4.047A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 346 removed outlier: 4.472A pdb=" N ASP C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 346 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 355 Processing helix chain 'C' and resid 357 through 370 Processing helix chain 'C' and resid 386 through 395 Processing helix chain 'C' and resid 401 through 416 Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 435 through 441 Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.667A pdb=" N LYS C 450 " --> pdb=" O LYS C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 480 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 494 through 497 Processing helix chain 'C' and resid 511 through 517 removed outlier: 3.647A pdb=" N LYS C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 530 removed outlier: 3.652A pdb=" N GLU C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 546 Processing helix chain 'C' and resid 549 through 558 Processing helix chain 'C' and resid 563 through 572 removed outlier: 3.667A pdb=" N LEU C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C 572 " --> pdb=" O GLU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 594 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 90 Processing helix chain 'D' and resid 107 through 121 Processing helix chain 'D' and resid 140 through 158 removed outlier: 3.803A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 228 through 240 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.835A pdb=" N MET D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 Processing helix chain 'D' and resid 318 through 331 Processing helix chain 'D' and resid 333 through 347 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 350 through 361 Processing helix chain 'D' and resid 361 through 372 removed outlier: 3.572A pdb=" N ASP D 365 " --> pdb=" O CYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 381 removed outlier: 3.638A pdb=" N GLN D 381 " --> pdb=" O THR D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 401 Processing helix chain 'D' and resid 407 through 424 Processing helix chain 'D' and resid 452 through 466 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 480 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 492 through 496 removed outlier: 3.601A pdb=" N MET D 496 " --> pdb=" O GLN D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.622A pdb=" N ARG D 502 " --> pdb=" O PHE D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 523 through 528 removed outlier: 3.566A pdb=" N TRP D 526 " --> pdb=" O TYR D 523 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN D 528 " --> pdb=" O SER D 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 22 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.756A pdb=" N THR E 29 " --> pdb=" O PRO E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 54 Processing helix chain 'E' and resid 63 through 67 Processing helix chain 'E' and resid 69 through 89 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 134 through 138 Processing helix chain 'E' and resid 144 through 151 removed outlier: 3.970A pdb=" N LYS E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) 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 155 Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.527A pdb=" N LEU E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 193 through 211 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 212 through 222 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 252 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 254 through 271 Proline residue: E 267 - end of helix Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'E' and resid 289 through 293 removed outlier: 3.797A pdb=" N LEU E 293 " --> pdb=" O LYS E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 341 Processing helix chain 'E' and resid 342 through 345 Processing helix chain 'E' and resid 346 through 351 removed outlier: 3.660A pdb=" N SER E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 382 through 394 Processing helix chain 'E' and resid 417 through 430 Processing helix chain 'E' and resid 455 through 466 Processing helix chain 'E' and resid 470 through 474 Processing helix chain 'F' and resid 281 through 291 removed outlier: 4.232A pdb=" N ILE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 309 removed outlier: 3.631A pdb=" N ASN F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 332 removed outlier: 3.721A pdb=" N LEU F 319 " --> pdb=" O CYS F 315 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 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 354 removed outlier: 4.189A pdb=" N HIS F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 374 removed outlier: 4.221A pdb=" N VAL F 362 " --> pdb=" O LYS F 358 " (cutoff:3.500A) 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 376 through 387 Processing helix chain 'F' and resid 393 through 403 removed outlier: 5.066A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 427 Processing helix chain 'I' and resid 54 through 62 Processing helix chain 'I' and resid 81 through 99 removed outlier: 4.543A pdb=" N SER I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 126 removed outlier: 3.673A pdb=" N PHE I 126 " --> pdb=" O ILE I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 180 through 188 Processing helix chain 'I' and resid 201 through 209 removed outlier: 3.845A pdb=" N LEU I 205 " --> pdb=" O ASN I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 229 Processing helix chain 'I' and resid 239 through 249 removed outlier: 3.583A pdb=" N LEU I 243 " --> pdb=" O VAL I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 292 through 304 Processing helix chain 'I' and resid 305 through 307 No H-bonds generated for 'chain 'I' and resid 305 through 307' Processing helix chain 'I' and resid 313 through 326 removed outlier: 4.040A pdb=" N GLY I 326 " --> pdb=" O LYS I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 349 removed outlier: 3.704A pdb=" N LEU I 334 " --> pdb=" O ASP I 330 " (cutoff:3.500A) 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 397 removed outlier: 3.893A pdb=" N ALA I 391 " --> pdb=" O LEU I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 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 411 through 429 Processing helix chain 'I' and resid 432 through 446 Processing helix chain 'I' and resid 454 through 469 Processing helix chain 'I' and resid 494 through 504 Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 412 Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 514 removed outlier: 6.499A pdb=" N THR A 473 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA A 597 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 475 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA A 599 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 477 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N ILE A 622 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR A 476 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE A 624 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA A 478 " --> pdb=" O PHE A 624 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, first strand: chain 'A' and resid 819 through 821 Processing sheet with id=AA5, first strand: chain 'B' and resid 475 through 479 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=AA6, first strand: chain 'C' and resid 124 through 131 removed outlier: 6.273A pdb=" N TYR C 125 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL C 202 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 127 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASN C 204 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE C 129 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASN C 103 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE C 238 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 105 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 240 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU C 107 " --> pdb=" O ILE C 240 " (cutoff:3.500A) 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) Processing sheet with id=AA7, first strand: chain 'C' and resid 293 through 294 removed outlier: 6.956A pdb=" N ASN C 293 " --> pdb=" O LEU C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 534 through 536 Processing sheet with id=AA9, first strand: chain 'D' and resid 127 through 133 Processing sheet with id=AB1, first strand: chain 'D' and resid 469 through 471 Processing sheet with id=AB2, first strand: chain 'E' and resid 59 through 62 removed outlier: 6.486A pdb=" N VAL E 60 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 33 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N MET E 170 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU E 35 " --> pdb=" O MET E 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 433 through 435 Processing sheet with id=AB4, first strand: chain 'I' and resid 152 through 154 Processing sheet with id=AB5, first strand: chain 'I' and resid 471 through 477 1141 hydrogen bonds defined for protein. 3246 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: 9.91 Time building geometry restraints manager: 7.01 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: 0.00 - 2.82: 32682 2.82 - 5.63: 503 5.63 - 8.45: 88 8.45 - 11.27: 15 11.27 - 14.09: 6 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: 326 2.64 - 3.21: 19882 3.21 - 3.77: 40232 3.77 - 4.34: 55217 4.34 - 4.90: 85895 Nonbonded interactions: 201552 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 201547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.010 Normalize map: mean=0, sd=1: 2.220 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: 1.020 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 60.180 Find NCS groups from input model: 0.460 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:14.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.200 ------------------------------------------------------------------------------- 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= 0.257 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 Details of bonding type rmsd hydrogen bonds : bond 0.16210 ( 1233) hydrogen bonds : angle 6.27514 ( 3430) covalent geometry : bond 0.00504 (24377) covalent geometry : angle 0.91299 (33294) *********************** 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 to be fit. rotamer outliers: 51 poor density : 438 time to evaluate : 2.565 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: 1.7273 time to fit residues: 919.0824 Evaluate side-chains 278 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 2.532 ------------------------------------------------------------------------------- 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: 1.9990 chunk 114 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 213 optimal weight: 20.0000 chunk 82 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 576 GLN A 856 ASN C 423 ASN C 454 HIS C 532 ASN D 120 GLN D 323 HIS F 290 ASN I 150 GLN I 263 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.106815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.073223 restraints weight = 39241.296| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.16 r_work: 0.2811 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1941 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= 0.136 Angle : 0.571 10.361 33294 Z= 0.309 Chirality : 0.041 0.168 3794 Planarity : 0.005 0.085 3884 Dihedral : 17.805 88.107 4005 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.52 % Allowed : 19.90 % Favored : 76.58 % 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: 0.03 (0.16), residues: 2633 helix: 0.45 (0.13), residues: 1496 sheet: 0.24 (0.31), residues: 267 loop : -0.61 (0.20), residues: 870 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 0.020 0.001 TYR C 528 ARG 0.007 0.001 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 1233) hydrogen bonds : angle 4.33976 ( 3430) covalent geometry : bond 0.00300 (24377) covalent geometry : angle 0.57113 (33294) *********************** 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 to be fit. rotamer outliers: 87 poor density : 274 time to evaluate : 2.718 Fit side-chains REVERT: A 380 LYS cc_start: 0.8971 (mmtm) cc_final: 0.8728 (mppt) REVERT: A 415 LYS cc_start: 0.8640 (mmpt) cc_final: 0.8392 (mmpt) REVERT: A 884 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8514 (tpt) REVERT: B 265 MET cc_start: 0.7813 (ptp) cc_final: 0.7431 (pmm) REVERT: B 271 ARG cc_start: 0.7564 (mmm160) cc_final: 0.6969 (mmm160) REVERT: B 287 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8293 (tppp) REVERT: C 56 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8849 (ptpp) REVERT: C 198 ASP cc_start: 0.8744 (m-30) cc_final: 0.8500 (m-30) REVERT: C 291 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.9024 (mtmt) REVERT: C 347 ASN cc_start: 0.7471 (t0) cc_final: 0.7125 (t0) REVERT: C 356 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7061 (mpp80) REVERT: C 555 ASN cc_start: 0.8782 (m-40) cc_final: 0.8492 (m-40) REVERT: C 592 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8683 (tm-30) REVERT: D 140 GLN cc_start: 0.8958 (mp10) cc_final: 0.8754 (mp10) REVERT: E 170 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.8763 (mmm) REVERT: E 368 LYS cc_start: 0.7938 (mttt) cc_final: 0.7577 (mtpp) REVERT: E 439 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7817 (pttt) REVERT: E 469 ASN cc_start: 0.7856 (p0) cc_final: 0.7474 (p0) REVERT: F 284 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7415 (tm-30) REVERT: F 287 ARG cc_start: 0.8602 (ttp-170) cc_final: 0.8266 (ttp80) REVERT: F 329 PHE cc_start: 0.8701 (m-80) cc_final: 0.8389 (m-80) REVERT: F 332 PHE cc_start: 0.8617 (m-10) cc_final: 0.8404 (m-80) REVERT: F 333 ASN cc_start: 0.8237 (p0) cc_final: 0.7950 (p0) REVERT: F 364 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7510 (pt0) REVERT: F 376 GLU cc_start: 0.8303 (mp0) cc_final: 0.7600 (mp0) REVERT: F 388 ASP cc_start: 0.7783 (t70) cc_final: 0.7259 (t0) REVERT: I 120 MET cc_start: 0.9331 (tpp) cc_final: 0.9074 (tpt) REVERT: I 341 SER cc_start: 0.9264 (m) cc_final: 0.9058 (p) REVERT: I 446 LYS cc_start: 0.8076 (tmmm) cc_final: 0.7873 (tmmm) outliers start: 87 outliers final: 16 residues processed: 342 average time/residue: 1.5680 time to fit residues: 606.1305 Evaluate side-chains 264 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 592 GLU 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 E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 463 SER 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 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 457 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 199 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 253 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 267 optimal weight: 0.0570 overall best weight: 2.2104 ------------------------------------------------------------------------------- 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 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 454 HIS E 248 HIS E 377 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.104062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.070528 restraints weight = 39263.510| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.14 r_work: 0.2755 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24377 Z= 0.180 Angle : 0.573 8.481 33294 Z= 0.308 Chirality : 0.042 0.143 3794 Planarity : 0.004 0.072 3884 Dihedral : 17.850 86.691 3985 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.79 % Allowed : 19.54 % Favored : 77.67 % 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: 0.66 (0.16), residues: 2633 helix: 1.06 (0.14), residues: 1485 sheet: 0.32 (0.32), residues: 259 loop : -0.45 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 58 HIS 0.005 0.001 HIS I 439 PHE 0.026 0.001 PHE C 462 TYR 0.024 0.002 TYR A 721 ARG 0.008 0.001 ARG D 425 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 1233) hydrogen bonds : angle 4.12967 ( 3430) covalent geometry : bond 0.00420 (24377) covalent geometry : angle 0.57319 (33294) *********************** 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 324 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 255 time to evaluate : 2.684 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8961 (mmtm) cc_final: 0.8690 (mppt) REVERT: A 415 LYS cc_start: 0.8737 (mmpt) cc_final: 0.8496 (mmpt) REVERT: A 468 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8716 (tt0) REVERT: A 633 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8447 (tmtm) REVERT: A 774 HIS cc_start: 0.7464 (t-90) cc_final: 0.7117 (t-90) REVERT: B 265 MET cc_start: 0.7887 (ptp) cc_final: 0.7454 (pmm) REVERT: B 287 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8326 (tppp) REVERT: C 56 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8818 (ptpp) REVERT: C 198 ASP cc_start: 0.8695 (m-30) cc_final: 0.8451 (m-30) REVERT: C 347 ASN cc_start: 0.7697 (t0) cc_final: 0.7342 (t0) REVERT: C 361 MET cc_start: 0.5781 (mmm) cc_final: 0.5251 (mmm) REVERT: C 411 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8067 (ptp90) REVERT: C 555 ASN cc_start: 0.8828 (m-40) cc_final: 0.8516 (m-40) REVERT: C 592 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8725 (tm-30) REVERT: D 353 SER cc_start: 0.9300 (OUTLIER) cc_final: 0.8910 (m) REVERT: E 211 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7871 (mm-30) REVERT: E 368 LYS cc_start: 0.8038 (mttt) cc_final: 0.7609 (mtpp) REVERT: E 469 ASN cc_start: 0.7994 (p0) cc_final: 0.7478 (p0) REVERT: F 284 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7333 (tm-30) REVERT: F 287 ARG cc_start: 0.8589 (ttp-170) cc_final: 0.8212 (ppp80) REVERT: F 296 ARG cc_start: 0.7751 (mmp-170) cc_final: 0.7328 (mmp-170) REVERT: F 329 PHE cc_start: 0.8695 (m-80) cc_final: 0.8307 (m-80) REVERT: F 333 ASN cc_start: 0.8290 (p0) cc_final: 0.7998 (p0) REVERT: F 364 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7553 (pt0) REVERT: F 376 GLU cc_start: 0.8383 (mp0) cc_final: 0.8044 (mp0) REVERT: F 388 ASP cc_start: 0.7774 (t70) cc_final: 0.7242 (t0) REVERT: I 120 MET cc_start: 0.9329 (tpp) cc_final: 0.9029 (tpt) REVERT: I 163 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6545 (mp0) REVERT: I 341 SER cc_start: 0.9274 (m) cc_final: 0.9055 (p) REVERT: I 460 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8031 (tt0) REVERT: I 488 LYS cc_start: 0.7824 (mtpm) cc_final: 0.7469 (mtmt) outliers start: 69 outliers final: 26 residues processed: 305 average time/residue: 1.6344 time to fit residues: 561.9375 Evaluate side-chains 270 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 2.865 ------------------------------------------------------------------------------- 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 633 LYS 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 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 C residue 56 LYS Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 457 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 176 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 260 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 312 HIS ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN D 79 GLN D 80 GLN D 120 GLN D 493 GLN F 290 ASN F 318 GLN F 383 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.102054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.068522 restraints weight = 39670.402| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.11 r_work: 0.2721 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 24377 Z= 0.234 Angle : 0.595 7.839 33294 Z= 0.320 Chirality : 0.044 0.140 3794 Planarity : 0.004 0.061 3884 Dihedral : 17.983 88.508 3983 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.79 % Allowed : 19.30 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 2633 helix: 1.21 (0.14), residues: 1485 sheet: 0.25 (0.32), residues: 259 loop : -0.41 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 539 HIS 0.006 0.001 HIS C 69 PHE 0.028 0.002 PHE C 462 TYR 0.024 0.002 TYR C 483 ARG 0.010 0.001 ARG B 271 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 1233) hydrogen bonds : angle 4.12107 ( 3430) covalent geometry : bond 0.00552 (24377) covalent geometry : angle 0.59527 (33294) *********************** 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 318 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 249 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8985 (mmtm) cc_final: 0.8677 (mppt) REVERT: A 415 LYS cc_start: 0.8782 (mmpt) cc_final: 0.8509 (mmpt) REVERT: A 468 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8695 (tt0) REVERT: A 633 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8514 (tmtm) REVERT: A 641 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8969 (ttmp) REVERT: A 774 HIS cc_start: 0.7539 (t-90) cc_final: 0.7255 (t-90) REVERT: B 265 MET cc_start: 0.7918 (ptp) cc_final: 0.7450 (pmm) REVERT: B 287 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8346 (tppp) REVERT: C 198 ASP cc_start: 0.8665 (m-30) cc_final: 0.8417 (m-30) REVERT: C 347 ASN cc_start: 0.7864 (t0) cc_final: 0.7539 (t0) REVERT: C 361 MET cc_start: 0.5972 (mmm) cc_final: 0.5707 (mmm) REVERT: C 411 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8238 (ptp90) REVERT: C 555 ASN cc_start: 0.8834 (m-40) cc_final: 0.8514 (m-40) REVERT: C 592 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8698 (tm-30) REVERT: D 118 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9096 (mp) REVERT: D 353 SER cc_start: 0.9322 (OUTLIER) cc_final: 0.8927 (m) REVERT: E 7 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: E 211 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7948 (mm-30) REVERT: E 276 GLU cc_start: 0.8455 (mp0) cc_final: 0.8129 (pm20) REVERT: E 437 MET cc_start: 0.8030 (tpp) cc_final: 0.7810 (tpp) REVERT: E 439 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7906 (pttt) REVERT: E 469 ASN cc_start: 0.7935 (p0) cc_final: 0.7446 (p0) REVERT: F 287 ARG cc_start: 0.8539 (ttp-170) cc_final: 0.8090 (ttp80) REVERT: F 329 PHE cc_start: 0.8746 (m-80) cc_final: 0.8396 (m-80) REVERT: F 333 ASN cc_start: 0.8297 (p0) cc_final: 0.8064 (p0) REVERT: F 364 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7555 (pt0) REVERT: F 376 GLU cc_start: 0.8412 (mp0) cc_final: 0.7972 (mp0) REVERT: F 385 ARG cc_start: 0.8472 (ptm-80) cc_final: 0.8230 (ptm160) REVERT: F 388 ASP cc_start: 0.7877 (t70) cc_final: 0.7391 (t0) REVERT: I 163 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: I 315 MET cc_start: 0.8807 (mpp) cc_final: 0.8505 (mpp) REVERT: I 341 SER cc_start: 0.9292 (m) cc_final: 0.9072 (p) REVERT: I 446 LYS cc_start: 0.8181 (tmmm) cc_final: 0.7940 (tmmm) REVERT: I 460 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8112 (tt0) REVERT: I 488 LYS cc_start: 0.7837 (mtpm) cc_final: 0.7510 (mtmt) outliers start: 69 outliers final: 28 residues processed: 304 average time/residue: 1.6367 time to fit residues: 560.6921 Evaluate side-chains 272 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 2.569 ------------------------------------------------------------------------------- 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 633 LYS 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 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 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 516 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 353 SER 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 7 GLU Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 163 GLU 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 457 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 255 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 262 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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** E 377 GLN F 383 GLN F 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.103584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.070359 restraints weight = 39599.185| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.14 r_work: 0.2755 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24377 Z= 0.140 Angle : 0.541 8.107 33294 Z= 0.292 Chirality : 0.041 0.135 3794 Planarity : 0.004 0.055 3884 Dihedral : 17.763 82.258 3982 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.71 % Allowed : 19.74 % Favored : 77.55 % 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: 1.07 (0.16), residues: 2633 helix: 1.47 (0.14), residues: 1483 sheet: 0.18 (0.31), residues: 263 loop : -0.34 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 539 HIS 0.006 0.001 HIS C 69 PHE 0.028 0.001 PHE C 462 TYR 0.023 0.001 TYR A 721 ARG 0.011 0.000 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 1233) hydrogen bonds : angle 3.95912 ( 3430) covalent geometry : bond 0.00321 (24377) covalent geometry : angle 0.54051 (33294) *********************** 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 320 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 253 time to evaluate : 2.716 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8637 (mppt) REVERT: A 391 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7773 (mp) REVERT: A 415 LYS cc_start: 0.8772 (mmpt) cc_final: 0.8498 (mmpt) REVERT: A 468 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8696 (tt0) REVERT: A 633 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8411 (tmtm) REVERT: A 641 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8918 (ttmp) REVERT: A 681 ARG cc_start: 0.7922 (ttp-110) cc_final: 0.7593 (ttm170) REVERT: A 683 ARG cc_start: 0.8194 (mtm110) cc_final: 0.7900 (ttm110) REVERT: A 774 HIS cc_start: 0.7502 (t-90) cc_final: 0.7192 (t-90) REVERT: B 265 MET cc_start: 0.8006 (ptp) cc_final: 0.7591 (pmm) REVERT: B 287 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8369 (tppp) REVERT: C 56 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8923 (mptp) REVERT: C 198 ASP cc_start: 0.8663 (m-30) cc_final: 0.8408 (m-30) REVERT: C 347 ASN cc_start: 0.7875 (t0) cc_final: 0.7538 (t0) REVERT: C 411 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8280 (ptp90) REVERT: C 449 TYR cc_start: 0.8687 (m-80) cc_final: 0.8358 (m-80) REVERT: C 555 ASN cc_start: 0.8788 (m-40) cc_final: 0.8478 (m-40) REVERT: D 239 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8067 (mm-30) REVERT: D 353 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.8943 (m) REVERT: D 420 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8221 (mppt) REVERT: E 2 ASN cc_start: 0.8581 (t0) cc_final: 0.8163 (p0) REVERT: E 7 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: E 211 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7971 (mm-30) REVERT: E 276 GLU cc_start: 0.8445 (mp0) cc_final: 0.8160 (pm20) REVERT: E 437 MET cc_start: 0.7970 (tpp) cc_final: 0.7722 (tpp) REVERT: E 439 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7863 (pttt) REVERT: E 469 ASN cc_start: 0.7936 (p0) cc_final: 0.7428 (p0) REVERT: F 287 ARG cc_start: 0.8546 (ttp-170) cc_final: 0.8101 (ttp80) REVERT: F 329 PHE cc_start: 0.8742 (m-10) cc_final: 0.8404 (m-80) REVERT: F 333 ASN cc_start: 0.8375 (p0) cc_final: 0.8098 (p0) REVERT: F 364 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7543 (pt0) REVERT: F 376 GLU cc_start: 0.8411 (mp0) cc_final: 0.7900 (mp0) REVERT: F 388 ASP cc_start: 0.7801 (t70) cc_final: 0.7299 (t0) REVERT: I 120 MET cc_start: 0.8965 (tpt) cc_final: 0.8545 (tpt) REVERT: I 163 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: I 341 SER cc_start: 0.9327 (m) cc_final: 0.9114 (p) REVERT: I 460 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8060 (tt0) REVERT: I 488 LYS cc_start: 0.7797 (mtpm) cc_final: 0.7494 (mtmt) outliers start: 67 outliers final: 30 residues processed: 303 average time/residue: 1.5821 time to fit residues: 540.6064 Evaluate side-chains 268 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 2.864 ------------------------------------------------------------------------------- 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 633 LYS Chi-restraints excluded: chain A residue 641 LYS 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 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 291 LYS 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 155 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 163 GLU 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 315 MET Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 489 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 169 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 725 HIS ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 ASN D 493 GLN E 438 ASN F 344 HIS F 383 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.103942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.070767 restraints weight = 39105.741| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.12 r_work: 0.2766 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2846 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= 0.135 Angle : 0.534 8.903 33294 Z= 0.288 Chirality : 0.040 0.139 3794 Planarity : 0.004 0.051 3884 Dihedral : 17.632 76.175 3980 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.47 % Allowed : 20.11 % 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: 1.21 (0.17), residues: 2633 helix: 1.60 (0.14), residues: 1485 sheet: 0.19 (0.31), residues: 259 loop : -0.28 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 539 HIS 0.006 0.001 HIS C 69 PHE 0.032 0.001 PHE C 408 TYR 0.023 0.001 TYR A 721 ARG 0.011 0.000 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 1233) hydrogen bonds : angle 3.88722 ( 3430) covalent geometry : bond 0.00311 (24377) covalent geometry : angle 0.53391 (33294) *********************** 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 to be fit. rotamer outliers: 61 poor density : 245 time to evaluate : 2.682 Fit side-chains REVERT: A 380 LYS cc_start: 0.8960 (mmtm) cc_final: 0.8639 (mppt) REVERT: A 415 LYS cc_start: 0.8769 (mmpt) cc_final: 0.8478 (mmpt) REVERT: A 468 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8692 (tt0) REVERT: A 641 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8915 (ttmp) REVERT: A 678 ARG cc_start: 0.7979 (mtp180) cc_final: 0.7332 (ttp80) REVERT: A 681 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7560 (ttm170) REVERT: A 683 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7895 (ttm110) REVERT: A 774 HIS cc_start: 0.7497 (t-90) cc_final: 0.7204 (t-90) REVERT: B 265 MET cc_start: 0.8012 (ptp) cc_final: 0.7591 (pmm) REVERT: B 287 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8321 (tppp) REVERT: C 198 ASP cc_start: 0.8682 (m-30) cc_final: 0.8443 (m-30) REVERT: C 347 ASN cc_start: 0.7922 (t0) cc_final: 0.7621 (t0) REVERT: C 411 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8221 (ptp90) REVERT: C 449 TYR cc_start: 0.8667 (m-80) cc_final: 0.8357 (m-80) REVERT: C 555 ASN cc_start: 0.8775 (m-40) cc_final: 0.8495 (m-40) REVERT: D 216 PHE cc_start: 0.8849 (t80) cc_final: 0.8636 (t80) REVERT: D 239 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8040 (mm-30) REVERT: D 353 SER cc_start: 0.9322 (OUTLIER) cc_final: 0.8946 (m) REVERT: D 420 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8173 (mppt) REVERT: E 2 ASN cc_start: 0.8557 (t0) cc_final: 0.8143 (p0) REVERT: E 7 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: E 211 GLU cc_start: 0.8220 (mm-30) cc_final: 0.8004 (mm-30) REVERT: E 276 GLU cc_start: 0.8523 (mp0) cc_final: 0.8257 (pm20) REVERT: E 368 LYS cc_start: 0.7941 (mttt) cc_final: 0.7658 (mtpp) REVERT: E 439 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7858 (ptmt) REVERT: E 469 ASN cc_start: 0.7889 (p0) cc_final: 0.7391 (p0) REVERT: F 287 ARG cc_start: 0.8531 (ttp-170) cc_final: 0.8087 (ttp80) REVERT: F 329 PHE cc_start: 0.8714 (m-10) cc_final: 0.8390 (m-80) REVERT: F 333 ASN cc_start: 0.8418 (p0) cc_final: 0.8121 (p0) REVERT: F 364 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7549 (pt0) REVERT: F 376 GLU cc_start: 0.8433 (mp0) cc_final: 0.7874 (mp0) REVERT: F 388 ASP cc_start: 0.7847 (t70) cc_final: 0.7326 (t0) REVERT: I 163 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: I 315 MET cc_start: 0.8831 (mpp) cc_final: 0.8588 (mpp) REVERT: I 341 SER cc_start: 0.9325 (m) cc_final: 0.9108 (p) REVERT: I 446 LYS cc_start: 0.8193 (tmmm) cc_final: 0.7989 (tmmm) REVERT: I 460 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8078 (tt0) outliers start: 61 outliers final: 28 residues processed: 289 average time/residue: 1.6847 time to fit residues: 554.8701 Evaluate side-chains 280 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 243 time to evaluate : 2.719 ------------------------------------------------------------------------------- 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 641 LYS Chi-restraints excluded: chain A residue 683 ARG 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 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 89 ASP 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 342 ASN Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 425 LEU Chi-restraints excluded: chain I residue 447 THR Chi-restraints excluded: chain I residue 457 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 62 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 196 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 HIS E 438 ASN I 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.067642 restraints weight = 39511.402| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.10 r_work: 0.2706 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 24377 Z= 0.268 Angle : 0.621 9.213 33294 Z= 0.330 Chirality : 0.045 0.143 3794 Planarity : 0.004 0.052 3884 Dihedral : 18.019 85.031 3980 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.87 % Allowed : 19.90 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.16), residues: 2633 helix: 1.45 (0.14), residues: 1482 sheet: 0.13 (0.31), residues: 257 loop : -0.42 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 539 HIS 0.007 0.001 HIS C 69 PHE 0.032 0.002 PHE C 462 TYR 0.025 0.002 TYR C 483 ARG 0.013 0.001 ARG F 341 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 1233) hydrogen bonds : angle 4.09976 ( 3430) covalent geometry : bond 0.00635 (24377) covalent geometry : angle 0.62074 (33294) *********************** 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 315 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 244 time to evaluate : 2.714 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8657 (mppt) REVERT: A 415 LYS cc_start: 0.8777 (mmpt) cc_final: 0.8494 (mmpt) REVERT: A 468 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8646 (tt0) REVERT: A 630 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: A 641 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8922 (ttmp) REVERT: A 678 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7370 (ttp80) REVERT: A 774 HIS cc_start: 0.7567 (t-90) cc_final: 0.7300 (t-90) REVERT: B 287 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8369 (tppp) REVERT: C 198 ASP cc_start: 0.8686 (m-30) cc_final: 0.8438 (m-30) REVERT: C 347 ASN cc_start: 0.7958 (t0) cc_final: 0.7638 (t0) REVERT: C 449 TYR cc_start: 0.8631 (m-80) cc_final: 0.8367 (m-80) REVERT: C 462 PHE cc_start: 0.7707 (p90) cc_final: 0.6860 (p90) REVERT: C 555 ASN cc_start: 0.8795 (m-40) cc_final: 0.8505 (m-40) REVERT: C 592 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8745 (tm-30) REVERT: D 239 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8080 (mm-30) REVERT: D 420 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8448 (mppt) REVERT: D 519 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8769 (mmtm) REVERT: E 2 ASN cc_start: 0.8611 (t0) cc_final: 0.8202 (p0) REVERT: E 211 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7981 (mm-30) REVERT: E 276 GLU cc_start: 0.8546 (mp0) cc_final: 0.8250 (pm20) REVERT: E 368 LYS cc_start: 0.8200 (mttt) cc_final: 0.7619 (mtpp) REVERT: E 461 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: E 469 ASN cc_start: 0.7918 (p0) cc_final: 0.7398 (p0) REVERT: F 287 ARG cc_start: 0.8532 (ttp-170) cc_final: 0.8103 (ttp80) REVERT: F 304 ASP cc_start: 0.8452 (m-30) cc_final: 0.7994 (m-30) REVERT: F 329 PHE cc_start: 0.8758 (m-10) cc_final: 0.8475 (m-80) REVERT: F 333 ASN cc_start: 0.8367 (p0) cc_final: 0.8073 (p0) REVERT: F 376 GLU cc_start: 0.8481 (mp0) cc_final: 0.7972 (mp0) REVERT: F 388 ASP cc_start: 0.7935 (t70) cc_final: 0.7436 (t0) REVERT: I 163 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: I 341 SER cc_start: 0.9299 (m) cc_final: 0.9062 (p) REVERT: I 446 LYS cc_start: 0.8251 (tmmm) cc_final: 0.8010 (tmmm) REVERT: I 453 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7320 (pp) REVERT: I 460 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8174 (tt0) outliers start: 71 outliers final: 36 residues processed: 296 average time/residue: 1.5088 time to fit residues: 507.8869 Evaluate side-chains 275 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 229 time to evaluate : 2.558 ------------------------------------------------------------------------------- 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 630 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 892 VAL Chi-restraints excluded: chain B residue 240 LEU 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 B residue 422 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 519 LYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 461 GLU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 163 GLU 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 315 MET Chi-restraints excluded: chain I residue 447 THR Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 457 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 116 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 224 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** E 377 GLN E 438 ASN F 383 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.102977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.069751 restraints weight = 39317.507| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.13 r_work: 0.2753 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24377 Z= 0.152 Angle : 0.567 10.255 33294 Z= 0.301 Chirality : 0.041 0.155 3794 Planarity : 0.004 0.051 3884 Dihedral : 17.793 86.452 3980 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.02 % Allowed : 21.04 % Favored : 76.94 % 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: 1.18 (0.16), residues: 2633 helix: 1.60 (0.14), residues: 1488 sheet: 0.13 (0.31), residues: 259 loop : -0.33 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 539 HIS 0.006 0.001 HIS C 69 PHE 0.029 0.001 PHE C 412 TYR 0.023 0.001 TYR A 721 ARG 0.013 0.000 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 1233) hydrogen bonds : angle 3.94233 ( 3430) covalent geometry : bond 0.00353 (24377) covalent geometry : angle 0.56666 (33294) *********************** 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 291 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 241 time to evaluate : 2.729 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8966 (mmtm) cc_final: 0.8642 (mppt) REVERT: A 415 LYS cc_start: 0.8762 (mmpt) cc_final: 0.8469 (mmpt) REVERT: A 468 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: A 641 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8903 (ttmp) REVERT: A 683 ARG cc_start: 0.8263 (mtm110) cc_final: 0.8006 (mtp85) REVERT: A 774 HIS cc_start: 0.7527 (t-90) cc_final: 0.7251 (t-90) REVERT: B 287 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8385 (tppp) REVERT: C 198 ASP cc_start: 0.8657 (m-30) cc_final: 0.8402 (m-30) REVERT: C 347 ASN cc_start: 0.8015 (t0) cc_final: 0.7750 (t0) REVERT: C 449 TYR cc_start: 0.8639 (m-80) cc_final: 0.8358 (m-80) REVERT: C 555 ASN cc_start: 0.8780 (m-40) cc_final: 0.8490 (m-40) REVERT: D 239 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7940 (mm-30) REVERT: D 420 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8326 (mppt) REVERT: E 2 ASN cc_start: 0.8550 (t0) cc_final: 0.8154 (p0) REVERT: E 123 GLN cc_start: 0.8895 (mp10) cc_final: 0.8478 (mm-40) REVERT: E 211 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8018 (mm-30) REVERT: E 276 GLU cc_start: 0.8550 (mp0) cc_final: 0.8276 (pm20) REVERT: E 368 LYS cc_start: 0.8046 (mttt) cc_final: 0.7694 (mtpp) REVERT: E 439 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7834 (ptmt) REVERT: E 469 ASN cc_start: 0.7925 (p0) cc_final: 0.7430 (p0) REVERT: F 284 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7280 (tm-30) REVERT: F 287 ARG cc_start: 0.8548 (ttp-170) cc_final: 0.8196 (ttp80) REVERT: F 300 TYR cc_start: 0.7394 (m-80) cc_final: 0.7188 (m-80) REVERT: F 329 PHE cc_start: 0.8773 (m-10) cc_final: 0.8490 (m-80) REVERT: F 333 ASN cc_start: 0.8402 (p0) cc_final: 0.8096 (p0) REVERT: F 341 ARG cc_start: 0.8441 (mmp-170) cc_final: 0.8222 (mmp80) REVERT: F 364 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7570 (pt0) REVERT: F 376 GLU cc_start: 0.8512 (mp0) cc_final: 0.7960 (mp0) REVERT: F 388 ASP cc_start: 0.7957 (t70) cc_final: 0.7437 (t0) REVERT: I 163 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: I 341 SER cc_start: 0.9334 (m) cc_final: 0.9121 (p) REVERT: I 446 LYS cc_start: 0.8290 (tmmm) cc_final: 0.8035 (tmmm) REVERT: I 460 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8142 (tt0) outliers start: 50 outliers final: 30 residues processed: 279 average time/residue: 1.5737 time to fit residues: 496.8877 Evaluate side-chains 266 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 2.825 ------------------------------------------------------------------------------- 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 641 LYS 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 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 342 ASN 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 155 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 457 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 108 optimal weight: 0.1980 chunk 270 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN B 425 HIS ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN E 377 GLN E 438 ASN F 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.103258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.070019 restraints weight = 39480.304| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.14 r_work: 0.2751 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24377 Z= 0.149 Angle : 0.566 11.455 33294 Z= 0.300 Chirality : 0.041 0.166 3794 Planarity : 0.004 0.069 3884 Dihedral : 17.700 78.918 3980 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.10 % Allowed : 21.24 % Favored : 76.66 % 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: 1.24 (0.17), residues: 2633 helix: 1.63 (0.14), residues: 1496 sheet: 0.16 (0.32), residues: 257 loop : -0.29 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 539 HIS 0.006 0.001 HIS C 69 PHE 0.041 0.001 PHE C 408 TYR 0.022 0.001 TYR A 721 ARG 0.018 0.000 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 1233) hydrogen bonds : angle 3.90745 ( 3430) covalent geometry : bond 0.00347 (24377) covalent geometry : angle 0.56598 (33294) *********************** 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 295 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 2.889 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8969 (mmtm) cc_final: 0.8636 (mppt) REVERT: A 415 LYS cc_start: 0.8755 (mmpt) cc_final: 0.8466 (mmpt) REVERT: A 468 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: A 641 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8896 (ttmp) REVERT: A 678 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7811 (ttp-170) REVERT: A 683 ARG cc_start: 0.8263 (mtm110) cc_final: 0.8017 (mtp85) REVERT: A 774 HIS cc_start: 0.7504 (t-90) cc_final: 0.7221 (t-90) REVERT: B 260 ARG cc_start: 0.7687 (mmp80) cc_final: 0.7405 (mmp80) REVERT: B 287 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8357 (tppp) REVERT: C 130 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8691 (mt-10) REVERT: C 198 ASP cc_start: 0.8648 (m-30) cc_final: 0.8393 (m-30) REVERT: C 347 ASN cc_start: 0.8001 (t0) cc_final: 0.7740 (t0) REVERT: C 448 GLU cc_start: 0.8621 (mp0) cc_final: 0.8098 (mp0) REVERT: C 449 TYR cc_start: 0.8652 (m-80) cc_final: 0.8236 (m-80) REVERT: C 555 ASN cc_start: 0.8766 (m-40) cc_final: 0.8487 (m-40) REVERT: D 239 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7919 (mm-30) REVERT: D 420 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8234 (mppt) REVERT: E 2 ASN cc_start: 0.8559 (t0) cc_final: 0.8178 (p0) REVERT: E 211 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7998 (mm-30) REVERT: E 216 ARG cc_start: 0.8596 (mmt90) cc_final: 0.8395 (mmt90) REVERT: E 276 GLU cc_start: 0.8552 (mp0) cc_final: 0.8306 (pm20) REVERT: E 367 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8401 (ptmm) REVERT: E 368 LYS cc_start: 0.8163 (mttt) cc_final: 0.7451 (mtpp) REVERT: E 437 MET cc_start: 0.8006 (tpp) cc_final: 0.7311 (ptt) REVERT: E 438 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.7633 (m110) REVERT: E 439 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7923 (ptmt) REVERT: E 461 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7285 (tp30) REVERT: E 469 ASN cc_start: 0.7941 (p0) cc_final: 0.7442 (p0) REVERT: F 280 MET cc_start: 0.6769 (mmt) cc_final: 0.6186 (mmt) REVERT: F 284 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7324 (tm-30) REVERT: F 287 ARG cc_start: 0.8543 (ttp-170) cc_final: 0.8190 (ttp80) REVERT: F 329 PHE cc_start: 0.8759 (m-10) cc_final: 0.8460 (m-80) REVERT: F 333 ASN cc_start: 0.8323 (p0) cc_final: 0.8006 (p0) REVERT: F 364 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7568 (pt0) REVERT: F 376 GLU cc_start: 0.8518 (mp0) cc_final: 0.7914 (mp0) REVERT: F 388 ASP cc_start: 0.7997 (t70) cc_final: 0.7471 (t0) REVERT: I 315 MET cc_start: 0.8818 (mpp) cc_final: 0.8591 (mpp) REVERT: I 341 SER cc_start: 0.9331 (m) cc_final: 0.9110 (p) REVERT: I 404 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7823 (mtp85) REVERT: I 446 LYS cc_start: 0.8280 (tmmm) cc_final: 0.8026 (tmmm) REVERT: I 453 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7228 (pp) REVERT: I 460 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8128 (tt0) REVERT: I 504 LYS cc_start: 0.8416 (ptpp) cc_final: 0.8212 (ptpp) outliers start: 52 outliers final: 31 residues processed: 283 average time/residue: 1.7280 time to fit residues: 557.1550 Evaluate side-chains 276 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 2.602 ------------------------------------------------------------------------------- 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 641 LYS 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 240 LEU 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 B residue 422 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 461 GLU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 413 VAL 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 453 LEU Chi-restraints excluded: chain I residue 457 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 168 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 GLN E 438 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.068230 restraints weight = 39846.028| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.14 r_work: 0.2722 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 24377 Z= 0.241 Angle : 0.626 12.513 33294 Z= 0.332 Chirality : 0.044 0.167 3794 Planarity : 0.004 0.082 3884 Dihedral : 17.911 89.607 3980 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.90 % Allowed : 21.36 % Favored : 76.74 % 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 (0.16), residues: 2633 helix: 1.51 (0.14), residues: 1496 sheet: 0.15 (0.32), residues: 256 loop : -0.33 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 539 HIS 0.007 0.001 HIS C 69 PHE 0.038 0.002 PHE C 412 TYR 0.023 0.002 TYR C 483 ARG 0.019 0.001 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 1233) hydrogen bonds : angle 4.02920 ( 3430) covalent geometry : bond 0.00572 (24377) covalent geometry : angle 0.62619 (33294) ********************** 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 278 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 231 time to evaluate : 3.235 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8986 (mmtm) cc_final: 0.8666 (mppt) REVERT: A 415 LYS cc_start: 0.8763 (mmpt) cc_final: 0.8468 (mmpt) REVERT: A 468 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8661 (tt0) REVERT: A 495 GLU cc_start: 0.8883 (tp30) cc_final: 0.8532 (tm-30) REVERT: A 641 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8937 (ttmp) REVERT: A 681 ARG cc_start: 0.7984 (ttp-110) cc_final: 0.7735 (ttm170) REVERT: A 683 ARG cc_start: 0.8280 (mtm110) cc_final: 0.7904 (ttm-80) REVERT: A 774 HIS cc_start: 0.7548 (t-90) cc_final: 0.7281 (t-90) REVERT: B 287 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8439 (tppp) REVERT: C 198 ASP cc_start: 0.8667 (m-30) cc_final: 0.8429 (m-30) REVERT: C 347 ASN cc_start: 0.8020 (t0) cc_final: 0.7752 (t0) REVERT: C 448 GLU cc_start: 0.8635 (mp0) cc_final: 0.8131 (mp0) REVERT: C 449 TYR cc_start: 0.8617 (m-80) cc_final: 0.8208 (m-80) REVERT: C 555 ASN cc_start: 0.8805 (m-40) cc_final: 0.8513 (m-40) REVERT: D 239 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8023 (mm-30) REVERT: D 420 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8369 (mppt) REVERT: E 2 ASN cc_start: 0.8563 (t0) cc_final: 0.8185 (p0) REVERT: E 123 GLN cc_start: 0.8836 (mp10) cc_final: 0.8371 (mm-40) REVERT: E 211 GLU cc_start: 0.8225 (mm-30) cc_final: 0.8003 (mm-30) REVERT: E 276 GLU cc_start: 0.8518 (mp0) cc_final: 0.8261 (pm20) REVERT: E 368 LYS cc_start: 0.8220 (mttt) cc_final: 0.7752 (mtpp) REVERT: E 437 MET cc_start: 0.8078 (tpp) cc_final: 0.7298 (ptm) REVERT: E 439 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7916 (ptmt) REVERT: E 461 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7284 (tp30) REVERT: E 469 ASN cc_start: 0.7894 (p0) cc_final: 0.7391 (p0) REVERT: F 287 ARG cc_start: 0.8506 (ttp-170) cc_final: 0.8063 (ttp80) REVERT: F 329 PHE cc_start: 0.8787 (m-10) cc_final: 0.8513 (m-80) REVERT: F 333 ASN cc_start: 0.8392 (p0) cc_final: 0.8085 (p0) REVERT: F 376 GLU cc_start: 0.8587 (mp0) cc_final: 0.8051 (mp0) REVERT: F 388 ASP cc_start: 0.8019 (t70) cc_final: 0.7493 (t0) REVERT: I 341 SER cc_start: 0.9327 (m) cc_final: 0.9103 (p) REVERT: I 404 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7844 (mtp85) REVERT: I 453 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7346 (pp) REVERT: I 460 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8192 (tt0) outliers start: 47 outliers final: 32 residues processed: 267 average time/residue: 1.5841 time to fit residues: 478.6256 Evaluate side-chains 267 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 2.626 ------------------------------------------------------------------------------- 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 641 LYS 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 240 LEU 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 B residue 422 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 461 GLU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 413 VAL 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 315 MET Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 457 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 6.9990 chunk 265 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 153 optimal weight: 0.0980 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.101968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.068653 restraints weight = 39544.590| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.14 r_work: 0.2732 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24377 Z= 0.201 Angle : 0.604 12.608 33294 Z= 0.320 Chirality : 0.042 0.157 3794 Planarity : 0.004 0.078 3884 Dihedral : 17.890 89.625 3980 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.70 % Allowed : 21.56 % Favored : 76.74 % 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: 1.14 (0.16), residues: 2633 helix: 1.54 (0.14), residues: 1496 sheet: 0.11 (0.31), residues: 258 loop : -0.30 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 539 HIS 0.007 0.001 HIS C 69 PHE 0.032 0.001 PHE C 462 TYR 0.024 0.002 TYR F 300 ARG 0.019 0.001 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 1233) hydrogen bonds : angle 4.00054 ( 3430) covalent geometry : bond 0.00476 (24377) covalent geometry : angle 0.60423 (33294) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26926.54 seconds wall clock time: 465 minutes 42.29 seconds (27942.29 seconds total)