Starting phenix.real_space_refine on Thu Mar 5 16:30:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjh_25925/03_2026/7tjh_25925.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjh_25925/03_2026/7tjh_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tjh_25925/03_2026/7tjh_25925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjh_25925/03_2026/7tjh_25925.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tjh_25925/03_2026/7tjh_25925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjh_25925/03_2026/7tjh_25925.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.30, per 1000 atoms: 0.22 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 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: 3.07 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: 5.24 Time building geometry restraints manager: 2.45 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: 0.000 Normalize map: mean=0, sd=1: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.680 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.840 ------------------------------------------------------------------------------- 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 : 3.49 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.020 0.001 ARG A 683 TYR 0.026 0.002 TYR C 328 PHE 0.031 0.002 PHE I 186 TRP 0.035 0.003 TRP E 456 HIS 0.010 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00504 (24377) covalent geometry : angle 0.91299 (33294) hydrogen bonds : bond 0.16210 ( 1233) hydrogen bonds : angle 6.27514 ( 3430) *********************** 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 : 0.823 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: 0.8334 time to fit residues: 441.0113 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 : 1.028 ------------------------------------------------------------------------------- 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 197 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 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 A 576 GLN A 634 ASN A 856 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 423 ASN C 454 HIS C 532 ASN D 120 GLN D 323 HIS E 248 HIS I 263 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.103170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.069370 restraints weight = 39620.333| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.17 r_work: 0.2733 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 24377 Z= 0.240 Angle : 0.630 9.499 33294 Z= 0.339 Chirality : 0.044 0.143 3794 Planarity : 0.005 0.085 3884 Dihedral : 18.122 89.820 4005 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.37 % Allowed : 19.58 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2633 helix: 0.44 (0.13), residues: 1491 sheet: 0.23 (0.31), residues: 264 loop : -0.59 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 607 TYR 0.025 0.002 TYR C 483 PHE 0.025 0.002 PHE C 360 TRP 0.013 0.002 TRP C 58 HIS 0.006 0.001 HIS I 439 Details of bonding type rmsd covalent geometry : bond 0.00562 (24377) covalent geometry : angle 0.62982 (33294) hydrogen bonds : bond 0.04880 ( 1233) hydrogen bonds : angle 4.36942 ( 3430) *********************** 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 370 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 262 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8972 (mmtm) cc_final: 0.8733 (mppt) REVERT: A 415 LYS cc_start: 0.8677 (mmpt) cc_final: 0.8422 (mmpt) REVERT: A 495 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8375 (tm-30) REVERT: A 607 ARG cc_start: 0.8353 (mtm110) cc_final: 0.8091 (mtm110) REVERT: A 633 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8564 (tmtm) REVERT: A 683 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7777 (ttp80) REVERT: A 774 HIS cc_start: 0.7499 (t-90) cc_final: 0.7174 (t-90) REVERT: A 884 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8622 (tpt) REVERT: B 251 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8378 (mttm) REVERT: B 265 MET cc_start: 0.7803 (ptp) cc_final: 0.7366 (pmm) REVERT: B 287 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8398 (tppp) REVERT: C 56 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8882 (ptpp) REVERT: C 198 ASP cc_start: 0.8695 (m-30) cc_final: 0.8436 (m-30) REVERT: C 347 ASN cc_start: 0.7496 (t0) cc_final: 0.7121 (t0) REVERT: C 356 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7130 (mpp80) REVERT: C 555 ASN cc_start: 0.8765 (m-40) cc_final: 0.8410 (m-40) REVERT: C 592 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8711 (tm-30) REVERT: D 140 GLN cc_start: 0.8989 (mp10) cc_final: 0.8786 (mp10) REVERT: D 239 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8172 (mm-30) REVERT: E 469 ASN cc_start: 0.7911 (p0) cc_final: 0.7548 (p0) REVERT: F 284 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7409 (tm-30) REVERT: F 287 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.8232 (ttp80) REVERT: F 329 PHE cc_start: 0.8694 (m-80) cc_final: 0.8234 (m-80) REVERT: F 332 PHE cc_start: 0.8639 (m-10) cc_final: 0.8419 (m-80) REVERT: F 333 ASN cc_start: 0.8234 (p0) cc_final: 0.7925 (p0) REVERT: F 376 GLU cc_start: 0.8325 (mp0) cc_final: 0.8077 (mp0) REVERT: F 388 ASP cc_start: 0.7861 (t70) cc_final: 0.7316 (t0) REVERT: I 57 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8849 (mtm180) REVERT: I 315 MET cc_start: 0.8838 (mpp) cc_final: 0.8552 (mpp) REVERT: I 460 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8038 (tt0) REVERT: I 502 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7490 (mmt) outliers start: 108 outliers final: 29 residues processed: 348 average time/residue: 0.7702 time to fit residues: 301.1691 Evaluate side-chains 272 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 495 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 884 MET Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 251 LYS 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 89 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 516 ILE 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 226 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 278 ILE 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 57 ARG Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 223 ASP 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 Chi-restraints excluded: chain I residue 502 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 C 593 ASN D 79 GLN D 80 GLN E 377 GLN F 344 HIS F 383 GLN F 407 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.103941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.070575 restraints weight = 39520.099| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.14 r_work: 0.2766 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2442 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= 0.156 Angle : 0.558 8.874 33294 Z= 0.301 Chirality : 0.041 0.141 3794 Planarity : 0.004 0.072 3884 Dihedral : 17.869 83.930 3987 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.83 % Allowed : 19.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.16), residues: 2633 helix: 1.11 (0.14), residues: 1482 sheet: 0.26 (0.31), residues: 260 loop : -0.45 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 425 TYR 0.020 0.001 TYR C 528 PHE 0.026 0.001 PHE C 462 TRP 0.013 0.001 TRP A 539 HIS 0.007 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00360 (24377) covalent geometry : angle 0.55766 (33294) hydrogen bonds : bond 0.04078 ( 1233) hydrogen bonds : angle 4.08817 ( 3430) *********************** 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 328 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 258 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8947 (mmtm) cc_final: 0.8696 (mppt) REVERT: A 415 LYS cc_start: 0.8794 (mmpt) cc_final: 0.8519 (mmpt) REVERT: A 468 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8748 (tt0) REVERT: A 495 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8432 (tm-30) REVERT: A 607 ARG cc_start: 0.8364 (mtm110) cc_final: 0.7963 (mtm110) REVERT: A 774 HIS cc_start: 0.7488 (t-90) cc_final: 0.7183 (t-90) REVERT: B 265 MET cc_start: 0.7918 (ptp) cc_final: 0.7458 (pmm) REVERT: B 287 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8400 (tppp) REVERT: C 56 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8854 (ptpp) REVERT: C 198 ASP cc_start: 0.8680 (m-30) cc_final: 0.8434 (m-30) REVERT: C 347 ASN cc_start: 0.7743 (t0) cc_final: 0.7381 (t0) REVERT: C 361 MET cc_start: 0.5810 (mmm) cc_final: 0.5329 (mmm) REVERT: C 411 ARG cc_start: 0.8386 (ttp80) cc_final: 0.8080 (ptp90) REVERT: C 555 ASN cc_start: 0.8815 (m-40) cc_final: 0.8557 (m-40) REVERT: D 239 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7943 (mm-30) REVERT: D 353 SER cc_start: 0.9326 (OUTLIER) cc_final: 0.8951 (m) REVERT: E 211 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7906 (mm-30) REVERT: E 276 GLU cc_start: 0.8424 (mp0) cc_final: 0.8144 (pm20) REVERT: E 439 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7872 (pttt) REVERT: E 469 ASN cc_start: 0.7994 (p0) cc_final: 0.7492 (p0) REVERT: F 280 MET cc_start: 0.6490 (mtt) cc_final: 0.5998 (mmt) REVERT: F 284 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7317 (tm-30) REVERT: F 287 ARG cc_start: 0.8573 (ttp-170) cc_final: 0.8156 (ppp80) REVERT: F 329 PHE cc_start: 0.8713 (m-80) cc_final: 0.8357 (m-80) REVERT: F 332 PHE cc_start: 0.8648 (m-10) cc_final: 0.8433 (m-80) REVERT: F 333 ASN cc_start: 0.8303 (p0) cc_final: 0.8004 (p0) REVERT: F 364 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7553 (pt0) REVERT: F 376 GLU cc_start: 0.8389 (mp0) cc_final: 0.8039 (mp0) REVERT: F 388 ASP cc_start: 0.7756 (t70) cc_final: 0.7244 (t0) REVERT: I 163 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: I 460 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8077 (tt0) REVERT: I 488 LYS cc_start: 0.7851 (mtpm) cc_final: 0.7501 (mtmt) outliers start: 70 outliers final: 26 residues processed: 309 average time/residue: 0.8109 time to fit residues: 281.0027 Evaluate side-chains 274 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 247 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 226 VAL Chi-restraints excluded: chain D residue 326 MET 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 439 LYS 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 223 ASP Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 315 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS D 120 GLN D 493 GLN F 318 GLN F 383 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.102518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.069101 restraints weight = 39520.690| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.13 r_work: 0.2730 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24377 Z= 0.201 Angle : 0.574 8.146 33294 Z= 0.309 Chirality : 0.042 0.138 3794 Planarity : 0.004 0.061 3884 Dihedral : 17.918 86.770 3984 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.79 % Allowed : 19.34 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2633 helix: 1.28 (0.14), residues: 1486 sheet: 0.15 (0.31), residues: 264 loop : -0.38 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 271 TYR 0.022 0.002 TYR C 528 PHE 0.025 0.001 PHE C 408 TRP 0.012 0.001 TRP A 539 HIS 0.007 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00470 (24377) covalent geometry : angle 0.57413 (33294) hydrogen bonds : bond 0.04303 ( 1233) hydrogen bonds : angle 4.06035 ( 3430) *********************** 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 315 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 246 time to evaluate : 0.891 Fit side-chains REVERT: A 380 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8666 (mppt) REVERT: A 415 LYS cc_start: 0.8797 (mmpt) cc_final: 0.8503 (mmpt) REVERT: A 468 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8727 (tt0) REVERT: A 495 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8414 (tm-30) REVERT: A 607 ARG cc_start: 0.8348 (mtm110) cc_final: 0.8086 (mtm110) REVERT: A 633 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8513 (tmtm) REVERT: A 774 HIS cc_start: 0.7538 (t-90) cc_final: 0.7246 (t-90) REVERT: B 251 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8428 (mttm) REVERT: B 265 MET cc_start: 0.7940 (ptp) cc_final: 0.7508 (pmm) REVERT: B 287 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8365 (tppp) REVERT: C 198 ASP cc_start: 0.8673 (m-30) cc_final: 0.8425 (m-30) REVERT: C 347 ASN cc_start: 0.7848 (t0) cc_final: 0.7517 (t0) REVERT: C 361 MET cc_start: 0.5924 (mmm) cc_final: 0.5635 (mmm) REVERT: C 411 ARG cc_start: 0.8377 (ttp80) cc_final: 0.8168 (ptp90) REVERT: C 555 ASN cc_start: 0.8817 (m-40) cc_final: 0.8520 (m-40) REVERT: C 592 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8719 (tm-30) REVERT: D 239 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7961 (mm-30) REVERT: D 353 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.8932 (m) REVERT: E 7 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: E 211 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7940 (mm-30) REVERT: E 276 GLU cc_start: 0.8492 (mp0) cc_final: 0.8200 (pm20) REVERT: E 368 LYS cc_start: 0.8123 (mttt) cc_final: 0.7706 (mtpp) REVERT: E 437 MET cc_start: 0.8014 (tpp) cc_final: 0.7716 (tpp) REVERT: E 439 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7850 (pttt) REVERT: E 469 ASN cc_start: 0.7905 (p0) cc_final: 0.7408 (p0) REVERT: F 280 MET cc_start: 0.6607 (mtt) cc_final: 0.6155 (mmt) REVERT: F 284 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7535 (tm-30) REVERT: F 287 ARG cc_start: 0.8528 (ttp-170) cc_final: 0.8076 (ttp80) REVERT: F 304 ASP cc_start: 0.8461 (m-30) cc_final: 0.8032 (m-30) REVERT: F 329 PHE cc_start: 0.8718 (m-80) cc_final: 0.8377 (m-80) REVERT: F 333 ASN cc_start: 0.8288 (p0) cc_final: 0.8032 (p0) REVERT: F 364 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7536 (pt0) REVERT: F 376 GLU cc_start: 0.8431 (mp0) cc_final: 0.7976 (mp0) REVERT: F 388 ASP cc_start: 0.7845 (t70) cc_final: 0.7342 (t0) REVERT: F 396 GLU cc_start: 0.7709 (tp30) cc_final: 0.7446 (tp30) REVERT: I 163 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: I 311 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8875 (pp) REVERT: I 460 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8069 (tt0) outliers start: 69 outliers final: 32 residues processed: 300 average time/residue: 0.7481 time to fit residues: 253.1554 Evaluate side-chains 277 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 495 GLU Chi-restraints excluded: chain A residue 633 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 238 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 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 550 LYS 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 226 VAL Chi-restraints excluded: chain D residue 326 MET 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 362 VAL 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 223 ASP Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 311 ILE Chi-restraints excluded: chain I residue 315 MET 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 37 optimal weight: 3.9990 chunk 256 optimal weight: 0.9980 chunk 242 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 173 optimal weight: 0.5980 chunk 249 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 268 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 312 HIS C 454 HIS C 563 ASN D 493 GLN E 377 GLN E 438 ASN F 383 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.071691 restraints weight = 39180.639| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.13 r_work: 0.2785 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24377 Z= 0.115 Angle : 0.522 9.426 33294 Z= 0.282 Chirality : 0.039 0.129 3794 Planarity : 0.003 0.056 3884 Dihedral : 17.606 74.976 3984 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.47 % Allowed : 19.74 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.17), residues: 2633 helix: 1.55 (0.14), residues: 1484 sheet: 0.12 (0.31), residues: 264 loop : -0.28 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 271 TYR 0.017 0.001 TYR C 528 PHE 0.030 0.001 PHE C 462 TRP 0.011 0.001 TRP A 539 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00254 (24377) covalent geometry : angle 0.52247 (33294) hydrogen bonds : bond 0.03521 ( 1233) hydrogen bonds : angle 3.87251 ( 3430) *********************** 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 321 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 260 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8932 (mmtm) cc_final: 0.8623 (mppt) REVERT: A 391 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 415 LYS cc_start: 0.8778 (mmpt) cc_final: 0.8467 (mmpt) REVERT: A 468 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8746 (tt0) REVERT: A 607 ARG cc_start: 0.8375 (mtm110) cc_final: 0.8100 (mtm110) REVERT: A 681 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7579 (ttm170) REVERT: A 683 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7903 (ttm110) REVERT: A 774 HIS cc_start: 0.7507 (t-90) cc_final: 0.7213 (t-90) REVERT: B 251 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8404 (mttm) REVERT: B 265 MET cc_start: 0.8011 (ptp) cc_final: 0.7589 (pmm) REVERT: B 287 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8353 (tppp) REVERT: C 198 ASP cc_start: 0.8624 (m-30) cc_final: 0.8375 (m-30) REVERT: C 347 ASN cc_start: 0.7887 (t0) cc_final: 0.7576 (t0) REVERT: C 361 MET cc_start: 0.5983 (mmm) cc_final: 0.5757 (mmm) REVERT: C 555 ASN cc_start: 0.8792 (m-40) cc_final: 0.8518 (m-40) REVERT: D 239 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7877 (mm-30) REVERT: D 353 SER cc_start: 0.9311 (OUTLIER) cc_final: 0.8939 (m) REVERT: E 2 ASN cc_start: 0.8570 (t0) cc_final: 0.8158 (p0) REVERT: E 7 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8083 (tm-30) REVERT: E 211 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7947 (mm-30) REVERT: E 276 GLU cc_start: 0.8460 (mp0) cc_final: 0.8209 (pm20) REVERT: E 437 MET cc_start: 0.7956 (tpp) cc_final: 0.7727 (tpp) REVERT: E 439 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7876 (ptmt) REVERT: E 469 ASN cc_start: 0.7894 (p0) cc_final: 0.7386 (p0) REVERT: F 284 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7580 (tm-30) REVERT: F 287 ARG cc_start: 0.8554 (ttp-170) cc_final: 0.8095 (ttp80) REVERT: F 304 ASP cc_start: 0.8472 (m-30) cc_final: 0.8026 (m-30) REVERT: F 329 PHE cc_start: 0.8729 (m-10) cc_final: 0.8413 (m-80) REVERT: F 333 ASN cc_start: 0.8338 (p0) cc_final: 0.8068 (p0) REVERT: F 364 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7544 (pt0) REVERT: F 376 GLU cc_start: 0.8412 (mp0) cc_final: 0.7903 (mp0) REVERT: F 388 ASP cc_start: 0.7816 (t70) cc_final: 0.7300 (t0) REVERT: F 396 GLU cc_start: 0.7737 (tp30) cc_final: 0.7459 (tp30) REVERT: I 311 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8876 (pp) REVERT: I 460 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8047 (tt0) REVERT: I 488 LYS cc_start: 0.7830 (mtpm) cc_final: 0.7490 (mtmt) outliers start: 61 outliers final: 23 residues processed: 307 average time/residue: 0.7390 time to fit residues: 256.0103 Evaluate side-chains 264 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 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 238 SER Chi-restraints excluded: chain B residue 251 LYS 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 122 SER Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 405 SER 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 F residue 311 SER Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 311 ILE Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 447 THR Chi-restraints excluded: chain I residue 457 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 131 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 HIS E 438 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.100864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.067473 restraints weight = 39506.668| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.11 r_work: 0.2703 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 24377 Z= 0.292 Angle : 0.626 9.612 33294 Z= 0.335 Chirality : 0.046 0.147 3794 Planarity : 0.004 0.052 3884 Dihedral : 18.041 84.061 3981 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.91 % Allowed : 19.62 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.16), residues: 2633 helix: 1.39 (0.14), residues: 1482 sheet: -0.02 (0.31), residues: 264 loop : -0.39 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 341 TYR 0.025 0.002 TYR C 483 PHE 0.030 0.002 PHE C 408 TRP 0.010 0.002 TRP A 539 HIS 0.007 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00691 (24377) covalent geometry : angle 0.62585 (33294) hydrogen bonds : bond 0.04791 ( 1233) hydrogen bonds : angle 4.10905 ( 3430) *********************** 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 302 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 230 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8979 (mmtm) cc_final: 0.8662 (mppt) REVERT: A 415 LYS cc_start: 0.8798 (mmpt) cc_final: 0.8498 (mmtt) REVERT: A 453 GLU cc_start: 0.7953 (mp0) cc_final: 0.7698 (mp0) REVERT: A 468 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8708 (tt0) REVERT: A 607 ARG cc_start: 0.8331 (mtm110) cc_final: 0.8008 (mtm110) REVERT: A 630 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: A 774 HIS cc_start: 0.7569 (t-90) cc_final: 0.7314 (t-90) REVERT: B 268 ASP cc_start: 0.8345 (m-30) cc_final: 0.8055 (t70) REVERT: B 287 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8392 (tppp) REVERT: C 121 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8148 (pt0) REVERT: C 198 ASP cc_start: 0.8666 (m-30) cc_final: 0.8412 (m-30) REVERT: C 347 ASN cc_start: 0.7934 (t0) cc_final: 0.7621 (t0) REVERT: C 462 PHE cc_start: 0.7703 (p90) cc_final: 0.6682 (p90) REVERT: C 555 ASN cc_start: 0.8801 (m-40) cc_final: 0.8500 (m-40) REVERT: C 592 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8760 (tm-30) REVERT: D 140 GLN cc_start: 0.8982 (mp10) cc_final: 0.8758 (mp10) REVERT: D 239 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7986 (mm-30) REVERT: D 353 SER cc_start: 0.9327 (OUTLIER) cc_final: 0.8915 (m) REVERT: D 420 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8379 (mppt) REVERT: D 519 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8781 (mmtm) REVERT: E 7 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: E 211 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7963 (mm-30) REVERT: E 230 ASP cc_start: 0.8693 (m-30) cc_final: 0.8130 (OUTLIER) REVERT: E 276 GLU cc_start: 0.8562 (mp0) cc_final: 0.8284 (pm20) REVERT: E 368 LYS cc_start: 0.8085 (mttt) cc_final: 0.7588 (mtpp) REVERT: E 461 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: E 469 ASN cc_start: 0.7934 (p0) cc_final: 0.7411 (p0) REVERT: F 280 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.5952 (mmt) REVERT: F 284 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7430 (tm-30) REVERT: F 287 ARG cc_start: 0.8544 (ttp-170) cc_final: 0.8108 (ttp80) REVERT: F 329 PHE cc_start: 0.8796 (m-10) cc_final: 0.8519 (m-80) REVERT: F 333 ASN cc_start: 0.8360 (p0) cc_final: 0.8082 (p0) REVERT: F 376 GLU cc_start: 0.8488 (mp0) cc_final: 0.7913 (mp0) REVERT: F 388 ASP cc_start: 0.7929 (t70) cc_final: 0.7420 (t0) REVERT: F 396 GLU cc_start: 0.7921 (tp30) cc_final: 0.7701 (tp30) REVERT: F 415 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8434 (m-30) REVERT: I 311 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8902 (pp) REVERT: I 453 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7335 (pp) REVERT: I 460 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8173 (tt0) REVERT: I 488 LYS cc_start: 0.7846 (mtpm) cc_final: 0.7571 (mtmt) outliers start: 72 outliers final: 32 residues processed: 283 average time/residue: 0.7417 time to fit residues: 236.8627 Evaluate side-chains 267 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 867 ASP Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 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 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 D residue 519 LYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 461 GLU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 280 MET Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 415 ASP Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 82 THR 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 311 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 184 optimal weight: 0.8980 chunk 239 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 51 optimal weight: 0.0370 chunk 103 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 454 HIS E 377 GLN E 438 ASN F 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.104047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.070971 restraints weight = 39373.323| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.13 r_work: 0.2769 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24377 Z= 0.129 Angle : 0.544 10.359 33294 Z= 0.290 Chirality : 0.040 0.152 3794 Planarity : 0.004 0.051 3884 Dihedral : 17.626 80.169 3981 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.06 % Allowed : 20.11 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.17), residues: 2633 helix: 1.62 (0.14), residues: 1487 sheet: 0.04 (0.31), residues: 264 loop : -0.30 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 271 TYR 0.019 0.001 TYR C 528 PHE 0.032 0.001 PHE C 408 TRP 0.013 0.001 TRP A 539 HIS 0.007 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00292 (24377) covalent geometry : angle 0.54400 (33294) hydrogen bonds : bond 0.03571 ( 1233) hydrogen bonds : angle 3.87756 ( 3430) *********************** 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 307 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8947 (mmtm) cc_final: 0.8613 (mppt) REVERT: A 415 LYS cc_start: 0.8767 (mmpt) cc_final: 0.8451 (mmpt) REVERT: A 453 GLU cc_start: 0.7856 (mp0) cc_final: 0.7616 (mp0) REVERT: A 468 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8719 (tt0) REVERT: A 607 ARG cc_start: 0.8359 (mtm110) cc_final: 0.8061 (mtm110) REVERT: A 681 ARG cc_start: 0.7907 (ttp-110) cc_final: 0.7589 (ttm170) REVERT: A 683 ARG cc_start: 0.8243 (mtm110) cc_final: 0.7913 (ttm110) REVERT: A 774 HIS cc_start: 0.7473 (t-90) cc_final: 0.7186 (t-90) REVERT: B 260 ARG cc_start: 0.7652 (mmt90) cc_final: 0.7359 (mmp80) REVERT: B 268 ASP cc_start: 0.8370 (m-30) cc_final: 0.8071 (t70) REVERT: B 287 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8354 (tppp) REVERT: C 198 ASP cc_start: 0.8655 (m-30) cc_final: 0.8398 (m-30) REVERT: C 347 ASN cc_start: 0.7992 (t0) cc_final: 0.7720 (t0) REVERT: C 449 TYR cc_start: 0.8661 (m-80) cc_final: 0.8348 (m-80) REVERT: C 555 ASN cc_start: 0.8776 (m-40) cc_final: 0.8495 (m-40) REVERT: D 239 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7896 (mm-30) REVERT: D 353 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.8946 (m) REVERT: D 420 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8324 (mppt) REVERT: E 2 ASN cc_start: 0.8538 (t0) cc_final: 0.8144 (p0) REVERT: E 7 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8091 (tm-30) REVERT: E 211 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8021 (mm-30) REVERT: E 276 GLU cc_start: 0.8585 (mp0) cc_final: 0.8337 (pm20) REVERT: E 437 MET cc_start: 0.8019 (tpp) cc_final: 0.7145 (ptm) REVERT: E 438 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7622 (m110) REVERT: E 439 LYS cc_start: 0.8147 (pttm) cc_final: 0.7745 (ptmt) REVERT: E 469 ASN cc_start: 0.7907 (p0) cc_final: 0.7417 (p0) REVERT: F 284 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7538 (tm-30) REVERT: F 287 ARG cc_start: 0.8519 (ttp-170) cc_final: 0.8073 (ttp80) REVERT: F 300 TYR cc_start: 0.7371 (m-80) cc_final: 0.6875 (m-80) REVERT: F 304 ASP cc_start: 0.8448 (m-30) cc_final: 0.7995 (m-30) REVERT: F 329 PHE cc_start: 0.8741 (m-10) cc_final: 0.8467 (m-80) REVERT: F 333 ASN cc_start: 0.8370 (p0) cc_final: 0.8098 (p0) REVERT: F 364 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7570 (pt0) REVERT: F 376 GLU cc_start: 0.8480 (mp0) cc_final: 0.7865 (mp0) REVERT: F 388 ASP cc_start: 0.7891 (t70) cc_final: 0.7353 (t0) REVERT: F 396 GLU cc_start: 0.7840 (tp30) cc_final: 0.7589 (tp30) REVERT: I 311 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8922 (pp) REVERT: I 460 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8121 (tt0) REVERT: I 488 LYS cc_start: 0.7821 (mtpm) cc_final: 0.7533 (mtmt) outliers start: 51 outliers final: 31 residues processed: 293 average time/residue: 0.7367 time to fit residues: 243.5277 Evaluate side-chains 274 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 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 B residue 484 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 616 ILE 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 282 LEU Chi-restraints excluded: chain E residue 438 ASN 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 414 THR Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 311 ILE Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 447 THR 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 139 optimal weight: 0.0870 chunk 226 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 overall best weight: 2.7162 ------------------------------------------------------------------------------- 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 E 377 GLN E 438 ASN F 318 GLN F 383 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.102096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.068624 restraints weight = 39077.732| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.13 r_work: 0.2726 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24377 Z= 0.206 Angle : 0.586 10.212 33294 Z= 0.311 Chirality : 0.043 0.138 3794 Planarity : 0.004 0.055 3884 Dihedral : 17.810 84.983 3981 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.39 % Allowed : 20.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.16), residues: 2633 helix: 1.58 (0.14), residues: 1488 sheet: -0.01 (0.31), residues: 263 loop : -0.30 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 271 TYR 0.022 0.002 TYR C 528 PHE 0.036 0.001 PHE C 408 TRP 0.010 0.001 TRP A 539 HIS 0.007 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00486 (24377) covalent geometry : angle 0.58583 (33294) hydrogen bonds : bond 0.04150 ( 1233) hydrogen bonds : angle 3.96492 ( 3430) *********************** 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 303 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8967 (mmtm) cc_final: 0.8634 (mppt) REVERT: A 415 LYS cc_start: 0.8774 (mmpt) cc_final: 0.8488 (mmpt) REVERT: A 453 GLU cc_start: 0.7930 (mp0) cc_final: 0.7641 (mp0) REVERT: A 468 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: A 607 ARG cc_start: 0.8338 (mtm110) cc_final: 0.8005 (mtm110) REVERT: A 619 PHE cc_start: 0.8813 (t80) cc_final: 0.8605 (t80) REVERT: A 623 MET cc_start: 0.8952 (tpt) cc_final: 0.8720 (tpt) REVERT: A 678 ARG cc_start: 0.7859 (ttp-170) cc_final: 0.7592 (ttp80) REVERT: A 681 ARG cc_start: 0.7983 (ttp-110) cc_final: 0.7651 (ttm170) REVERT: A 683 ARG cc_start: 0.8278 (mtm110) cc_final: 0.7933 (ttm110) REVERT: A 774 HIS cc_start: 0.7533 (t-90) cc_final: 0.7257 (t-90) REVERT: B 268 ASP cc_start: 0.8374 (m-30) cc_final: 0.8092 (t70) REVERT: B 287 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8316 (tppp) REVERT: C 121 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: C 130 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8676 (mt-10) REVERT: C 198 ASP cc_start: 0.8663 (m-30) cc_final: 0.8407 (m-30) REVERT: C 347 ASN cc_start: 0.8001 (t0) cc_final: 0.7725 (t0) REVERT: C 449 TYR cc_start: 0.8676 (m-80) cc_final: 0.8425 (m-80) REVERT: C 462 PHE cc_start: 0.7703 (p90) cc_final: 0.6743 (p90) REVERT: C 555 ASN cc_start: 0.8778 (m-40) cc_final: 0.8513 (m-40) REVERT: C 592 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8706 (tm-30) REVERT: D 239 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7946 (mm-30) REVERT: D 353 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.8928 (m) REVERT: D 420 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8362 (mppt) REVERT: E 2 ASN cc_start: 0.8570 (t0) cc_final: 0.8198 (p0) REVERT: E 7 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8100 (tm-30) REVERT: E 123 GLN cc_start: 0.8868 (mp10) cc_final: 0.8402 (mm-40) REVERT: E 211 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8022 (mm-30) REVERT: E 276 GLU cc_start: 0.8568 (mp0) cc_final: 0.8308 (pm20) REVERT: E 439 LYS cc_start: 0.8113 (pttm) cc_final: 0.7647 (ptmt) REVERT: E 469 ASN cc_start: 0.7909 (p0) cc_final: 0.7392 (p0) REVERT: F 284 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7401 (tm-30) REVERT: F 287 ARG cc_start: 0.8532 (ttp-170) cc_final: 0.8100 (ttp80) REVERT: F 304 ASP cc_start: 0.8474 (m-30) cc_final: 0.8002 (m-30) REVERT: F 329 PHE cc_start: 0.8756 (m-10) cc_final: 0.8458 (m-80) REVERT: F 333 ASN cc_start: 0.8320 (p0) cc_final: 0.8025 (p0) REVERT: F 364 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7573 (pt0) REVERT: F 376 GLU cc_start: 0.8548 (mp0) cc_final: 0.7953 (mp0) REVERT: F 388 ASP cc_start: 0.7944 (t70) cc_final: 0.7416 (t0) REVERT: F 396 GLU cc_start: 0.7876 (tp30) cc_final: 0.7515 (tp30) REVERT: I 311 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8939 (pp) REVERT: I 453 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7232 (pp) REVERT: I 488 LYS cc_start: 0.7815 (mtpm) cc_final: 0.7504 (mtmt) outliers start: 59 outliers final: 34 residues processed: 286 average time/residue: 0.7322 time to fit residues: 236.7022 Evaluate side-chains 277 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 867 ASP Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 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 121 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 533 MET 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 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 282 LEU 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 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 309 THR Chi-restraints excluded: chain I residue 311 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 40 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 196 optimal weight: 0.5980 chunk 236 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 167 optimal weight: 0.4980 chunk 165 optimal weight: 0.4980 chunk 205 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN C 454 HIS E 233 GLN E 377 GLN E 438 ASN F 383 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.071340 restraints weight = 39527.837| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.13 r_work: 0.2777 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.3048 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= 0.120 Angle : 0.543 11.421 33294 Z= 0.288 Chirality : 0.040 0.155 3794 Planarity : 0.003 0.054 3884 Dihedral : 17.514 76.741 3981 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.82 % Allowed : 21.08 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.17), residues: 2633 helix: 1.73 (0.14), residues: 1481 sheet: 0.03 (0.31), residues: 264 loop : -0.19 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 271 TYR 0.018 0.001 TYR C 528 PHE 0.032 0.001 PHE C 462 TRP 0.012 0.001 TRP A 539 HIS 0.006 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00269 (24377) covalent geometry : angle 0.54288 (33294) hydrogen bonds : bond 0.03447 ( 1233) hydrogen bonds : angle 3.84452 ( 3430) *********************** 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 290 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8951 (mmtm) cc_final: 0.8613 (mppt) REVERT: A 415 LYS cc_start: 0.8754 (mmpt) cc_final: 0.8456 (mmtt) REVERT: A 453 GLU cc_start: 0.7866 (mp0) cc_final: 0.7561 (mp0) REVERT: A 468 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8722 (tt0) REVERT: A 607 ARG cc_start: 0.8386 (mtm110) cc_final: 0.8119 (mtm110) REVERT: A 681 ARG cc_start: 0.7907 (ttp-110) cc_final: 0.7650 (ttm170) REVERT: A 683 ARG cc_start: 0.8259 (mtm110) cc_final: 0.7892 (ttm-80) REVERT: A 774 HIS cc_start: 0.7458 (t-90) cc_final: 0.7181 (t-90) REVERT: B 260 ARG cc_start: 0.7665 (mmt90) cc_final: 0.7370 (mmp80) REVERT: B 268 ASP cc_start: 0.8305 (m-30) cc_final: 0.8004 (t70) REVERT: B 272 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7725 (mp0) REVERT: B 287 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8331 (tppp) REVERT: C 121 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8070 (pt0) REVERT: C 198 ASP cc_start: 0.8641 (m-30) cc_final: 0.8382 (m-30) REVERT: C 347 ASN cc_start: 0.8033 (t0) cc_final: 0.7767 (t0) REVERT: C 416 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8226 (mp0) REVERT: C 448 GLU cc_start: 0.8688 (mp0) cc_final: 0.8244 (mp0) REVERT: C 449 TYR cc_start: 0.8702 (m-80) cc_final: 0.8261 (m-80) REVERT: C 555 ASN cc_start: 0.8754 (m-40) cc_final: 0.8469 (m-40) REVERT: D 239 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7905 (mm-30) REVERT: D 353 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.8938 (m) REVERT: D 420 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8330 (mppt) REVERT: E 2 ASN cc_start: 0.8553 (t0) cc_final: 0.8180 (p0) REVERT: E 7 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8073 (tm-30) REVERT: E 211 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8005 (mm-30) REVERT: E 216 ARG cc_start: 0.8558 (mmt90) cc_final: 0.8354 (mmt90) REVERT: E 276 GLU cc_start: 0.8552 (mp0) cc_final: 0.8301 (pm20) REVERT: E 437 MET cc_start: 0.8024 (tpp) cc_final: 0.7265 (ptt) REVERT: E 438 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7638 (m110) REVERT: E 439 LYS cc_start: 0.8078 (pttm) cc_final: 0.7783 (ptmt) REVERT: E 469 ASN cc_start: 0.7921 (p0) cc_final: 0.7421 (p0) REVERT: F 284 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7569 (tm-30) REVERT: F 287 ARG cc_start: 0.8475 (ttp-170) cc_final: 0.8050 (ttp80) REVERT: F 329 PHE cc_start: 0.8754 (m-10) cc_final: 0.8440 (m-80) REVERT: F 333 ASN cc_start: 0.8311 (p0) cc_final: 0.8042 (p0) REVERT: F 376 GLU cc_start: 0.8519 (mp0) cc_final: 0.7857 (mp0) REVERT: F 388 ASP cc_start: 0.7898 (t70) cc_final: 0.7382 (t0) REVERT: F 396 GLU cc_start: 0.7857 (tp30) cc_final: 0.7595 (tp30) REVERT: I 311 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8920 (pp) REVERT: I 453 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7154 (pp) REVERT: I 488 LYS cc_start: 0.7808 (mtpm) cc_final: 0.7521 (mtmt) outliers start: 45 outliers final: 29 residues processed: 280 average time/residue: 0.7709 time to fit residues: 242.6207 Evaluate side-chains 277 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 867 ASP Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 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 282 LEU Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 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 311 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 66 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 F 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.102213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.068782 restraints weight = 39394.498| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.14 r_work: 0.2729 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24377 Z= 0.200 Angle : 0.597 10.778 33294 Z= 0.316 Chirality : 0.042 0.144 3794 Planarity : 0.004 0.061 3884 Dihedral : 17.741 83.216 3981 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.70 % Allowed : 21.24 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.16), residues: 2633 helix: 1.60 (0.14), residues: 1494 sheet: -0.03 (0.31), residues: 259 loop : -0.21 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 271 TYR 0.021 0.002 TYR C 528 PHE 0.039 0.001 PHE C 462 TRP 0.010 0.001 TRP A 539 HIS 0.007 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00473 (24377) covalent geometry : angle 0.59694 (33294) hydrogen bonds : bond 0.04072 ( 1233) hydrogen bonds : angle 3.93795 ( 3430) ********************** 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 283 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8979 (mmtm) cc_final: 0.8638 (mppt) REVERT: A 415 LYS cc_start: 0.8752 (mmpt) cc_final: 0.8461 (mmpt) REVERT: A 453 GLU cc_start: 0.7945 (mp0) cc_final: 0.7636 (mp0) REVERT: A 468 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8723 (tt0) REVERT: A 607 ARG cc_start: 0.8360 (mtm110) cc_final: 0.8036 (mtm110) REVERT: A 619 PHE cc_start: 0.8793 (t80) cc_final: 0.8539 (t80) REVERT: A 678 ARG cc_start: 0.7844 (ttp-170) cc_final: 0.7354 (ttp-170) REVERT: A 681 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7596 (ttm170) REVERT: A 683 ARG cc_start: 0.8258 (mtm110) cc_final: 0.7920 (ttm110) REVERT: A 690 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8755 (tm-30) REVERT: A 774 HIS cc_start: 0.7550 (t-90) cc_final: 0.7273 (t-90) REVERT: B 268 ASP cc_start: 0.8324 (m-30) cc_final: 0.8031 (t70) REVERT: B 287 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8304 (tppp) REVERT: C 121 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: C 198 ASP cc_start: 0.8663 (m-30) cc_final: 0.8405 (m-30) REVERT: C 347 ASN cc_start: 0.8024 (t0) cc_final: 0.7755 (t0) REVERT: C 416 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8267 (mp0) REVERT: C 449 TYR cc_start: 0.8676 (m-80) cc_final: 0.8382 (m-80) REVERT: C 555 ASN cc_start: 0.8768 (m-40) cc_final: 0.8497 (m-40) REVERT: D 239 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7940 (mm-30) REVERT: D 353 SER cc_start: 0.9317 (OUTLIER) cc_final: 0.8926 (m) REVERT: D 420 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8385 (mptt) REVERT: E 2 ASN cc_start: 0.8546 (t0) cc_final: 0.8183 (p0) REVERT: E 7 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8111 (tm-30) REVERT: E 123 GLN cc_start: 0.8847 (mp10) cc_final: 0.8363 (mm-40) REVERT: E 211 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7998 (mm-30) REVERT: E 276 GLU cc_start: 0.8604 (mp0) cc_final: 0.8343 (pm20) REVERT: E 437 MET cc_start: 0.8101 (tpp) cc_final: 0.7273 (ptm) REVERT: E 438 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7673 (m110) REVERT: E 439 LYS cc_start: 0.8168 (pttm) cc_final: 0.7797 (ptmt) REVERT: E 469 ASN cc_start: 0.7914 (p0) cc_final: 0.7405 (p0) REVERT: F 284 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7462 (tm-30) REVERT: F 287 ARG cc_start: 0.8516 (ttp-170) cc_final: 0.8089 (ttp80) REVERT: F 329 PHE cc_start: 0.8744 (m-10) cc_final: 0.8506 (m-80) REVERT: F 333 ASN cc_start: 0.8298 (p0) cc_final: 0.8013 (p0) REVERT: F 341 ARG cc_start: 0.8407 (mmm160) cc_final: 0.8055 (mmp80) REVERT: F 376 GLU cc_start: 0.8557 (mp0) cc_final: 0.7933 (mp0) REVERT: F 385 ARG cc_start: 0.8522 (ptm-80) cc_final: 0.8204 (ptm160) REVERT: F 388 ASP cc_start: 0.8003 (t70) cc_final: 0.7486 (t0) REVERT: F 396 GLU cc_start: 0.7891 (tp30) cc_final: 0.7513 (tp30) REVERT: I 311 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8914 (pp) REVERT: I 453 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7260 (pp) REVERT: I 488 LYS cc_start: 0.7800 (mtpm) cc_final: 0.7523 (mtmt) outliers start: 42 outliers final: 29 residues processed: 277 average time/residue: 0.8007 time to fit residues: 249.4721 Evaluate side-chains 276 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 238 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 690 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 LYS 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 121 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 460 THR 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 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 195 ASP Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 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 311 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 214 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 179 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 E 377 GLN E 438 ASN F 383 GLN I 313 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.103678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.070633 restraints weight = 39040.222| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.11 r_work: 0.2762 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24377 Z= 0.133 Angle : 0.563 10.679 33294 Z= 0.298 Chirality : 0.040 0.140 3794 Planarity : 0.004 0.063 3884 Dihedral : 17.607 76.790 3981 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.62 % Allowed : 21.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.17), residues: 2633 helix: 1.70 (0.14), residues: 1487 sheet: -0.00 (0.32), residues: 253 loop : -0.14 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 337 TYR 0.026 0.001 TYR F 300 PHE 0.042 0.001 PHE C 408 TRP 0.012 0.001 TRP A 539 HIS 0.006 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00307 (24377) covalent geometry : angle 0.56317 (33294) hydrogen bonds : bond 0.03608 ( 1233) hydrogen bonds : angle 3.87091 ( 3430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11502.35 seconds wall clock time: 195 minutes 48.28 seconds (11748.28 seconds total)