Starting phenix.real_space_refine on Sat Aug 8 16:38:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9whu_65977/08_2026/9whu_65977.cif Found real_map, /net/cci-nas-00/data/ceres_data/9whu_65977/08_2026/9whu_65977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9whu_65977/08_2026/9whu_65977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9whu_65977/08_2026/9whu_65977.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9whu_65977/08_2026/9whu_65977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9whu_65977/08_2026/9whu_65977.map" } resolution = 3.5 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= 0.011 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: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 87 5.16 5 C 18128 2.51 5 N 4750 2.21 5 O 5323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28311 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2303 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain: "B" Number of atoms: 6973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6973 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 828} Chain: "D" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2303 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain: "E" Number of atoms: 6973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6973 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 828} Chain: "F" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain breaks: 1 Chain: "G" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2303 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain: "H" Number of atoms: 6973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6973 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 828} Chain: "I" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain breaks: 1 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain breaks: 1 Time building chain proxies: 6.38, per 1000 atoms: 0.23 Number of scatterers: 28311 At special positions: 0 Unit cell: (110.908, 134.208, 202.244, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 P 23 15.00 O 5323 8.00 N 4750 7.00 C 18128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 273 " distance=2.03 Simple disulfide: pdb=" SG CYS G 251 " - pdb=" SG CYS G 273 " distance=2.01 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6582 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 18 sheets defined 58.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 282 through 295 Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.828A pdb=" N GLU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 330 through 343 Processing helix chain 'A' and resid 386 through 401 Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.616A pdb=" N GLU A 417 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.959A pdb=" N SER A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 468 through 488 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.534A pdb=" N LEU A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 14 Processing helix chain 'B' and resid 15 through 34 Processing helix chain 'B' and resid 43 through 59 Processing helix chain 'B' and resid 62 through 77 Processing helix chain 'B' and resid 78 through 83 removed outlier: 5.192A pdb=" N ASP B 81 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS B 82 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 78 through 83' Processing helix chain 'B' and resid 86 through 98 Processing helix chain 'B' and resid 110 through 124 Processing helix chain 'B' and resid 133 through 145 removed outlier: 3.673A pdb=" N LYS B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 158 through 174 removed outlier: 3.673A pdb=" N ILE B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 199 Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.673A pdb=" N LEU B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 283 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.500A pdb=" N LEU B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 removed outlier: 4.003A pdb=" N THR B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 367 Processing helix chain 'B' and resid 376 through 391 removed outlier: 3.606A pdb=" N ARG B 391 " --> pdb=" O PHE B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.528A pdb=" N ILE B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 424 Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 458 through 464 removed outlier: 4.125A pdb=" N GLU B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 458 through 464' Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.556A pdb=" N LEU B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 546 through 558 Processing helix chain 'B' and resid 566 through 569 Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 592 through 601 removed outlier: 4.193A pdb=" N LYS B 597 " --> pdb=" O PHE B 593 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE B 598 " --> pdb=" O VAL B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 618 removed outlier: 3.515A pdb=" N LEU B 607 " --> pdb=" O ARG B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 628 removed outlier: 3.971A pdb=" N ILE B 625 " --> pdb=" O PRO B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 Processing helix chain 'B' and resid 646 through 650 Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.839A pdb=" N THR B 676 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 677 " --> pdb=" O TRP B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 677' Processing helix chain 'B' and resid 683 through 699 removed outlier: 3.559A pdb=" N ASN B 699 " --> pdb=" O ASN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 712 removed outlier: 3.757A pdb=" N ASP B 712 " --> pdb=" O ASN B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 750 Processing helix chain 'B' and resid 753 through 770 removed outlier: 4.008A pdb=" N TYR B 758 " --> pdb=" O PHE B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 785 removed outlier: 3.664A pdb=" N PHE B 782 " --> pdb=" O ASN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 801 through 811 removed outlier: 3.883A pdb=" N SER B 811 " --> pdb=" O ILE B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 816 Processing helix chain 'B' and resid 822 through 825 Processing helix chain 'B' and resid 831 through 838 Processing helix chain 'B' and resid 843 through 850 Processing helix chain 'D' and resid 282 through 297 Proline residue: D 293 - end of helix Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 313 through 325 Processing helix chain 'D' and resid 329 through 343 removed outlier: 4.587A pdb=" N GLU D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 401 removed outlier: 3.999A pdb=" N SER D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 418 Processing helix chain 'D' and resid 421 through 433 Processing helix chain 'D' and resid 461 through 465 removed outlier: 4.074A pdb=" N ASN D 465 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 488 removed outlier: 3.798A pdb=" N LEU D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 495 Processing helix chain 'D' and resid 496 through 498 No H-bonds generated for 'chain 'D' and resid 496 through 498' Processing helix chain 'D' and resid 511 through 522 Processing helix chain 'E' and resid 4 through 14 Processing helix chain 'E' and resid 15 through 36 Processing helix chain 'E' and resid 43 through 59 removed outlier: 3.894A pdb=" N ASP E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 84 through 97 removed outlier: 4.457A pdb=" N LEU E 88 " --> pdb=" O GLY E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 124 Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.539A pdb=" N THR E 129 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 Processing helix chain 'E' and resid 154 through 157 Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'E' and resid 184 through 199 Processing helix chain 'E' and resid 199 through 206 Processing helix chain 'E' and resid 232 through 241 removed outlier: 3.679A pdb=" N LEU E 237 " --> pdb=" O PRO E 233 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 261 removed outlier: 3.881A pdb=" N LEU E 259 " --> pdb=" O ALA E 256 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN E 261 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 355 through 367 Processing helix chain 'E' and resid 376 through 391 Processing helix chain 'E' and resid 399 through 413 Processing helix chain 'E' and resid 417 through 424 Processing helix chain 'E' and resid 435 through 448 removed outlier: 3.814A pdb=" N LYS E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 461 Processing helix chain 'E' and resid 487 through 500 Processing helix chain 'E' and resid 526 through 530 Processing helix chain 'E' and resid 538 through 546 Processing helix chain 'E' and resid 546 through 559 removed outlier: 4.033A pdb=" N ASP E 559 " --> pdb=" O ARG E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 585 Processing helix chain 'E' and resid 588 through 591 Processing helix chain 'E' and resid 592 through 601 Processing helix chain 'E' and resid 604 through 617 removed outlier: 3.962A pdb=" N SER E 608 " --> pdb=" O GLU E 604 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU E 612 " --> pdb=" O SER E 608 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS E 613 " --> pdb=" O LEU E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 628 removed outlier: 3.722A pdb=" N ILE E 625 " --> pdb=" O PRO E 621 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 628 " --> pdb=" O ILE E 624 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 645 removed outlier: 3.574A pdb=" N VAL E 645 " --> pdb=" O ASP E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 651 removed outlier: 3.569A pdb=" N LYS E 651 " --> pdb=" O PRO E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 671 Processing helix chain 'E' and resid 672 through 677 Processing helix chain 'E' and resid 683 through 698 Processing helix chain 'E' and resid 702 through 714 Processing helix chain 'E' and resid 732 through 749 Processing helix chain 'E' and resid 753 through 770 Processing helix chain 'E' and resid 778 through 784 removed outlier: 3.659A pdb=" N PHE E 782 " --> pdb=" O ASN E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 789 through 799 Processing helix chain 'E' and resid 801 through 811 Processing helix chain 'E' and resid 811 through 816 Processing helix chain 'E' and resid 831 through 839 Processing helix chain 'E' and resid 845 through 852 Processing helix chain 'G' and resid 280 through 297 removed outlier: 3.577A pdb=" N ILE G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Proline residue: G 293 - end of helix Processing helix chain 'G' and resid 298 through 307 Processing helix chain 'G' and resid 309 through 326 Processing helix chain 'G' and resid 330 through 343 removed outlier: 3.694A pdb=" N MET G 334 " --> pdb=" O LYS G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 401 Processing helix chain 'G' and resid 402 through 407 removed outlier: 6.023A pdb=" N ARG G 405 " --> pdb=" O PRO G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 421 through 433 Processing helix chain 'G' and resid 468 through 488 Processing helix chain 'G' and resid 488 through 496 removed outlier: 3.659A pdb=" N ILE G 492 " --> pdb=" O ARG G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 523 Processing helix chain 'H' and resid 4 through 14 Processing helix chain 'H' and resid 15 through 36 Processing helix chain 'H' and resid 43 through 59 removed outlier: 3.559A pdb=" N ASP H 49 " --> pdb=" O THR H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 77 Processing helix chain 'H' and resid 78 through 84 removed outlier: 5.012A pdb=" N ASP H 81 " --> pdb=" O PRO H 78 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY H 84 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 removed outlier: 3.585A pdb=" N SER H 91 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 97 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 124 Processing helix chain 'H' and resid 125 through 129 removed outlier: 3.626A pdb=" N THR H 129 " --> pdb=" O PHE H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 145 Processing helix chain 'H' and resid 154 through 157 Processing helix chain 'H' and resid 158 through 173 removed outlier: 3.540A pdb=" N ASN H 173 " --> pdb=" O GLU H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 199 Processing helix chain 'H' and resid 199 through 206 removed outlier: 3.500A pdb=" N PHE H 206 " --> pdb=" O LEU H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 241 Processing helix chain 'H' and resid 256 through 261 Processing helix chain 'H' and resid 267 through 283 Processing helix chain 'H' and resid 299 through 305 removed outlier: 3.520A pdb=" N PHE H 305 " --> pdb=" O PHE H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 352 removed outlier: 4.267A pdb=" N THR H 352 " --> pdb=" O GLY H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 367 removed outlier: 4.116A pdb=" N ARG H 366 " --> pdb=" O ASN H 362 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS H 367 " --> pdb=" O ILE H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 391 Processing helix chain 'H' and resid 401 through 413 Processing helix chain 'H' and resid 417 through 423 Processing helix chain 'H' and resid 435 through 448 removed outlier: 3.595A pdb=" N LYS H 448 " --> pdb=" O GLU H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 458 through 463 removed outlier: 3.802A pdb=" N GLU H 462 " --> pdb=" O PRO H 458 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY H 463 " --> pdb=" O THR H 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 458 through 463' Processing helix chain 'H' and resid 487 through 500 Processing helix chain 'H' and resid 525 through 530 removed outlier: 3.931A pdb=" N ILE H 528 " --> pdb=" O ASN H 525 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 546 Processing helix chain 'H' and resid 546 through 559 Processing helix chain 'H' and resid 568 through 585 removed outlier: 3.619A pdb=" N ILE H 583 " --> pdb=" O ALA H 579 " (cutoff:3.500A) Processing helix chain 'H' and resid 592 through 601 Processing helix chain 'H' and resid 604 through 615 Processing helix chain 'H' and resid 621 through 628 removed outlier: 3.752A pdb=" N ILE H 625 " --> pdb=" O PRO H 621 " (cutoff:3.500A) Processing helix chain 'H' and resid 632 through 645 Processing helix chain 'H' and resid 656 through 671 Processing helix chain 'H' and resid 683 through 698 Processing helix chain 'H' and resid 702 through 711 Processing helix chain 'H' and resid 732 through 751 Processing helix chain 'H' and resid 753 through 770 removed outlier: 3.609A pdb=" N LYS H 757 " --> pdb=" O PHE H 753 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR H 758 " --> pdb=" O PHE H 754 " (cutoff:3.500A) Processing helix chain 'H' and resid 778 through 786 removed outlier: 3.802A pdb=" N PHE H 782 " --> pdb=" O ASN H 778 " (cutoff:3.500A) Processing helix chain 'H' and resid 789 through 799 Processing helix chain 'H' and resid 801 through 811 removed outlier: 3.711A pdb=" N SER H 811 " --> pdb=" O ILE H 807 " (cutoff:3.500A) Processing helix chain 'H' and resid 813 through 816 Processing helix chain 'H' and resid 822 through 825 removed outlier: 4.047A pdb=" N TYR H 825 " --> pdb=" O GLU H 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 822 through 825' Processing helix chain 'H' and resid 831 through 839 Processing helix chain 'H' and resid 845 through 853 removed outlier: 3.619A pdb=" N VAL H 849 " --> pdb=" O GLU H 845 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE H 851 " --> pdb=" O GLY H 847 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 350 removed outlier: 6.395A pdb=" N ALA A 363 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 383 removed outlier: 6.581A pdb=" N ILE A 449 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL A 507 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 451 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE A 509 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N TYR A 453 " --> pdb=" O PHE A 509 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 209 through 211 removed outlier: 6.269A pdb=" N LYS B 209 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE B 230 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 211 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY B 153 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER B 150 " --> pdb=" O SER B 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 344 through 345 removed outlier: 4.627A pdb=" N ILE B 334 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU B 324 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER B 321 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE B 513 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN B 323 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N CYS B 515 " --> pdb=" O ASN B 323 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR B 325 " --> pdb=" O CYS B 515 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 716 through 717 Processing sheet with id=AA6, first strand: chain 'B' and resid 818 through 821 removed outlier: 7.039A pdb=" N LYS B 819 " --> pdb=" O ILE B 828 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 269 through 271 removed outlier: 3.574A pdb=" N TYR D 453 " --> pdb=" O VAL D 507 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY D 362 " --> pdb=" O SER D 378 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA D 363 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 209 through 211 removed outlier: 6.454A pdb=" N LYS E 209 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE E 230 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL E 211 " --> pdb=" O ILE E 230 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE E 178 " --> pdb=" O PHE E 229 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU E 231 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE E 180 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN E 177 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR E 250 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP E 249 " --> pdb=" O LYS E 287 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL E 289 " --> pdb=" O ASP E 249 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU E 251 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N SER E 291 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL E 253 " --> pdb=" O SER E 291 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER E 313 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 321 through 325 removed outlier: 6.720A pdb=" N SER E 321 " --> pdb=" O GLY E 511 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE E 513 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASN E 323 " --> pdb=" O ILE E 513 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS E 515 " --> pdb=" O ASN E 323 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR E 325 " --> pdb=" O CYS E 515 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE E 471 " --> pdb=" O PHE E 514 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU E 516 " --> pdb=" O ILE E 471 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE E 473 " --> pdb=" O LEU E 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 334 through 337 removed outlier: 3.962A pdb=" N ILE E 334 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 716 through 717 Processing sheet with id=AB3, first strand: chain 'E' and resid 818 through 821 removed outlier: 6.921A pdb=" N ASN E 821 " --> pdb=" O ILE E 827 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE E 827 " --> pdb=" O ASN E 821 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 270 through 271 removed outlier: 6.766A pdb=" N LEU G 447 " --> pdb=" O ASP G 503 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N PHE G 505 " --> pdb=" O LEU G 447 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE G 449 " --> pdb=" O PHE G 505 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL G 507 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE G 451 " --> pdb=" O VAL G 507 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE G 509 " --> pdb=" O ILE G 451 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR G 453 " --> pdb=" O PHE G 509 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 366 through 367 Processing sheet with id=AB6, first strand: chain 'H' and resid 209 through 211 removed outlier: 6.532A pdb=" N ILE H 178 " --> pdb=" O PHE H 229 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU H 231 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE H 180 " --> pdb=" O LEU H 231 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN H 177 " --> pdb=" O ILE H 248 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR H 250 " --> pdb=" O ASN H 177 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 179 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TYR H 149 " --> pdb=" O PHE H 290 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER H 292 " --> pdb=" O TYR H 149 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE H 151 " --> pdb=" O SER H 292 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 321 through 325 removed outlier: 6.462A pdb=" N ILE H 471 " --> pdb=" O PHE H 514 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET H 371 " --> pdb=" O PHE H 472 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN H 370 " --> pdb=" O ILE H 454 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N CYS H 456 " --> pdb=" O ASN H 370 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE H 372 " --> pdb=" O CYS H 456 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA H 428 " --> pdb=" O PHE H 455 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 334 through 337 removed outlier: 4.443A pdb=" N ILE H 334 " --> pdb=" O ILE H 345 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 818 through 821 removed outlier: 5.968A pdb=" N ASN H 821 " --> pdb=" O ILE H 827 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE H 827 " --> pdb=" O ASN H 821 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3909 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.13 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9081 1.35 - 1.47: 7106 1.47 - 1.60: 12595 1.60 - 1.72: 39 1.72 - 1.85: 126 Bond restraints: 28947 Sorted by residual: bond pdb=" N9 DA F 7 " pdb=" C4 DA F 7 " ideal model delta sigma weight residual 1.374 1.394 -0.020 6.00e-03 2.78e+04 1.12e+01 bond pdb=" C3' DA C 6 " pdb=" C2' DA C 6 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.42e+00 bond pdb=" C3' DA F 7 " pdb=" C2' DA F 7 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.33e+00 bond pdb=" C3' DA C 13 " pdb=" C2' DA C 13 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.91e+00 bond pdb=" C3' DA F 13 " pdb=" C2' DA F 13 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.76e+00 ... (remaining 28942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 38910 3.02 - 6.04: 223 6.04 - 9.06: 27 9.06 - 12.08: 8 12.08 - 15.10: 2 Bond angle restraints: 39170 Sorted by residual: angle pdb=" CB MET G 255 " pdb=" CG MET G 255 " pdb=" SD MET G 255 " ideal model delta sigma weight residual 112.70 127.80 -15.10 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C HIS A 455 " pdb=" N LYS A 456 " pdb=" CA LYS A 456 " ideal model delta sigma weight residual 121.54 130.59 -9.05 1.91e+00 2.74e-01 2.24e+01 angle pdb=" CA CYS G 251 " pdb=" CB CYS G 251 " pdb=" SG CYS G 251 " ideal model delta sigma weight residual 114.40 124.86 -10.46 2.30e+00 1.89e-01 2.07e+01 angle pdb=" CA CYS G 273 " pdb=" CB CYS G 273 " pdb=" SG CYS G 273 " ideal model delta sigma weight residual 114.40 123.29 -8.89 2.30e+00 1.89e-01 1.49e+01 angle pdb=" N HIS A 455 " pdb=" CA HIS A 455 " pdb=" C HIS A 455 " ideal model delta sigma weight residual 112.54 107.86 4.68 1.22e+00 6.72e-01 1.47e+01 ... (remaining 39165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 14562 17.84 - 35.68: 2122 35.68 - 53.52: 630 53.52 - 71.36: 139 71.36 - 89.20: 47 Dihedral angle restraints: 17500 sinusoidal: 7348 harmonic: 10152 Sorted by residual: dihedral pdb=" CB CYS D 251 " pdb=" SG CYS D 251 " pdb=" SG CYS D 273 " pdb=" CB CYS D 273 " ideal model delta sinusoidal sigma weight residual -86.00 -167.85 81.85 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS G 251 " pdb=" SG CYS G 251 " pdb=" SG CYS G 273 " pdb=" CB CYS G 273 " ideal model delta sinusoidal sigma weight residual 93.00 152.92 -59.92 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS A 251 " pdb=" SG CYS A 251 " pdb=" SG CYS A 273 " pdb=" CB CYS A 273 " ideal model delta sinusoidal sigma weight residual 93.00 135.52 -42.52 1 1.00e+01 1.00e-02 2.52e+01 ... (remaining 17497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3861 0.066 - 0.131: 458 0.131 - 0.197: 27 0.197 - 0.262: 5 0.262 - 0.328: 1 Chirality restraints: 4352 Sorted by residual: chirality pdb=" CG LEU E 21 " pdb=" CB LEU E 21 " pdb=" CD1 LEU E 21 " pdb=" CD2 LEU E 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CG LEU G 479 " pdb=" CB LEU G 479 " pdb=" CD1 LEU G 479 " pdb=" CD2 LEU G 479 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU A 316 " pdb=" CB LEU A 316 " pdb=" CD1 LEU A 316 " pdb=" CD2 LEU A 316 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 4349 not shown) Planarity restraints: 4919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 292 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO H 293 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO H 293 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 293 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 63 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C GLN E 63 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN E 63 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN E 64 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 292 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO E 293 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO E 293 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 293 " 0.039 5.00e-02 4.00e+02 ... (remaining 4916 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 9766 2.85 - 3.36: 30541 3.36 - 3.88: 50001 3.88 - 4.39: 57338 4.39 - 4.90: 94156 Nonbonded interactions: 241802 Sorted by model distance: nonbonded pdb=" O ASN A 280 " pdb=" ND2 ASN A 280 " model vdw 2.338 3.120 nonbonded pdb=" O SER B 127 " pdb=" OD1 ASN B 128 " model vdw 2.509 3.040 nonbonded pdb=" O LYS H 379 " pdb=" OD1 ASP H 382 " model vdw 2.550 3.040 nonbonded pdb=" N VAL H 464 " pdb=" O VAL H 464 " model vdw 2.565 2.496 nonbonded pdb=" N HIS A 455 " pdb=" N LYS A 456 " model vdw 2.573 2.560 ... (remaining 241797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = (chain 'C' and resid 7 through 15) selection = chain 'F' selection = (chain 'I' and resid 7 through 14) } 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 group one per residue 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: 16.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 27.180 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.003 0.041 28950 Z= 0.150 Angle : 0.633 15.099 39176 Z= 0.334 Chirality : 0.043 0.328 4352 Planarity : 0.004 0.095 4919 Dihedral : 18.753 89.201 10909 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.40 % Favored : 92.28 % Rotamer: Outliers : 3.15 % Allowed : 30.63 % Favored : 66.22 % 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: -0.44 (0.15), residues: 3393 helix: 1.09 (0.13), residues: 1783 sheet: -1.09 (0.27), residues: 376 loop : -2.12 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 405 TYR 0.019 0.001 TYR B 565 PHE 0.019 0.001 PHE H 126 TRP 0.019 0.001 TRP E 697 HIS 0.004 0.001 HIS D 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (28947) covalent geometry : angle 0.63084 / 0.33 (39170) SS BOND : bond 0.01094 / 0.33 ( 3) SS BOND : angle 4.20551 / 2.54 ( 6) hydrogen bonds : bond 0.13156 / 8.52 ( 1344) hydrogen bonds : angle 6.05675 / 4.29 ( 3909) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 296 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.3753 (mpp) cc_final: 0.3548 (mpp) REVERT: A 268 ASN cc_start: 0.7763 (m-40) cc_final: 0.7245 (t0) REVERT: A 272 LEU cc_start: 0.8221 (tp) cc_final: 0.8004 (tp) REVERT: A 303 MET cc_start: 0.8023 (mmm) cc_final: 0.7549 (mpp) REVERT: A 340 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9000 (mm) REVERT: A 422 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: B 117 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.7667 (m-40) REVERT: B 203 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9073 (mp) REVERT: B 309 LYS cc_start: 0.7006 (mmtt) cc_final: 0.6769 (mmtt) REVERT: B 424 MET cc_start: 0.8017 (mtp) cc_final: 0.7608 (mtt) REVERT: B 466 MET cc_start: 0.8140 (tpt) cc_final: 0.7823 (tpt) REVERT: B 596 ARG cc_start: 0.9033 (ttp80) cc_final: 0.8794 (ttm110) REVERT: B 754 PHE cc_start: 0.8461 (t80) cc_final: 0.8064 (t80) REVERT: D 278 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6383 (mtpm) REVERT: D 290 ASP cc_start: 0.9120 (t0) cc_final: 0.8733 (t0) REVERT: D 311 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6022 (m-80) REVERT: D 334 MET cc_start: 0.8939 (mmm) cc_final: 0.8638 (mpp) REVERT: D 340 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8388 (mm) REVERT: D 350 TYR cc_start: 0.8088 (m-10) cc_final: 0.7845 (m-80) REVERT: D 463 TYR cc_start: 0.8155 (m-80) cc_final: 0.7714 (t80) REVERT: D 483 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: E 67 MET cc_start: 0.8683 (mmm) cc_final: 0.7988 (mmm) REVERT: E 113 GLN cc_start: 0.8566 (tp40) cc_final: 0.8262 (tp40) REVERT: E 296 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7548 (tm-30) REVERT: E 418 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7550 (m-10) REVERT: E 531 GLU cc_start: 0.8209 (pm20) cc_final: 0.7823 (pm20) REVERT: E 694 MET cc_start: 0.7259 (mmm) cc_final: 0.7011 (mmm) REVERT: E 750 ILE cc_start: 0.9183 (mm) cc_final: 0.8957 (mp) REVERT: G 249 MET cc_start: 0.7109 (mmp) cc_final: 0.6822 (mmm) REVERT: G 337 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7724 (tm-30) REVERT: G 457 ILE cc_start: 0.3556 (OUTLIER) cc_final: 0.3272 (tp) REVERT: H 46 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8007 (mt-10) REVERT: H 255 GLU cc_start: 0.8810 (mm-30) cc_final: 0.7998 (mp0) REVERT: H 394 GLU cc_start: 0.7642 (pm20) cc_final: 0.7283 (pp20) REVERT: H 418 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6431 (m-10) REVERT: H 845 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7699 (pm20) outliers start: 98 outliers final: 65 residues processed: 365 average time/residue: 0.1701 time to fit residues: 104.2389 Evaluate side-chains 353 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 276 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 602 HIS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 311 PHE Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 578 MET Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 760 ASN Chi-restraints excluded: chain E residue 820 PHE Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 367 PHE Chi-restraints excluded: chain G residue 396 VAL Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 457 ILE Chi-restraints excluded: chain G residue 460 SER Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 418 TYR Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 521 ASN Chi-restraints excluded: chain H residue 556 TYR Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 844 VAL Chi-restraints excluded: chain H residue 845 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 761 HIS D 413 ASN ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 372 ASN H 632 ASN H 837 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.089123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.072776 restraints weight = 109052.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.074954 restraints weight = 60511.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.076422 restraints weight = 40507.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.077426 restraints weight = 30457.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.078170 restraints weight = 24970.812| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28950 Z= 0.182 Angle : 0.599 13.528 39176 Z= 0.316 Chirality : 0.043 0.278 4352 Planarity : 0.004 0.060 4919 Dihedral : 11.219 88.442 4175 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.93 % Favored : 91.75 % Rotamer: Outliers : 6.05 % Allowed : 27.32 % Favored : 66.63 % 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: -0.47 (0.15), residues: 3393 helix: 1.09 (0.12), residues: 1821 sheet: -1.21 (0.27), residues: 381 loop : -2.24 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 555 TYR 0.014 0.001 TYR A 270 PHE 0.021 0.002 PHE G 248 TRP 0.018 0.001 TRP E 697 HIS 0.004 0.001 HIS H 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (28947) covalent geometry : angle 0.59668 / 0.32 (39170) SS BOND : bond 0.00178 / 0.08 ( 3) SS BOND : angle 3.82176 / 2.28 ( 6) hydrogen bonds : bond 0.04039 / 2.69 ( 1344) hydrogen bonds : angle 5.09758 / 3.59 ( 3909) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 280 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.3863 (mpp) cc_final: 0.3647 (mpp) REVERT: A 268 ASN cc_start: 0.7745 (m-40) cc_final: 0.7507 (t0) REVERT: A 340 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9009 (mm) REVERT: A 422 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: B 424 MET cc_start: 0.7938 (mtp) cc_final: 0.7551 (mtt) REVERT: B 466 MET cc_start: 0.8157 (tpt) cc_final: 0.7744 (tpt) REVERT: B 596 ARG cc_start: 0.9058 (ttp80) cc_final: 0.8828 (ttm110) REVERT: B 754 PHE cc_start: 0.8410 (t80) cc_final: 0.8130 (t80) REVERT: B 756 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: D 290 ASP cc_start: 0.9126 (t0) cc_final: 0.8765 (t0) REVERT: D 311 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.5983 (m-80) REVERT: D 334 MET cc_start: 0.8998 (mmm) cc_final: 0.8556 (mpp) REVERT: D 340 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8292 (mm) REVERT: D 426 GLN cc_start: 0.8713 (pp30) cc_final: 0.8372 (pp30) REVERT: D 463 TYR cc_start: 0.8173 (m-80) cc_final: 0.7686 (t80) REVERT: D 483 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: E 67 MET cc_start: 0.8757 (mmm) cc_final: 0.8048 (mmm) REVERT: E 296 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7543 (tm-30) REVERT: E 394 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: E 486 LYS cc_start: 0.9416 (mmmm) cc_final: 0.9172 (mmmm) REVERT: E 531 GLU cc_start: 0.8203 (pm20) cc_final: 0.7842 (pm20) REVERT: E 541 ASP cc_start: 0.8570 (t0) cc_final: 0.8332 (t0) REVERT: E 718 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7868 (p) REVERT: G 249 MET cc_start: 0.7024 (mmp) cc_final: 0.6780 (mmm) REVERT: G 337 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7810 (tm-30) REVERT: G 514 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8411 (tttp) REVERT: H 46 GLU cc_start: 0.8696 (mt-10) cc_final: 0.7913 (mt-10) REVERT: H 53 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: H 255 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8025 (mp0) REVERT: H 394 GLU cc_start: 0.7562 (pm20) cc_final: 0.7253 (pp20) REVERT: H 418 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.6489 (m-10) outliers start: 188 outliers final: 119 residues processed: 427 average time/residue: 0.1614 time to fit residues: 116.5641 Evaluate side-chains 396 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 266 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 602 HIS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 311 PHE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 503 ASP Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 448 LYS Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 820 PHE Chi-restraints excluded: chain E residue 829 SER Chi-restraints excluded: chain E residue 853 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 334 MET Chi-restraints excluded: chain G residue 396 VAL Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain G residue 514 LYS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 418 TYR Chi-restraints excluded: chain H residue 419 LEU Chi-restraints excluded: chain H residue 454 ILE Chi-restraints excluded: chain H residue 521 ASN Chi-restraints excluded: chain H residue 541 ASP Chi-restraints excluded: chain H residue 556 TYR Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 801 SER Chi-restraints excluded: chain H residue 814 LEU Chi-restraints excluded: chain H residue 837 ASN Chi-restraints excluded: chain H residue 844 VAL Chi-restraints excluded: chain H residue 849 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 210 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 328 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 281 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 GLN ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 GLN E 649 ASN G 337 GLN ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 761 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.089317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.073037 restraints weight = 108937.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.075205 restraints weight = 60157.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.076721 restraints weight = 40157.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.077786 restraints weight = 30047.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.078450 restraints weight = 24401.008| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28950 Z= 0.154 Angle : 0.574 13.327 39176 Z= 0.299 Chirality : 0.042 0.334 4352 Planarity : 0.004 0.063 4919 Dihedral : 10.815 88.413 4101 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.69 % Favored : 92.01 % Rotamer: Outliers : 5.89 % Allowed : 27.93 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.42 (0.15), residues: 3393 helix: 1.14 (0.13), residues: 1803 sheet: -1.22 (0.27), residues: 383 loop : -2.19 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 265 TYR 0.014 0.001 TYR H 762 PHE 0.020 0.001 PHE G 248 TRP 0.018 0.001 TRP E 697 HIS 0.009 0.001 HIS H 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (28947) covalent geometry : angle 0.57336 / 0.30 (39170) SS BOND : bond 0.00134 / 0.06 ( 3) SS BOND : angle 2.84368 / 1.72 ( 6) hydrogen bonds : bond 0.03782 / 2.52 ( 1344) hydrogen bonds : angle 4.91201 / 3.46 ( 3909) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 281 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASN cc_start: 0.7715 (m-40) cc_final: 0.7508 (t0) REVERT: A 340 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9045 (mt) REVERT: B 13 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.6806 (m-10) REVERT: B 424 MET cc_start: 0.7882 (mtp) cc_final: 0.7500 (mtt) REVERT: B 466 MET cc_start: 0.8162 (tpt) cc_final: 0.7801 (tpt) REVERT: B 596 ARG cc_start: 0.9055 (ttp80) cc_final: 0.8816 (ttm110) REVERT: B 756 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: D 256 GLU cc_start: 0.8121 (pm20) cc_final: 0.7909 (pm20) REVERT: D 278 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6482 (mtpm) REVERT: D 290 ASP cc_start: 0.9124 (t0) cc_final: 0.8754 (t0) REVERT: D 311 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.5954 (m-80) REVERT: D 334 MET cc_start: 0.8983 (mmm) cc_final: 0.8644 (mpp) REVERT: D 340 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8295 (mm) REVERT: D 463 TYR cc_start: 0.8189 (m-80) cc_final: 0.7728 (t80) REVERT: D 483 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: E 67 MET cc_start: 0.8745 (mmm) cc_final: 0.8061 (mmm) REVERT: E 296 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7515 (tm-30) REVERT: E 394 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: E 486 LYS cc_start: 0.9423 (mmmm) cc_final: 0.9181 (mmmm) REVERT: E 531 GLU cc_start: 0.8184 (pm20) cc_final: 0.7826 (pm20) REVERT: E 541 ASP cc_start: 0.8538 (t0) cc_final: 0.8316 (t0) REVERT: E 718 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7889 (p) REVERT: G 249 MET cc_start: 0.6911 (mmp) cc_final: 0.6630 (mmm) REVERT: G 337 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: G 514 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8457 (tttp) REVERT: H 23 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8773 (ttmm) REVERT: H 46 GLU cc_start: 0.8583 (mt-10) cc_final: 0.7884 (mt-10) REVERT: H 254 ASP cc_start: 0.7159 (t0) cc_final: 0.6938 (t0) REVERT: H 255 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8390 (mp0) REVERT: H 418 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6502 (m-10) REVERT: H 845 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7393 (mt-10) outliers start: 183 outliers final: 124 residues processed: 417 average time/residue: 0.1595 time to fit residues: 111.3594 Evaluate side-chains 402 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 264 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 602 HIS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 311 PHE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 448 LYS Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 820 PHE Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 334 MET Chi-restraints excluded: chain G residue 337 GLN Chi-restraints excluded: chain G residue 396 VAL Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain G residue 514 LYS Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 418 TYR Chi-restraints excluded: chain H residue 419 LEU Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 520 SER Chi-restraints excluded: chain H residue 521 ASN Chi-restraints excluded: chain H residue 541 ASP Chi-restraints excluded: chain H residue 556 TYR Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 801 SER Chi-restraints excluded: chain H residue 814 LEU Chi-restraints excluded: chain H residue 844 VAL Chi-restraints excluded: chain H residue 845 GLU Chi-restraints excluded: chain H residue 849 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 329 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 211 optimal weight: 0.3980 chunk 267 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 240 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 HIS A 480 ASN B 200 HIS ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 710 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.089828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.073504 restraints weight = 108468.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.075723 restraints weight = 59846.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.077253 restraints weight = 39812.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.078288 restraints weight = 29753.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.078923 restraints weight = 24206.959| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28950 Z= 0.133 Angle : 0.564 13.277 39176 Z= 0.292 Chirality : 0.042 0.343 4352 Planarity : 0.004 0.067 4919 Dihedral : 10.719 87.855 4090 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.52 % Favored : 92.19 % Rotamer: Outliers : 6.24 % Allowed : 27.90 % Favored : 65.86 % 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: -0.36 (0.15), residues: 3393 helix: 1.21 (0.13), residues: 1800 sheet: -1.18 (0.27), residues: 383 loop : -2.20 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 265 TYR 0.017 0.001 TYR H 505 PHE 0.020 0.001 PHE G 450 TRP 0.016 0.001 TRP E 697 HIS 0.006 0.001 HIS H 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (28947) covalent geometry : angle 0.56326 / 0.29 (39170) SS BOND : bond 0.00212 / 0.07 ( 3) SS BOND : angle 1.97186 / 1.17 ( 6) hydrogen bonds : bond 0.03518 / 2.34 ( 1344) hydrogen bonds : angle 4.78924 / 3.38 ( 3909) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 277 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8090 (mmm) cc_final: 0.7883 (mmm) REVERT: A 340 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9046 (mt) REVERT: A 422 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: B 13 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.6808 (m-10) REVERT: B 424 MET cc_start: 0.7821 (mtp) cc_final: 0.7470 (mtt) REVERT: B 466 MET cc_start: 0.8162 (tpt) cc_final: 0.7681 (tpt) REVERT: B 590 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7739 (mtmm) REVERT: B 596 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8823 (ttm110) REVERT: B 756 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6405 (mp0) REVERT: D 278 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6475 (mtpm) REVERT: D 290 ASP cc_start: 0.9113 (t0) cc_final: 0.8748 (t0) REVERT: D 311 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.5888 (m-80) REVERT: D 340 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8273 (mm) REVERT: D 426 GLN cc_start: 0.8713 (pp30) cc_final: 0.8413 (pp30) REVERT: D 432 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7889 (mm) REVERT: D 463 TYR cc_start: 0.8206 (m-80) cc_final: 0.7730 (t80) REVERT: D 483 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: E 67 MET cc_start: 0.8720 (mmm) cc_final: 0.8052 (mmm) REVERT: E 296 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7495 (tm-30) REVERT: E 394 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: E 418 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7422 (m-10) REVERT: E 486 LYS cc_start: 0.9420 (mmmm) cc_final: 0.9178 (mmmm) REVERT: E 531 GLU cc_start: 0.8174 (pm20) cc_final: 0.7813 (pm20) REVERT: G 249 MET cc_start: 0.6898 (mmp) cc_final: 0.6636 (mmm) REVERT: G 337 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8034 (tm-30) REVERT: H 23 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8762 (ttmm) REVERT: H 41 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7876 (p0) REVERT: H 46 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7862 (mt-10) REVERT: H 254 ASP cc_start: 0.7125 (t0) cc_final: 0.6899 (t0) REVERT: H 418 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6462 (m-10) outliers start: 194 outliers final: 124 residues processed: 430 average time/residue: 0.1526 time to fit residues: 110.6016 Evaluate side-chains 401 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 262 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 602 HIS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 311 PHE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 448 LYS Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 820 PHE Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 334 MET Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 406 SER Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 418 TYR Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 521 ASN Chi-restraints excluded: chain H residue 541 ASP Chi-restraints excluded: chain H residue 556 TYR Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 801 SER Chi-restraints excluded: chain H residue 814 LEU Chi-restraints excluded: chain H residue 844 VAL Chi-restraints excluded: chain H residue 845 GLU Chi-restraints excluded: chain H residue 849 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 149 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 257 optimal weight: 0.0470 chunk 154 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 312 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 HIS A 480 ASN ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.088460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.072192 restraints weight = 109379.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.074344 restraints weight = 60827.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.075825 restraints weight = 40737.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.076801 restraints weight = 30567.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.077543 restraints weight = 25049.777| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28950 Z= 0.198 Angle : 0.608 13.231 39176 Z= 0.317 Chirality : 0.044 0.353 4352 Planarity : 0.004 0.069 4919 Dihedral : 10.767 87.884 4084 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.19 % Favored : 91.54 % Rotamer: Outliers : 6.82 % Allowed : 27.25 % Favored : 65.93 % 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: -0.51 (0.15), residues: 3393 helix: 1.07 (0.13), residues: 1806 sheet: -1.24 (0.27), residues: 383 loop : -2.24 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.030 0.001 TYR H 505 PHE 0.021 0.002 PHE G 450 TRP 0.018 0.002 TRP E 697 HIS 0.006 0.001 HIS H 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (28947) covalent geometry : angle 0.60541 / 0.32 (39170) SS BOND : bond 0.00236 / 0.12 ( 3) SS BOND : angle 4.20982 / 2.60 ( 6) hydrogen bonds : bond 0.03645 / 2.43 ( 1344) hydrogen bonds : angle 4.83602 / 3.41 ( 3909) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 261 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9083 (mm) REVERT: A 422 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: B 13 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.6938 (m-10) REVERT: B 173 ASN cc_start: 0.7502 (OUTLIER) cc_final: 0.7116 (p0) REVERT: B 203 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9057 (mp) REVERT: B 424 MET cc_start: 0.7881 (mtp) cc_final: 0.7528 (mtt) REVERT: B 466 MET cc_start: 0.8177 (tpt) cc_final: 0.7694 (tpt) REVERT: B 590 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7741 (mtmm) REVERT: B 596 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8827 (ttm110) REVERT: B 756 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: D 278 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6509 (mtpm) REVERT: D 290 ASP cc_start: 0.9126 (t0) cc_final: 0.8772 (t0) REVERT: D 334 MET cc_start: 0.8993 (mmm) cc_final: 0.8696 (mpp) REVERT: D 340 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8355 (mm) REVERT: D 432 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8088 (mm) REVERT: D 444 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8373 (mm-30) REVERT: D 483 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: E 296 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7554 (tm-30) REVERT: E 394 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: E 418 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7550 (m-10) REVERT: E 486 LYS cc_start: 0.9420 (mmmm) cc_final: 0.9184 (mmmm) REVERT: E 531 GLU cc_start: 0.8217 (pm20) cc_final: 0.7886 (pm20) REVERT: E 718 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7928 (p) REVERT: G 337 GLN cc_start: 0.8543 (tm-30) cc_final: 0.7870 (tm-30) REVERT: H 23 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8784 (ttmm) REVERT: H 41 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7926 (p0) REVERT: H 46 GLU cc_start: 0.8599 (mt-10) cc_final: 0.7831 (mt-10) REVERT: H 219 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8205 (pttp) REVERT: H 255 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8417 (mp0) REVERT: H 418 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6608 (m-10) REVERT: H 845 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7898 (pm20) outliers start: 212 outliers final: 157 residues processed: 423 average time/residue: 0.1608 time to fit residues: 114.6306 Evaluate side-chains 435 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 258 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 602 HIS Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 311 PHE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 448 LYS Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 591 ASP Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 760 ASN Chi-restraints excluded: chain E residue 820 PHE Chi-restraints excluded: chain E residue 829 SER Chi-restraints excluded: chain E residue 853 LEU Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 334 MET Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 396 VAL Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 406 SER Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain G residue 507 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 219 LYS Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 318 SER Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 371 MET Chi-restraints excluded: chain H residue 418 TYR Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 454 ILE Chi-restraints excluded: chain H residue 520 SER Chi-restraints excluded: chain H residue 521 ASN Chi-restraints excluded: chain H residue 541 ASP Chi-restraints excluded: chain H residue 556 TYR Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 693 LEU Chi-restraints excluded: chain H residue 781 THR Chi-restraints excluded: chain H residue 801 SER Chi-restraints excluded: chain H residue 814 LEU Chi-restraints excluded: chain H residue 844 VAL Chi-restraints excluded: chain H residue 845 GLU Chi-restraints excluded: chain H residue 849 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 305 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 chunk 279 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 285 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN ** H 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.088271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.071874 restraints weight = 110072.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.074040 restraints weight = 61222.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.075507 restraints weight = 41026.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.076507 restraints weight = 30922.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.077255 restraints weight = 25300.326| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28950 Z= 0.194 Angle : 0.610 12.957 39176 Z= 0.316 Chirality : 0.043 0.286 4352 Planarity : 0.004 0.063 4919 Dihedral : 10.801 88.111 4082 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.10 % Favored : 91.63 % Rotamer: Outliers : 6.89 % Allowed : 27.57 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.63 (0.15), residues: 3393 helix: 0.95 (0.12), residues: 1821 sheet: -1.27 (0.27), residues: 383 loop : -2.31 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.022 0.001 TYR B 166 PHE 0.021 0.002 PHE G 450 TRP 0.019 0.002 TRP E 697 HIS 0.006 0.001 HIS H 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (28947) covalent geometry : angle 0.60842 / 0.32 (39170) SS BOND : bond 0.00343 / 0.16 ( 3) SS BOND : angle 3.03162 / 1.83 ( 6) hydrogen bonds : bond 0.03644 / 2.42 ( 1344) hydrogen bonds : angle 4.81114 / 3.39 ( 3909) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 266 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.5895 (OUTLIER) cc_final: 0.5664 (m-10) REVERT: A 303 MET cc_start: 0.8115 (mmm) cc_final: 0.7912 (mmm) REVERT: A 340 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9048 (mm) REVERT: A 422 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: B 13 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7029 (m-10) REVERT: B 203 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9081 (mp) REVERT: B 424 MET cc_start: 0.7913 (mtp) cc_final: 0.7525 (mtt) REVERT: B 466 MET cc_start: 0.8174 (tpt) cc_final: 0.7689 (tpt) REVERT: B 590 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7775 (mtmm) REVERT: B 596 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8832 (ttm110) REVERT: B 756 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: D 278 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6560 (mtpm) REVERT: D 290 ASP cc_start: 0.9127 (t0) cc_final: 0.8776 (t0) REVERT: D 334 MET cc_start: 0.8971 (mmm) cc_final: 0.8700 (mpp) REVERT: D 340 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8407 (mm) REVERT: D 372 ASN cc_start: 0.8129 (t0) cc_final: 0.7826 (t0) REVERT: D 426 GLN cc_start: 0.8713 (pp30) cc_final: 0.8416 (pp30) REVERT: D 432 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8075 (mm) REVERT: D 457 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6401 (mm) REVERT: D 483 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: E 296 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7557 (tm-30) REVERT: E 394 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: E 418 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7572 (m-10) REVERT: E 486 LYS cc_start: 0.9420 (mmmm) cc_final: 0.9193 (mmmm) REVERT: E 531 GLU cc_start: 0.8208 (pm20) cc_final: 0.7913 (pm20) REVERT: E 718 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7996 (p) REVERT: G 337 GLN cc_start: 0.8539 (tm-30) cc_final: 0.7899 (tm-30) REVERT: H 23 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8785 (ttmm) REVERT: H 40 PHE cc_start: 0.7170 (t80) cc_final: 0.6954 (t80) REVERT: H 41 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7867 (p0) REVERT: H 46 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7868 (mt-10) REVERT: H 99 LEU cc_start: 0.8727 (mp) cc_final: 0.8492 (mp) REVERT: H 219 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8195 (pttp) REVERT: H 255 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8311 (mp0) REVERT: H 418 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6530 (m-10) REVERT: H 845 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8015 (pm20) outliers start: 214 outliers final: 163 residues processed: 428 average time/residue: 0.1689 time to fit residues: 122.0347 Evaluate side-chains 439 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 256 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 602 HIS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 311 PHE Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 448 LYS Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 591 ASP Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 650 LYS Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 760 ASN Chi-restraints excluded: chain E residue 820 PHE Chi-restraints excluded: chain E residue 829 SER Chi-restraints excluded: chain E residue 853 LEU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 334 MET Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 396 VAL Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 406 SER Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain G residue 507 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 219 LYS Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 318 SER Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 371 MET Chi-restraints excluded: chain H residue 418 TYR Chi-restraints excluded: chain H residue 419 LEU Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 492 THR Chi-restraints excluded: chain H residue 520 SER Chi-restraints excluded: chain H residue 521 ASN Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 541 ASP Chi-restraints excluded: chain H residue 556 TYR Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 693 LEU Chi-restraints excluded: chain H residue 781 THR Chi-restraints excluded: chain H residue 801 SER Chi-restraints excluded: chain H residue 814 LEU Chi-restraints excluded: chain H residue 844 VAL Chi-restraints excluded: chain H residue 845 GLU Chi-restraints excluded: chain H residue 849 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 131 optimal weight: 0.6980 chunk 250 optimal weight: 2.9990 chunk 310 optimal weight: 10.0000 chunk 268 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 195 optimal weight: 0.6980 chunk 300 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 ASN ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.089800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.073519 restraints weight = 107574.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.075717 restraints weight = 59352.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.077258 restraints weight = 39504.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.078281 restraints weight = 29517.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.078999 restraints weight = 24094.944| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28950 Z= 0.126 Angle : 0.585 13.350 39176 Z= 0.298 Chirality : 0.042 0.368 4352 Planarity : 0.004 0.058 4919 Dihedral : 10.703 87.964 4078 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.43 % Favored : 92.28 % Rotamer: Outliers : 5.92 % Allowed : 28.73 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.40 (0.15), residues: 3393 helix: 1.15 (0.13), residues: 1803 sheet: -1.19 (0.27), residues: 383 loop : -2.17 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 268 TYR 0.014 0.001 TYR H 762 PHE 0.022 0.001 PHE A 339 TRP 0.017 0.001 TRP E 697 HIS 0.005 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (28947) covalent geometry : angle 0.58477 / 0.30 (39170) SS BOND : bond 0.00242 / 0.11 ( 3) SS BOND : angle 2.37683 / 1.46 ( 6) hydrogen bonds : bond 0.03348 / 2.23 ( 1344) hydrogen bonds : angle 4.65335 / 3.29 ( 3909) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 277 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8994 (mt) REVERT: A 422 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: B 13 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6853 (m-10) REVERT: B 203 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.9035 (mp) REVERT: B 424 MET cc_start: 0.7831 (mtp) cc_final: 0.7468 (mtt) REVERT: B 466 MET cc_start: 0.8167 (tpt) cc_final: 0.7728 (tpt) REVERT: B 590 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7709 (mtmm) REVERT: B 596 ARG cc_start: 0.9033 (ttp80) cc_final: 0.8810 (ttm110) REVERT: B 756 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6211 (mp0) REVERT: D 254 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6598 (mtp85) REVERT: D 278 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6529 (mtpm) REVERT: D 290 ASP cc_start: 0.9121 (t0) cc_final: 0.8775 (t0) REVERT: D 311 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6021 (m-80) REVERT: D 340 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8288 (mm) REVERT: D 372 ASN cc_start: 0.8125 (t0) cc_final: 0.7839 (t0) REVERT: D 432 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8056 (mm) REVERT: D 457 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.6356 (mm) REVERT: D 483 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: E 296 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7539 (tm-30) REVERT: E 394 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: E 418 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7486 (m-10) REVERT: E 486 LYS cc_start: 0.9416 (mmmm) cc_final: 0.9166 (mmmm) REVERT: E 531 GLU cc_start: 0.8180 (pm20) cc_final: 0.7845 (pm20) REVERT: E 694 MET cc_start: 0.7357 (mmm) cc_final: 0.7067 (mmm) REVERT: G 250 GLU cc_start: 0.6796 (mt-10) cc_final: 0.5920 (pm20) REVERT: G 337 GLN cc_start: 0.8500 (tm-30) cc_final: 0.7802 (tm-30) REVERT: H 23 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8748 (ttmm) REVERT: H 39 HIS cc_start: 0.7663 (OUTLIER) cc_final: 0.7291 (p90) REVERT: H 46 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7826 (mt-10) REVERT: H 255 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8264 (mp0) REVERT: H 316 ILE cc_start: 0.8736 (mm) cc_final: 0.8478 (mp) REVERT: H 418 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6480 (m-10) REVERT: H 845 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7986 (pm20) outliers start: 184 outliers final: 132 residues processed: 421 average time/residue: 0.1690 time to fit residues: 118.5712 Evaluate side-chains 415 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 264 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 602 HIS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 311 PHE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 448 LYS Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 591 ASP Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 760 ASN Chi-restraints excluded: chain E residue 820 PHE Chi-restraints excluded: chain E residue 827 ILE Chi-restraints excluded: chain E residue 829 SER Chi-restraints excluded: chain E residue 853 LEU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 334 MET Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 396 VAL Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 406 SER Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 39 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 390 ILE Chi-restraints excluded: chain H residue 418 TYR Chi-restraints excluded: chain H residue 419 LEU Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 520 SER Chi-restraints excluded: chain H residue 521 ASN Chi-restraints excluded: chain H residue 541 ASP Chi-restraints excluded: chain H residue 556 TYR Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 693 LEU Chi-restraints excluded: chain H residue 781 THR Chi-restraints excluded: chain H residue 801 SER Chi-restraints excluded: chain H residue 814 LEU Chi-restraints excluded: chain H residue 844 VAL Chi-restraints excluded: chain H residue 845 GLU Chi-restraints excluded: chain H residue 849 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 288 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 228 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.089314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.073038 restraints weight = 108307.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.075233 restraints weight = 59737.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.076769 restraints weight = 39729.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.077748 restraints weight = 29632.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.078508 restraints weight = 24250.863| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28950 Z= 0.148 Angle : 0.607 13.381 39176 Z= 0.308 Chirality : 0.043 0.312 4352 Planarity : 0.004 0.076 4919 Dihedral : 10.691 87.385 4078 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.78 % Favored : 91.92 % Rotamer: Outliers : 5.66 % Allowed : 28.70 % Favored : 65.64 % 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: -0.40 (0.15), residues: 3393 helix: 1.14 (0.13), residues: 1806 sheet: -1.19 (0.27), residues: 383 loop : -2.16 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 271 TYR 0.020 0.001 TYR A 270 PHE 0.022 0.001 PHE G 248 TRP 0.017 0.001 TRP E 697 HIS 0.004 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (28947) covalent geometry : angle 0.60530 / 0.31 (39170) SS BOND : bond 0.00141 / 0.07 ( 3) SS BOND : angle 4.01421 / 2.35 ( 6) hydrogen bonds : bond 0.03363 / 2.23 ( 1344) hydrogen bonds : angle 4.63429 / 3.27 ( 3909) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 266 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.7630 (mmt180) cc_final: 0.7427 (mmt90) REVERT: A 340 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9064 (mm) REVERT: A 422 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: B 13 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.6875 (m-10) REVERT: B 173 ASN cc_start: 0.7438 (OUTLIER) cc_final: 0.7010 (p0) REVERT: B 203 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9032 (mp) REVERT: B 424 MET cc_start: 0.7838 (mtp) cc_final: 0.7463 (mtt) REVERT: B 466 MET cc_start: 0.8231 (tpt) cc_final: 0.7792 (tpt) REVERT: B 590 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7734 (mtmm) REVERT: B 596 ARG cc_start: 0.9030 (ttp80) cc_final: 0.8803 (ttm110) REVERT: B 756 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6458 (mp0) REVERT: D 278 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6527 (mtpm) REVERT: D 290 ASP cc_start: 0.9123 (t0) cc_final: 0.8776 (t0) REVERT: D 311 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6152 (m-80) REVERT: D 340 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8290 (mm) REVERT: D 372 ASN cc_start: 0.8169 (t0) cc_final: 0.7884 (t0) REVERT: D 432 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8101 (mm) REVERT: D 457 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.6303 (mm) REVERT: D 483 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: E 296 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7494 (tm-30) REVERT: E 394 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: E 418 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7583 (m-10) REVERT: E 486 LYS cc_start: 0.9402 (mmmm) cc_final: 0.9178 (mmmm) REVERT: E 531 GLU cc_start: 0.8198 (pm20) cc_final: 0.7862 (pm20) REVERT: G 250 GLU cc_start: 0.6622 (mt-10) cc_final: 0.5793 (pm20) REVERT: G 252 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7474 (t80) REVERT: G 337 GLN cc_start: 0.8514 (tm-30) cc_final: 0.7860 (tm-30) REVERT: H 23 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8751 (ttmm) REVERT: H 46 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7839 (mt-10) REVERT: H 255 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8288 (mp0) REVERT: H 316 ILE cc_start: 0.8747 (mm) cc_final: 0.8518 (mp) REVERT: H 418 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6521 (m-10) REVERT: H 845 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7982 (pm20) outliers start: 176 outliers final: 141 residues processed: 408 average time/residue: 0.1704 time to fit residues: 117.1663 Evaluate side-chains 422 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 262 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 602 HIS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 311 PHE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 448 LYS Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 650 LYS Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 760 ASN Chi-restraints excluded: chain E residue 820 PHE Chi-restraints excluded: chain E residue 829 SER Chi-restraints excluded: chain E residue 853 LEU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 252 PHE Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 334 MET Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 396 VAL Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 406 SER Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 390 ILE Chi-restraints excluded: chain H residue 418 TYR Chi-restraints excluded: chain H residue 419 LEU Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 520 SER Chi-restraints excluded: chain H residue 521 ASN Chi-restraints excluded: chain H residue 541 ASP Chi-restraints excluded: chain H residue 556 TYR Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 693 LEU Chi-restraints excluded: chain H residue 781 THR Chi-restraints excluded: chain H residue 801 SER Chi-restraints excluded: chain H residue 814 LEU Chi-restraints excluded: chain H residue 844 VAL Chi-restraints excluded: chain H residue 845 GLU Chi-restraints excluded: chain H residue 849 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 213 optimal weight: 0.4980 chunk 220 optimal weight: 0.0570 chunk 37 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 303 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.090281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.073956 restraints weight = 107839.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.076197 restraints weight = 59164.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.077744 restraints weight = 39269.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.078743 restraints weight = 29262.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.079524 restraints weight = 23865.682| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28950 Z= 0.118 Angle : 0.606 13.678 39176 Z= 0.302 Chirality : 0.042 0.366 4352 Planarity : 0.004 0.076 4919 Dihedral : 10.641 87.286 4078 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.31 % Favored : 92.40 % Rotamer: Outliers : 5.02 % Allowed : 29.28 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.29 (0.15), residues: 3393 helix: 1.23 (0.13), residues: 1803 sheet: -1.15 (0.27), residues: 383 loop : -2.11 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 254 TYR 0.017 0.001 TYR A 270 PHE 0.021 0.001 PHE G 248 TRP 0.017 0.001 TRP E 697 HIS 0.005 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (28947) covalent geometry : angle 0.60405 / 0.30 (39170) SS BOND : bond 0.00168 / 0.06 ( 3) SS BOND : angle 3.82865 / 2.24 ( 6) hydrogen bonds : bond 0.03210 / 2.14 ( 1344) hydrogen bonds : angle 4.55189 / 3.22 ( 3909) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 282 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9010 (mt) REVERT: A 422 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: B 13 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.6962 (m-10) REVERT: B 173 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.7061 (p0) REVERT: B 203 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.9018 (mp) REVERT: B 424 MET cc_start: 0.7836 (mtp) cc_final: 0.7474 (mtt) REVERT: B 466 MET cc_start: 0.8266 (tpt) cc_final: 0.7861 (tpt) REVERT: B 590 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7996 (mtmm) REVERT: B 756 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: D 254 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6635 (mtp85) REVERT: D 278 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6522 (mtpm) REVERT: D 290 ASP cc_start: 0.9118 (t0) cc_final: 0.8763 (t0) REVERT: D 311 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6156 (m-80) REVERT: D 340 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8317 (mm) REVERT: D 372 ASN cc_start: 0.8161 (t0) cc_final: 0.7883 (t0) REVERT: D 432 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7944 (mm) REVERT: D 457 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6250 (mm) REVERT: D 483 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: E 296 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7499 (tm-30) REVERT: E 394 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: E 418 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: E 486 LYS cc_start: 0.9411 (mmmm) cc_final: 0.9186 (mmmm) REVERT: E 531 GLU cc_start: 0.8159 (pm20) cc_final: 0.7792 (pm20) REVERT: E 694 MET cc_start: 0.7253 (mmm) cc_final: 0.7018 (mmm) REVERT: G 249 MET cc_start: 0.4557 (mtt) cc_final: 0.3769 (tmm) REVERT: G 250 GLU cc_start: 0.6507 (mt-10) cc_final: 0.6114 (pm20) REVERT: G 252 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7420 (t80) REVERT: G 337 GLN cc_start: 0.8482 (tm-30) cc_final: 0.7825 (tm-30) REVERT: G 506 PHE cc_start: 0.7740 (m-10) cc_final: 0.7504 (m-10) REVERT: H 23 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8764 (ttmm) REVERT: H 39 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.7276 (p90) REVERT: H 46 GLU cc_start: 0.8504 (mt-10) cc_final: 0.7828 (mt-10) REVERT: H 255 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8352 (mp0) REVERT: H 316 ILE cc_start: 0.8725 (mm) cc_final: 0.8524 (mp) REVERT: H 418 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6448 (m-10) REVERT: H 845 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7982 (pm20) outliers start: 156 outliers final: 125 residues processed: 404 average time/residue: 0.1729 time to fit residues: 118.1509 Evaluate side-chains 412 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 266 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 602 HIS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 311 PHE Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 448 LYS Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 760 ASN Chi-restraints excluded: chain E residue 820 PHE Chi-restraints excluded: chain E residue 829 SER Chi-restraints excluded: chain E residue 853 LEU Chi-restraints excluded: chain G residue 252 PHE Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 334 MET Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 406 SER Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 39 HIS Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 390 ILE Chi-restraints excluded: chain H residue 418 TYR Chi-restraints excluded: chain H residue 419 LEU Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 520 SER Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 541 ASP Chi-restraints excluded: chain H residue 556 TYR Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 693 LEU Chi-restraints excluded: chain H residue 781 THR Chi-restraints excluded: chain H residue 801 SER Chi-restraints excluded: chain H residue 814 LEU Chi-restraints excluded: chain H residue 844 VAL Chi-restraints excluded: chain H residue 845 GLU Chi-restraints excluded: chain H residue 849 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 236 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 249 optimal weight: 0.9990 chunk 325 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 210 optimal weight: 0.5980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.090468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.074082 restraints weight = 107160.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.076310 restraints weight = 58948.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.077843 restraints weight = 39215.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.078868 restraints weight = 29275.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.079641 restraints weight = 23863.988| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28950 Z= 0.120 Angle : 0.613 13.406 39176 Z= 0.306 Chirality : 0.043 0.350 4352 Planarity : 0.004 0.077 4919 Dihedral : 10.591 87.509 4072 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.22 % Favored : 92.48 % Rotamer: Outliers : 4.63 % Allowed : 29.79 % Favored : 65.57 % 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: -0.26 (0.15), residues: 3393 helix: 1.27 (0.13), residues: 1800 sheet: -1.15 (0.27), residues: 383 loop : -2.11 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 596 TYR 0.015 0.001 TYR A 270 PHE 0.022 0.001 PHE G 248 TRP 0.017 0.001 TRP E 697 HIS 0.004 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (28947) covalent geometry : angle 0.61175 / 0.31 (39170) SS BOND : bond 0.00106 / 0.04 ( 3) SS BOND : angle 3.59224 / 2.14 ( 6) hydrogen bonds : bond 0.03182 / 2.11 ( 1344) hydrogen bonds : angle 4.53738 / 3.20 ( 3909) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 275 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9026 (mt) REVERT: A 422 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 503 ASP cc_start: 0.7482 (m-30) cc_final: 0.7251 (m-30) REVERT: B 13 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6886 (m-10) REVERT: B 173 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.7026 (p0) REVERT: B 203 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9024 (mp) REVERT: B 424 MET cc_start: 0.7810 (mtp) cc_final: 0.7454 (mtt) REVERT: B 466 MET cc_start: 0.8278 (tpt) cc_final: 0.7876 (tpt) REVERT: B 596 ARG cc_start: 0.9036 (mtp-110) cc_final: 0.8725 (mtp-110) REVERT: B 756 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6335 (mp0) REVERT: D 278 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6446 (mtpm) REVERT: D 290 ASP cc_start: 0.9120 (t0) cc_final: 0.8765 (t0) REVERT: D 311 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6228 (m-80) REVERT: D 340 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8365 (mm) REVERT: D 372 ASN cc_start: 0.8166 (t0) cc_final: 0.7886 (t0) REVERT: D 432 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7955 (mm) REVERT: D 457 ILE cc_start: 0.6625 (OUTLIER) cc_final: 0.6286 (mm) REVERT: D 483 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: E 296 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7471 (tm-30) REVERT: E 394 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: E 418 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7560 (m-10) REVERT: E 486 LYS cc_start: 0.9404 (mmmm) cc_final: 0.9184 (mmmm) REVERT: E 531 GLU cc_start: 0.8183 (pm20) cc_final: 0.7813 (pm20) REVERT: E 694 MET cc_start: 0.7289 (mmm) cc_final: 0.7046 (mmm) REVERT: E 818 LEU cc_start: 0.8732 (tp) cc_final: 0.8497 (pp) REVERT: G 250 GLU cc_start: 0.6543 (mt-10) cc_final: 0.5805 (pm20) REVERT: G 252 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7417 (t80) REVERT: G 337 GLN cc_start: 0.8486 (tm-30) cc_final: 0.7829 (tm-30) REVERT: G 506 PHE cc_start: 0.7529 (m-10) cc_final: 0.7287 (m-10) REVERT: H 23 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8764 (ttmm) REVERT: H 39 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7294 (p90) REVERT: H 46 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7833 (mt-10) REVERT: H 255 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8321 (mp0) REVERT: H 316 ILE cc_start: 0.8720 (mm) cc_final: 0.8518 (mp) REVERT: H 418 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6375 (m-10) REVERT: H 845 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7989 (pm20) outliers start: 144 outliers final: 118 residues processed: 389 average time/residue: 0.1701 time to fit residues: 111.6734 Evaluate side-chains 402 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 265 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 602 HIS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 311 PHE Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 448 LYS Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 760 ASN Chi-restraints excluded: chain E residue 820 PHE Chi-restraints excluded: chain E residue 829 SER Chi-restraints excluded: chain E residue 853 LEU Chi-restraints excluded: chain G residue 252 PHE Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 334 MET Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 39 HIS Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 418 TYR Chi-restraints excluded: chain H residue 419 LEU Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 541 ASP Chi-restraints excluded: chain H residue 556 TYR Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 801 SER Chi-restraints excluded: chain H residue 814 LEU Chi-restraints excluded: chain H residue 844 VAL Chi-restraints excluded: chain H residue 845 GLU Chi-restraints excluded: chain H residue 849 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 300 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 195 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 273 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.090159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.073693 restraints weight = 107633.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.075912 restraints weight = 59299.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.077442 restraints weight = 39454.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.078463 restraints weight = 29492.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.079237 restraints weight = 24115.000| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28950 Z= 0.129 Angle : 0.614 13.354 39176 Z= 0.306 Chirality : 0.043 0.354 4352 Planarity : 0.004 0.077 4919 Dihedral : 10.573 87.126 4070 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.34 % Favored : 92.37 % Rotamer: Outliers : 4.76 % Allowed : 29.86 % Favored : 65.38 % 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: -0.27 (0.15), residues: 3393 helix: 1.24 (0.13), residues: 1806 sheet: -1.12 (0.27), residues: 383 loop : -2.10 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 596 TYR 0.014 0.001 TYR B 166 PHE 0.023 0.001 PHE G 509 TRP 0.017 0.001 TRP E 697 HIS 0.004 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (28947) covalent geometry : angle 0.61208 / 0.31 (39170) SS BOND : bond 0.00112 / 0.05 ( 3) SS BOND : angle 3.48831 / 2.07 ( 6) hydrogen bonds : bond 0.03184 / 2.11 ( 1344) hydrogen bonds : angle 4.52253 / 3.19 ( 3909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5500.60 seconds wall clock time: 96 minutes 29.02 seconds (5789.02 seconds total)