Starting phenix.real_space_refine on Sun Jul 5 17:04:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9whu_65977/07_2026/9whu_65977.cif Found real_map, /net/cci-nas-00/data/ceres_data/9whu_65977/07_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_65977/07_2026/9whu_65977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9whu_65977/07_2026/9whu_65977.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9whu_65977/07_2026/9whu_65977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9whu_65977/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 5.84, per 1000 atoms: 0.21 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: 2.51 Conformation dependent library (CDL) restraints added in 1.3 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: 1.01 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: 5.83 Time building geometry restraints manager: 3.33 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: 9.560 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.800 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- 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 0.63073 / 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 : 1.105 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: 0.1707 time to fit residues: 104.6201 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 : 1.161 ------------------------------------------------------------------------------- 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** ** 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 = 0.4050 r_free = 0.4050 target = 0.089205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.072849 restraints weight = 108993.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.075013 restraints weight = 60465.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.076508 restraints weight = 40525.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.077495 restraints weight = 30473.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.078234 restraints weight = 24955.877| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.0637 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= 0.181 Angle : 0.596 13.498 39176 Z= 0.315 Chirality : 0.043 0.275 4352 Planarity : 0.004 0.060 4919 Dihedral : 11.212 88.475 4175 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.90 % Favored : 91.78 % Rotamer: Outliers : 5.82 % Allowed : 27.70 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 3393 helix: 1.09 (0.12), residues: 1821 sheet: -1.19 (0.27), residues: 381 loop : -2.23 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 405 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 0.00403 / 0.18 (28947) covalent geometry : angle 0.59361 / 0.31 (39170) SS BOND : bond 0.00157 / 0.07 ( 3) SS BOND : angle 3.87834 / 2.31 ( 6) hydrogen bonds : bond 0.04152 / 2.77 ( 1344) hydrogen bonds : angle 5.11174 / 3.60 ( 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 461 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 280 time to evaluate : 1.093 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: 0.3858 (mpp) cc_final: 0.3639 (mpp) REVERT: A 268 ASN cc_start: 0.7747 (m-40) cc_final: 0.7508 (t0) REVERT: A 340 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9012 (mm) REVERT: A 422 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: B 424 MET cc_start: 0.7938 (mtp) cc_final: 0.7547 (mtt) REVERT: B 466 MET cc_start: 0.8159 (tpt) cc_final: 0.7748 (tpt) REVERT: B 596 ARG cc_start: 0.9055 (ttp80) cc_final: 0.8837 (ttm110) REVERT: B 754 PHE cc_start: 0.8415 (t80) cc_final: 0.8128 (t80) REVERT: B 756 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: D 290 ASP cc_start: 0.9126 (t0) cc_final: 0.8765 (t0) REVERT: D 311 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6017 (m-80) REVERT: D 334 MET cc_start: 0.9000 (mmm) cc_final: 0.8557 (mpp) REVERT: D 340 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8292 (mm) REVERT: D 426 GLN cc_start: 0.8715 (pp30) cc_final: 0.8377 (pp30) REVERT: D 463 TYR cc_start: 0.8183 (m-80) cc_final: 0.7688 (t80) REVERT: D 483 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: E 67 MET cc_start: 0.8755 (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: 0.8066 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: E 486 LYS cc_start: 0.9407 (mmmm) cc_final: 0.9160 (mmmm) REVERT: E 531 GLU cc_start: 0.8201 (pm20) cc_final: 0.7841 (pm20) REVERT: E 541 ASP cc_start: 0.8568 (t0) cc_final: 0.8327 (t0) REVERT: E 718 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7863 (p) REVERT: G 249 MET cc_start: 0.6934 (mmp) cc_final: 0.6712 (mmm) REVERT: G 337 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7818 (tm-30) REVERT: G 514 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8442 (tttp) REVERT: H 46 GLU cc_start: 0.8699 (mt-10) cc_final: 0.7919 (mt-10) REVERT: H 53 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: H 255 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8023 (mp0) REVERT: H 394 GLU cc_start: 0.7563 (pm20) cc_final: 0.7252 (pp20) REVERT: H 418 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6477 (m-10) outliers start: 181 outliers final: 115 residues processed: 419 average time/residue: 0.1653 time to fit residues: 116.9144 Evaluate side-chains 391 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 265 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 431 LEU 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 414 THR 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 409 ILE 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 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 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 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: 1.9990 chunk 89 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 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: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 HIS ** 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 E 517 GLN E 649 ASN ** G 337 GLN ** 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 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 761 HIS ** H 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.087578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.071252 restraints weight = 110781.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.073356 restraints weight = 62064.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.074836 restraints weight = 41813.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.075837 restraints weight = 31532.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.076496 restraints weight = 25791.425| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28950 Z= 0.242 Angle : 0.631 13.343 39176 Z= 0.333 Chirality : 0.044 0.322 4352 Planarity : 0.004 0.066 4919 Dihedral : 10.927 89.189 4103 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.28 % Favored : 91.39 % Rotamer: Outliers : 7.11 % Allowed : 26.83 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.15), residues: 3393 helix: 0.85 (0.12), residues: 1842 sheet: -1.31 (0.27), residues: 383 loop : -2.33 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 265 TYR 0.019 0.001 TYR B 166 PHE 0.020 0.002 PHE G 450 TRP 0.021 0.002 TRP E 697 HIS 0.010 0.001 HIS H 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 (28947) covalent geometry : angle 0.62976 / 0.33 (39170) SS BOND : bond 0.00265 / 0.12 ( 3) SS BOND : angle 2.80887 / 1.68 ( 6) hydrogen bonds : bond 0.04124 / 2.75 ( 1344) hydrogen bonds : angle 5.08485 / 3.58 ( 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 491 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 270 time to evaluate : 1.190 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 268 ASN cc_start: 0.7817 (m-40) cc_final: 0.7598 (t0) REVERT: A 340 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9044 (mm) REVERT: B 13 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6973 (m-10) REVERT: B 35 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8489 (mp0) REVERT: B 203 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9077 (mp) REVERT: B 424 MET cc_start: 0.7949 (mtp) cc_final: 0.7576 (mtt) REVERT: B 466 MET cc_start: 0.8171 (tpt) cc_final: 0.7781 (tpt) REVERT: B 590 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7789 (mtmm) REVERT: B 596 ARG cc_start: 0.9077 (ttp80) cc_final: 0.8839 (ttm110) REVERT: B 756 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6403 (mp0) REVERT: D 278 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6550 (mtpm) REVERT: D 290 ASP cc_start: 0.9133 (t0) cc_final: 0.8782 (t0) REVERT: D 309 ASN cc_start: 0.6980 (t0) cc_final: 0.6761 (t0) REVERT: D 311 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.5901 (m-80) REVERT: D 334 MET cc_start: 0.9037 (mmm) cc_final: 0.8576 (mpp) REVERT: D 340 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8359 (mm) REVERT: D 463 TYR cc_start: 0.8212 (m-80) cc_final: 0.7743 (t80) REVERT: D 483 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: E 296 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7556 (tm-30) REVERT: E 394 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: E 418 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7521 (m-10) REVERT: E 486 LYS cc_start: 0.9418 (mmmm) cc_final: 0.9188 (mmmm) REVERT: E 531 GLU cc_start: 0.8225 (pm20) cc_final: 0.7936 (pm20) REVERT: E 541 ASP cc_start: 0.8590 (t0) cc_final: 0.8328 (t0) REVERT: E 718 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7904 (p) REVERT: G 249 MET cc_start: 0.6938 (mmp) cc_final: 0.6646 (mmm) REVERT: G 514 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8454 (tttp) REVERT: H 23 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8792 (ttmm) REVERT: H 46 GLU cc_start: 0.8652 (mt-10) cc_final: 0.7954 (mt-10) REVERT: H 255 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8081 (mp0) REVERT: H 418 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6569 (m-10) REVERT: H 845 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7392 (mt-10) outliers start: 221 outliers final: 156 residues processed: 436 average time/residue: 0.1717 time to fit residues: 125.4506 Evaluate side-chains 429 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 256 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 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 438 SER 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 A residue 497 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 35 GLU 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 234 GLU 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 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 706 ILE 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 411 LEU Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 433 ILE 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 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 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 291 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 382 ASP 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 589 LEU 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 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 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 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 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 G residue 514 LYS 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 88 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 212 THR 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 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 454 ILE Chi-restraints excluded: chain H residue 492 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 329 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 211 optimal weight: 0.0470 chunk 267 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 ASN B 190 GLN 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** G 337 GLN ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN H 710 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.089883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.073621 restraints weight = 107657.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.075835 restraints weight = 59344.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.077369 restraints weight = 39524.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.078421 restraints weight = 29546.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.079176 restraints weight = 23976.089| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28950 Z= 0.119 Angle : 0.567 13.242 39176 Z= 0.293 Chirality : 0.042 0.360 4352 Planarity : 0.004 0.057 4919 Dihedral : 10.805 88.211 4094 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.40 % Favored : 92.31 % Rotamer: Outliers : 5.95 % Allowed : 28.38 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.13 (0.13), residues: 1821 sheet: -1.21 (0.27), residues: 383 loop : -2.21 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 555 TYR 0.014 0.001 TYR H 762 PHE 0.018 0.001 PHE G 248 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 0.00259 / 0.12 (28947) covalent geometry : angle 0.56656 / 0.29 (39170) SS BOND : bond 0.00158 / 0.06 ( 3) SS BOND : angle 1.93942 / 1.16 ( 6) hydrogen bonds : bond 0.03511 / 2.34 ( 1344) hydrogen bonds : angle 4.78082 / 3.37 ( 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 468 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 283 time to evaluate : 1.148 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: 0.9297 (OUTLIER) cc_final: 0.9036 (mt) REVERT: B 13 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6866 (m-10) REVERT: B 424 MET cc_start: 0.7853 (mtp) cc_final: 0.7469 (mtt) REVERT: B 466 MET cc_start: 0.8167 (tpt) cc_final: 0.7824 (tpt) REVERT: B 590 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7717 (mtmm) REVERT: B 596 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8855 (ttm110) REVERT: B 756 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: D 278 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6480 (mtpm) REVERT: D 290 ASP cc_start: 0.9126 (t0) cc_final: 0.8749 (t0) REVERT: D 311 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6047 (m-80) REVERT: D 334 MET cc_start: 0.8965 (mmm) cc_final: 0.8521 (mpp) REVERT: D 340 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8278 (mm) REVERT: D 426 GLN cc_start: 0.8731 (pp30) cc_final: 0.8463 (pp30) REVERT: D 432 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7885 (mm) REVERT: D 444 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8266 (mm-30) REVERT: D 483 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: E 296 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7515 (tm-30) REVERT: E 394 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7640 (tm-30) REVERT: E 486 LYS cc_start: 0.9408 (mmmm) cc_final: 0.9160 (mmmm) REVERT: E 531 GLU cc_start: 0.8173 (pm20) cc_final: 0.7841 (pm20) REVERT: G 249 MET cc_start: 0.6921 (mmp) cc_final: 0.6677 (mmm) REVERT: G 337 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: G 514 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8446 (tttp) REVERT: H 23 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8754 (ttmm) REVERT: H 41 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7853 (p0) REVERT: H 46 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7785 (mt-10) REVERT: H 254 ASP cc_start: 0.7098 (t0) cc_final: 0.6428 (t0) REVERT: H 255 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8169 (mp0) REVERT: H 418 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.6501 (m-10) REVERT: H 845 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7324 (mt-10) outliers start: 185 outliers final: 111 residues processed: 427 average time/residue: 0.1609 time to fit residues: 115.2066 Evaluate side-chains 387 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 259 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 431 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 234 GLU 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 349 SER 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 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 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 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 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 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 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 174 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 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 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 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 747 ILE Chi-restraints excluded: chain E residue 820 PHE Chi-restraints excluded: chain E residue 853 LEU Chi-restraints excluded: chain G residue 253 VAL 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 41 ASN Chi-restraints excluded: chain H residue 109 LEU 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 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 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: 0.5980 chunk 249 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 316 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 312 optimal weight: 0.8980 chunk 324 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 323 ASN ** 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 = 0.4049 r_free = 0.4049 target = 0.089113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.072731 restraints weight = 108662.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.074906 restraints weight = 60264.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.076417 restraints weight = 40303.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.077418 restraints weight = 30205.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.078176 restraints weight = 24723.529| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1065 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= 0.157 Angle : 0.587 13.259 39176 Z= 0.303 Chirality : 0.043 0.275 4352 Planarity : 0.004 0.070 4919 Dihedral : 10.757 87.745 4084 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.93 % Favored : 91.81 % Rotamer: Outliers : 6.05 % Allowed : 28.47 % Favored : 65.48 % 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: 1.12 (0.13), residues: 1806 sheet: -1.21 (0.27), residues: 383 loop : -2.20 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 265 TYR 0.017 0.001 TYR B 166 PHE 0.020 0.001 PHE G 248 TRP 0.017 0.001 TRP E 697 HIS 0.005 0.001 HIS H 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (28947) covalent geometry : angle 0.58494 / 0.30 (39170) SS BOND : bond 0.00204 / 0.10 ( 3) SS BOND : angle 4.46030 / 2.76 ( 6) hydrogen bonds : bond 0.03542 / 2.36 ( 1344) hydrogen bonds : angle 4.76977 / 3.36 ( 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 453 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 265 time to evaluate : 1.244 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 303 MET cc_start: 0.8061 (mmm) cc_final: 0.7858 (mmm) REVERT: A 340 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9038 (mt) REVERT: A 422 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: B 13 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.6953 (m-10) REVERT: B 173 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7107 (p0) REVERT: B 424 MET cc_start: 0.7844 (mtp) cc_final: 0.7479 (mtt) REVERT: B 466 MET cc_start: 0.8171 (tpt) cc_final: 0.7824 (tpt) REVERT: B 590 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7717 (mtmm) REVERT: B 596 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8832 (ttm110) REVERT: B 756 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: D 278 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6517 (mtpm) REVERT: D 290 ASP cc_start: 0.9120 (t0) cc_final: 0.8760 (t0) REVERT: D 311 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6076 (m-80) REVERT: D 334 MET cc_start: 0.8993 (mmm) cc_final: 0.8652 (mpp) REVERT: D 340 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8327 (mm) REVERT: D 432 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8046 (mm) REVERT: D 444 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8356 (mm-30) REVERT: D 483 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: E 296 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7504 (tm-30) REVERT: E 394 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: E 418 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7504 (m-10) REVERT: E 486 LYS cc_start: 0.9413 (mmmm) cc_final: 0.9168 (mmmm) REVERT: E 531 GLU cc_start: 0.8202 (pm20) cc_final: 0.7870 (pm20) REVERT: H 23 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8767 (ttmm) REVERT: H 41 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7898 (p0) REVERT: H 46 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7828 (mt-10) REVERT: H 254 ASP cc_start: 0.7142 (t0) cc_final: 0.6813 (t0) REVERT: H 255 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8312 (mp0) REVERT: H 418 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6530 (m-10) outliers start: 188 outliers final: 136 residues processed: 409 average time/residue: 0.1688 time to fit residues: 115.8744 Evaluate side-chains 413 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 260 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 139 ILE Chi-restraints excluded: chain B residue 173 ASN 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 234 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 ILE 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 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 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 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 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 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 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 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 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 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 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 88 LEU 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 305 optimal weight: 0.7980 chunk 284 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 285 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 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** ** 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 = 0.4048 r_free = 0.4048 target = 0.089142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.072388 restraints weight = 111117.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.074615 restraints weight = 61758.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.076175 restraints weight = 41346.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.077204 restraints weight = 31126.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.077926 restraints weight = 25494.746| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28950 Z= 0.161 Angle : 0.590 13.327 39176 Z= 0.304 Chirality : 0.043 0.334 4352 Planarity : 0.004 0.072 4919 Dihedral : 10.733 87.742 4082 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.84 % Favored : 91.90 % Rotamer: Outliers : 6.60 % Allowed : 28.09 % Favored : 65.32 % 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: -0.46 (0.15), residues: 3393 helix: 1.10 (0.13), residues: 1806 sheet: -1.23 (0.27), residues: 383 loop : -2.20 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.022 0.001 TYR H 505 PHE 0.019 0.001 PHE G 248 TRP 0.017 0.001 TRP E 697 HIS 0.005 0.001 HIS H 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (28947) covalent geometry : angle 0.58873 / 0.30 (39170) SS BOND : bond 0.00262 / 0.12 ( 3) SS BOND : angle 3.15017 / 1.92 ( 6) hydrogen bonds : bond 0.03492 / 2.32 ( 1344) hydrogen bonds : angle 4.73791 / 3.34 ( 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 472 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 267 time to evaluate : 1.152 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: A 248 PHE cc_start: 0.5953 (OUTLIER) cc_final: 0.5719 (m-10) REVERT: A 340 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9026 (mt) REVERT: A 422 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: B 13 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.6967 (m-10) REVERT: B 173 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.7072 (p0) REVERT: B 203 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9028 (mp) REVERT: B 424 MET cc_start: 0.7866 (mtp) cc_final: 0.7477 (mtt) REVERT: B 466 MET cc_start: 0.8177 (tpt) cc_final: 0.7689 (tpt) REVERT: B 590 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7740 (mtmm) REVERT: B 596 ARG cc_start: 0.9079 (ttp80) cc_final: 0.8827 (ttm110) REVERT: B 756 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6291 (mp0) REVERT: D 278 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6515 (mtpm) REVERT: D 290 ASP cc_start: 0.9120 (t0) cc_final: 0.8766 (t0) REVERT: D 311 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6121 (m-80) REVERT: D 334 MET cc_start: 0.9020 (mmm) cc_final: 0.8704 (mpp) REVERT: D 340 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8359 (mm) REVERT: D 372 ASN cc_start: 0.8153 (t0) cc_final: 0.7832 (t0) REVERT: D 426 GLN cc_start: 0.8725 (pp30) cc_final: 0.8422 (pp30) REVERT: D 432 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8107 (mm) REVERT: D 457 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.6362 (mm) REVERT: D 483 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: E 296 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7508 (tm-30) REVERT: E 394 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: E 418 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7556 (m-10) REVERT: E 486 LYS cc_start: 0.9426 (mmmm) cc_final: 0.9186 (mmmm) REVERT: E 531 GLU cc_start: 0.8201 (pm20) cc_final: 0.7871 (pm20) REVERT: H 23 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8770 (ttmm) REVERT: H 41 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7859 (p0) REVERT: H 46 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7840 (mt-10) REVERT: H 254 ASP cc_start: 0.7128 (t0) cc_final: 0.6807 (t0) REVERT: H 255 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8313 (mp0) REVERT: H 418 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.6585 (m-10) REVERT: H 424 MET cc_start: 0.8470 (mpp) cc_final: 0.8262 (mpp) outliers start: 205 outliers final: 152 residues processed: 421 average time/residue: 0.1616 time to fit residues: 113.9335 Evaluate side-chains 430 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 259 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 391 SER 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 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 234 GLU 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 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 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 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 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 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 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 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 291 SER 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 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 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 451 ILE 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 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 88 LEU 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 143 MET 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 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 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 520 SER Chi-restraints excluded: chain H residue 521 ASN Chi-restraints excluded: chain H residue 524 ASP 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 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: 0.9980 chunk 250 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 268 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 300 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN H 837 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.089492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.073094 restraints weight = 107718.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.075284 restraints weight = 59803.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.076809 restraints weight = 39985.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.077800 restraints weight = 29979.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.078559 restraints weight = 24543.588| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28950 Z= 0.140 Angle : 0.584 13.433 39176 Z= 0.299 Chirality : 0.042 0.271 4352 Planarity : 0.004 0.074 4919 Dihedral : 10.713 87.771 4082 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.75 % Favored : 91.95 % Rotamer: Outliers : 6.02 % Allowed : 28.41 % 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: -0.41 (0.15), residues: 3393 helix: 1.16 (0.13), residues: 1803 sheet: -1.21 (0.27), residues: 383 loop : -2.19 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 268 TYR 0.029 0.001 TYR H 505 PHE 0.023 0.001 PHE A 339 TRP 0.018 0.001 TRP E 697 HIS 0.005 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (28947) covalent geometry : angle 0.58279 / 0.30 (39170) SS BOND : bond 0.00193 / 0.08 ( 3) SS BOND : angle 2.52107 / 1.54 ( 6) hydrogen bonds : bond 0.03382 / 2.25 ( 1344) hydrogen bonds : angle 4.66595 / 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 460 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 273 time to evaluate : 1.188 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: 0.7616 (mmt180) cc_final: 0.7411 (mmt90) REVERT: A 340 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9008 (mt) REVERT: A 422 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: B 13 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6922 (m-10) REVERT: B 173 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.7074 (p0) REVERT: B 203 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.9046 (mp) REVERT: B 424 MET cc_start: 0.7846 (mtp) cc_final: 0.7469 (mtt) REVERT: B 466 MET cc_start: 0.8168 (tpt) cc_final: 0.7705 (tpt) REVERT: B 590 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7710 (mtmm) REVERT: B 596 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8817 (ttm110) REVERT: B 694 MET cc_start: 0.7118 (mmm) cc_final: 0.6867 (mmm) REVERT: B 756 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: D 254 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6670 (mtp85) REVERT: D 278 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6536 (mtpm) REVERT: D 290 ASP cc_start: 0.9121 (t0) cc_final: 0.8774 (t0) REVERT: D 311 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6186 (m-80) REVERT: D 340 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8313 (mm) REVERT: D 372 ASN cc_start: 0.8150 (t0) cc_final: 0.7835 (t0) REVERT: D 432 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8092 (mm) REVERT: D 457 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6314 (mm) REVERT: D 483 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: E 296 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7500 (tm-30) REVERT: E 394 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: E 418 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7563 (m-10) REVERT: E 486 LYS cc_start: 0.9407 (mmmm) cc_final: 0.9169 (mmmm) REVERT: E 531 GLU cc_start: 0.8190 (pm20) cc_final: 0.7856 (pm20) REVERT: E 694 MET cc_start: 0.7335 (mmm) cc_final: 0.7049 (mmm) REVERT: G 250 GLU cc_start: 0.6864 (mt-10) cc_final: 0.5931 (pm20) REVERT: H 23 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8769 (ttmm) REVERT: H 41 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7830 (p0) REVERT: H 46 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7821 (mt-10) REVERT: H 254 ASP cc_start: 0.7119 (t0) cc_final: 0.6890 (t0) REVERT: H 418 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6450 (m-10) REVERT: H 424 MET cc_start: 0.8413 (mpp) cc_final: 0.8027 (mpp) REVERT: H 845 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8007 (pm20) outliers start: 187 outliers final: 136 residues processed: 420 average time/residue: 0.1631 time to fit residues: 115.1347 Evaluate side-chains 414 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 258 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 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 234 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 349 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 403 ILE Chi-restraints excluded: chain B residue 493 LEU 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 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 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 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 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 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 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 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 351 SER 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 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 88 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 171 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 253 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 318 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 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 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 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: 7.9990 chunk 74 optimal weight: 8.9990 chunk 288 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 228 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 211 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 323 ASN ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN H 837 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.088932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.072183 restraints weight = 111351.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.074402 restraints weight = 61631.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.075951 restraints weight = 41249.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.076987 restraints weight = 31032.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.077734 restraints weight = 25326.603| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28950 Z= 0.178 Angle : 0.619 13.417 39176 Z= 0.315 Chirality : 0.043 0.351 4352 Planarity : 0.004 0.077 4919 Dihedral : 10.732 87.623 4081 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.08 % Favored : 91.63 % Rotamer: Outliers : 6.34 % Allowed : 28.15 % Favored : 65.51 % 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 (0.13), residues: 1806 sheet: -1.25 (0.27), residues: 383 loop : -2.20 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 265 TYR 0.023 0.001 TYR H 505 PHE 0.022 0.002 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 0.00404 / 0.18 (28947) covalent geometry : angle 0.61733 / 0.31 (39170) SS BOND : bond 0.00205 / 0.10 ( 3) SS BOND : angle 4.07314 / 2.37 ( 6) hydrogen bonds : bond 0.03488 / 2.31 ( 1344) hydrogen bonds : angle 4.71629 / 3.33 ( 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 456 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 259 time to evaluate : 0.909 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: A 303 MET cc_start: 0.8347 (mmm) cc_final: 0.8116 (mmm) REVERT: A 340 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9081 (mm) REVERT: A 422 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: B 13 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6890 (m-10) REVERT: B 173 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.7037 (p0) REVERT: B 203 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9037 (mp) REVERT: B 424 MET cc_start: 0.7866 (mtp) cc_final: 0.7478 (mtt) REVERT: B 466 MET cc_start: 0.8161 (tpt) cc_final: 0.7702 (tpt) REVERT: B 590 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7752 (mtmm) REVERT: B 596 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8822 (ttm110) REVERT: B 694 MET cc_start: 0.7308 (mmm) cc_final: 0.7054 (mmm) REVERT: B 756 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: D 254 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6744 (mtp85) REVERT: D 278 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6546 (mtpm) REVERT: D 290 ASP cc_start: 0.9126 (t0) cc_final: 0.8778 (t0) REVERT: D 311 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6215 (m-10) REVERT: D 334 MET cc_start: 0.8932 (mmm) cc_final: 0.8678 (mpp) REVERT: D 372 ASN cc_start: 0.8166 (t0) cc_final: 0.7859 (t0) REVERT: D 426 GLN cc_start: 0.8700 (pp30) cc_final: 0.8413 (pp30) REVERT: D 432 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8122 (mm) REVERT: D 457 ILE cc_start: 0.6598 (OUTLIER) cc_final: 0.6341 (mm) REVERT: D 483 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: E 296 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7495 (tm-30) REVERT: E 394 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: E 418 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7591 (m-10) REVERT: E 486 LYS cc_start: 0.9402 (mmmm) cc_final: 0.9182 (mmmm) REVERT: E 531 GLU cc_start: 0.8196 (pm20) cc_final: 0.7896 (pm20) REVERT: E 718 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7992 (p) REVERT: G 250 GLU cc_start: 0.6867 (mt-10) cc_final: 0.5910 (pm20) REVERT: G 252 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7288 (t80) REVERT: H 23 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8778 (ttmm) REVERT: H 39 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7289 (p90) REVERT: H 41 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7806 (p0) REVERT: H 46 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7821 (mt-10) REVERT: H 254 ASP cc_start: 0.7107 (t0) cc_final: 0.6445 (t0) REVERT: H 255 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8200 (mp0) REVERT: H 418 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6444 (m-10) REVERT: H 424 MET cc_start: 0.8403 (mpp) cc_final: 0.8173 (mpp) REVERT: H 845 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8033 (pm20) outliers start: 197 outliers final: 153 residues processed: 414 average time/residue: 0.1536 time to fit residues: 107.2644 Evaluate side-chains 431 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 256 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 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 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 234 GLU 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 324 LEU 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 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 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 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 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 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 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 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 G residue 247 ASP Chi-restraints excluded: chain G residue 252 PHE 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 451 ILE 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 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 39 HIS Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 88 LEU 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 171 ILE Chi-restraints excluded: chain H residue 184 THR 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 318 SER Chi-restraints excluded: chain H residue 338 SER 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 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 839 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: 0.9990 chunk 73 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 303 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** ** 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 = 0.4069 r_free = 0.4069 target = 0.090006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.073570 restraints weight = 108011.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.075783 restraints weight = 59612.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.077326 restraints weight = 39693.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.078381 restraints weight = 29689.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.079122 restraints weight = 24064.139| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28950 Z= 0.125 Angle : 0.607 13.311 39176 Z= 0.304 Chirality : 0.042 0.336 4352 Planarity : 0.004 0.077 4919 Dihedral : 10.673 87.630 4079 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.69 % Favored : 92.01 % Rotamer: Outliers : 5.21 % Allowed : 29.15 % 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: -0.35 (0.15), residues: 3393 helix: 1.20 (0.13), residues: 1803 sheet: -1.20 (0.27), residues: 383 loop : -2.14 (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 0.023 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 0.00281 / 0.13 (28947) covalent geometry : angle 0.60498 / 0.30 (39170) SS BOND : bond 0.00142 / 0.06 ( 3) SS BOND : angle 3.59203 / 2.11 ( 6) hydrogen bonds : bond 0.03300 / 2.20 ( 1344) hydrogen bonds : angle 4.61105 / 3.26 ( 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 433 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 271 time to evaluate : 1.118 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 255 MET cc_start: 0.3178 (mpp) cc_final: 0.2914 (mpp) REVERT: A 303 MET cc_start: 0.8374 (mmm) cc_final: 0.8127 (mmm) REVERT: A 340 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9029 (mt) REVERT: A 422 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: B 13 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6953 (m-10) REVERT: B 203 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9018 (mp) REVERT: B 424 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7445 (mtt) REVERT: B 466 MET cc_start: 0.8258 (tpt) cc_final: 0.7831 (tpt) REVERT: B 590 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8004 (mtmm) REVERT: B 756 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: D 254 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6678 (mtp85) REVERT: D 278 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6531 (mtpm) REVERT: D 290 ASP cc_start: 0.9123 (t0) cc_final: 0.8764 (t0) REVERT: D 311 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6477 (m-10) REVERT: D 340 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8336 (mm) REVERT: D 372 ASN cc_start: 0.8172 (t0) cc_final: 0.7893 (t0) REVERT: D 426 GLN cc_start: 0.8705 (pp30) cc_final: 0.8400 (pp30) REVERT: D 432 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7960 (mm) REVERT: D 457 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6238 (mm) REVERT: D 483 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: E 296 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7516 (tm-30) REVERT: E 394 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: E 418 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7493 (m-10) REVERT: E 486 LYS cc_start: 0.9412 (mmmm) cc_final: 0.9173 (mmmm) REVERT: E 531 GLU cc_start: 0.8167 (pm20) cc_final: 0.7821 (pm20) REVERT: E 694 MET cc_start: 0.7270 (mmm) cc_final: 0.7031 (mmm) REVERT: G 250 GLU cc_start: 0.6744 (mt-10) cc_final: 0.5901 (pm20) REVERT: G 252 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7204 (t80) REVERT: G 254 ARG cc_start: 0.7215 (pmt170) cc_final: 0.6856 (pmt170) REVERT: G 506 PHE cc_start: 0.7702 (m-10) cc_final: 0.7461 (m-10) REVERT: H 23 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8768 (ttmm) REVERT: H 39 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7313 (p90) REVERT: H 46 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7799 (mt-10) REVERT: H 254 ASP cc_start: 0.7091 (t0) cc_final: 0.6687 (t0) REVERT: H 255 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8389 (mt-10) REVERT: H 418 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6359 (m-10) REVERT: H 424 MET cc_start: 0.8392 (mpp) cc_final: 0.8190 (mpp) REVERT: H 845 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7988 (pm20) outliers start: 162 outliers final: 126 residues processed: 400 average time/residue: 0.1699 time to fit residues: 113.2978 Evaluate side-chains 409 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 262 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 481 VAL Chi-restraints excluded: chain B residue 13 PHE 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 234 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 324 LEU 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 424 MET 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 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 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 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 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 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 G residue 247 ASP 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 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 451 ILE Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 473 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 88 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 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 338 SER 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 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: 2.9990 chunk 183 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 325 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 160 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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** ** G 337 GLN ** 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 = 0.4065 r_free = 0.4065 target = 0.089804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.073172 restraints weight = 109585.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.075398 restraints weight = 60660.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.076949 restraints weight = 40653.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.077983 restraints weight = 30566.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.078748 restraints weight = 24993.665| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1374 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= 0.140 Angle : 0.622 13.451 39176 Z= 0.312 Chirality : 0.042 0.322 4352 Planarity : 0.004 0.078 4919 Dihedral : 10.637 87.065 4076 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.54 % Favored : 92.13 % Rotamer: Outliers : 5.02 % Allowed : 29.47 % Favored : 65.51 % 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: -0.32 (0.15), residues: 3393 helix: 1.22 (0.13), residues: 1803 sheet: -1.16 (0.27), residues: 383 loop : -2.14 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 405 TYR 0.014 0.001 TYR B 166 PHE 0.023 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 0.00318 / 0.14 (28947) covalent geometry : angle 0.62090 / 0.31 (39170) SS BOND : bond 0.00173 / 0.07 ( 3) SS BOND : angle 3.57881 / 2.09 ( 6) hydrogen bonds : bond 0.03295 / 2.19 ( 1344) hydrogen bonds : angle 4.60469 / 3.25 ( 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 418 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 262 time to evaluate : 0.863 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 308 ARG cc_start: 0.7612 (mmt90) cc_final: 0.7376 (mmt90) REVERT: A 340 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9075 (mm) REVERT: B 13 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6967 (m-10) REVERT: B 203 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.9023 (mp) REVERT: B 424 MET cc_start: 0.7816 (mtp) cc_final: 0.7441 (mtt) REVERT: B 466 MET cc_start: 0.8268 (tpt) cc_final: 0.7836 (tpt) REVERT: B 596 ARG cc_start: 0.9082 (mtp-110) cc_final: 0.8765 (mtp-110) REVERT: B 756 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: D 254 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6645 (mtp85) REVERT: D 278 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6525 (mtpm) REVERT: D 290 ASP cc_start: 0.9124 (t0) cc_final: 0.8772 (t0) REVERT: D 311 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6578 (m-10) REVERT: D 340 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8383 (mm) REVERT: D 372 ASN cc_start: 0.8175 (t0) cc_final: 0.7900 (t0) REVERT: D 426 GLN cc_start: 0.8730 (pp30) cc_final: 0.8420 (pp30) REVERT: D 432 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8071 (mm) REVERT: D 457 ILE cc_start: 0.6587 (OUTLIER) cc_final: 0.6330 (mm) REVERT: D 483 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: E 296 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7511 (tm-30) REVERT: E 346 GLU cc_start: 0.8085 (pp20) cc_final: 0.7735 (pp20) REVERT: E 394 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: E 418 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7588 (m-10) REVERT: E 486 LYS cc_start: 0.9429 (mmmm) cc_final: 0.9210 (mmmm) REVERT: E 531 GLU cc_start: 0.8179 (pm20) cc_final: 0.7831 (pm20) REVERT: E 694 MET cc_start: 0.7293 (mmm) cc_final: 0.7043 (mmm) REVERT: G 250 GLU cc_start: 0.6830 (mt-10) cc_final: 0.5823 (pm20) REVERT: G 252 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7187 (t80) REVERT: G 254 ARG cc_start: 0.7218 (pmt170) cc_final: 0.6846 (pmt170) REVERT: G 506 PHE cc_start: 0.7772 (m-10) cc_final: 0.7540 (m-10) REVERT: H 23 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8767 (ttmm) REVERT: H 39 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.7344 (p90) REVERT: H 46 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7815 (mt-10) REVERT: H 254 ASP cc_start: 0.7091 (t0) cc_final: 0.6704 (t0) REVERT: H 255 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8398 (mt-10) REVERT: H 418 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6361 (m-10) REVERT: H 845 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8007 (pm20) outliers start: 156 outliers final: 129 residues processed: 387 average time/residue: 0.1553 time to fit residues: 100.7843 Evaluate side-chains 404 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 257 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 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 431 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain B residue 13 PHE 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 234 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 324 LEU 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 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 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 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 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 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 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 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 G residue 247 ASP 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 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 451 ILE Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 473 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 88 LEU 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 353 LEU Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 390 ILE 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 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 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: 2.9990 chunk 156 optimal weight: 1.9990 chunk 249 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 195 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 273 optimal weight: 0.8980 chunk 270 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** D 413 ASN ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 796 GLN ** 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 = 0.4026 r_free = 0.4026 target = 0.088080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.071496 restraints weight = 111284.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.073667 restraints weight = 62454.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.075143 restraints weight = 42175.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.076134 restraints weight = 31904.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.076874 restraints weight = 26293.642| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28950 Z= 0.213 Angle : 0.672 13.502 39176 Z= 0.342 Chirality : 0.044 0.341 4352 Planarity : 0.004 0.079 4919 Dihedral : 10.714 87.399 4076 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.66 % Favored : 90.98 % Rotamer: Outliers : 5.24 % Allowed : 29.28 % Favored : 65.48 % 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: -0.61 (0.15), residues: 3393 helix: 0.95 (0.12), residues: 1821 sheet: -1.27 (0.27), residues: 383 loop : -2.27 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 596 TYR 0.026 0.001 TYR B 166 PHE 0.025 0.002 PHE G 248 TRP 0.016 0.002 TRP E 697 HIS 0.029 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (28947) covalent geometry : angle 0.67059 / 0.34 (39170) SS BOND : bond 0.00264 / 0.13 ( 3) SS BOND : angle 3.35584 / 1.96 ( 6) hydrogen bonds : bond 0.03639 / 2.41 ( 1344) hydrogen bonds : angle 4.77833 / 3.36 ( 3909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5513.50 seconds wall clock time: 96 minutes 42.56 seconds (5802.56 seconds total)