Starting phenix.real_space_refine on Tue Jul 7 05:31:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gj6_51383/07_2026/9gj6_51383.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gj6_51383/07_2026/9gj6_51383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gj6_51383/07_2026/9gj6_51383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gj6_51383/07_2026/9gj6_51383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gj6_51383/07_2026/9gj6_51383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gj6_51383/07_2026/9gj6_51383.map" } resolution = 3.91 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= -0.001 sd= 0.115 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 622 5.49 5 S 152 5.16 5 C 24931 2.51 5 N 7912 2.21 5 O 9671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s 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: 43288 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1496 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 6, 'TRANS': 177} Chain: "D" Number of atoms: 6874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6874 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 28, 'TRANS': 804} Chain: "1" Number of atoms: 11798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 11798 Classifications: {'RNA': 552} Modifications used: {'rna2p_pur': 53, 'rna2p_pyr': 55, 'rna3p_pur': 230, 'rna3p_pyr': 214} Link IDs: {'rna2p': 108, 'rna3p': 443} Chain breaks: 10 Chain: "8" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1237 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 22, 'rna3p_pyr': 22} Link IDs: {'rna2p': 14, 'rna3p': 43} Chain: "LC" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2908 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 18, 'TRANS': 346} Chain: "LE" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1724 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Chain: "Lk" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "LY" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1075 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "Lh" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "LX" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 950 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 107} Chain: "LR" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1281 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain: "Lr" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "B" Number of atoms: 6914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 839, 6914 Classifications: {'peptide': 839} Link IDs: {'PTRANS': 30, 'TRANS': 808} Chain: "C" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1444 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "LU" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 799 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "Ld" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "LP" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.28, per 1000 atoms: 0.19 Number of scatterers: 43288 At special positions: 0 Unit cell: (215.248, 227.478, 254.384, 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 152 16.00 P 622 15.00 O 9671 8.00 N 7912 7.00 C 24931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.4 seconds 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7066 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 22 sheets defined 62.6% alpha, 7.5% beta 180 base pairs and 283 stacking pairs defined. Time for finding SS restraints: 5.91 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 removed outlier: 3.874A pdb=" N MET A 12 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 38 removed outlier: 3.508A pdb=" N TYR A 31 " --> pdb=" O GLN A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 82 Processing helix chain 'A' and resid 85 through 103 Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 151 through 178 removed outlier: 4.261A pdb=" N ASP A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.513A pdb=" N ARG D 19 " --> pdb=" O LYS D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 37 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'D' and resid 61 through 76 removed outlier: 3.503A pdb=" N ALA D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 95 through 110 removed outlier: 3.506A pdb=" N ALA D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP D 109 " --> pdb=" O ASN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 127 removed outlier: 3.655A pdb=" N LEU D 122 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 144 Processing helix chain 'D' and resid 147 through 161 removed outlier: 3.861A pdb=" N TRP D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR D 158 " --> pdb=" O TYR D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 178 removed outlier: 3.713A pdb=" N ALA D 167 " --> pdb=" O ASP D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 203 Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.800A pdb=" N GLU D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.641A pdb=" N GLU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 235 " --> pdb=" O GLY D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 254 Processing helix chain 'D' and resid 257 through 269 removed outlier: 4.071A pdb=" N TYR D 261 " --> pdb=" O ASN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 287 removed outlier: 4.329A pdb=" N LEU D 277 " --> pdb=" O MET D 273 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 278 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 296 through 301 removed outlier: 4.377A pdb=" N PHE D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 321 Processing helix chain 'D' and resid 324 through 330 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 335 through 357 Processing helix chain 'D' and resid 369 through 387 removed outlier: 3.905A pdb=" N LEU D 373 " --> pdb=" O PRO D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 403 removed outlier: 3.621A pdb=" N GLU D 402 " --> pdb=" O ASN D 398 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 403 " --> pdb=" O THR D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 422 removed outlier: 3.716A pdb=" N LEU D 412 " --> pdb=" O ILE D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 438 removed outlier: 3.676A pdb=" N ASP D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 455 removed outlier: 3.677A pdb=" N ASN D 445 " --> pdb=" O ASP D 441 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 450 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR D 451 " --> pdb=" O LYS D 447 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET D 452 " --> pdb=" O CYS D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 467 removed outlier: 3.874A pdb=" N ALA D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 463 " --> pdb=" O LYS D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 482 Processing helix chain 'D' and resid 484 through 498 removed outlier: 3.523A pdb=" N ALA D 497 " --> pdb=" O GLN D 493 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 522 removed outlier: 3.592A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN D 522 " --> pdb=" O ILE D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 533 removed outlier: 4.366A pdb=" N MET D 530 " --> pdb=" O HIS D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 547 removed outlier: 3.763A pdb=" N LYS D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 550 No H-bonds generated for 'chain 'D' and resid 548 through 550' Processing helix chain 'D' and resid 551 through 571 removed outlier: 3.595A pdb=" N PHE D 555 " --> pdb=" O HIS D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 586 removed outlier: 3.673A pdb=" N GLU D 579 " --> pdb=" O ASP D 575 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 585 " --> pdb=" O GLU D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 626 Processing helix chain 'D' and resid 643 through 649 Processing helix chain 'D' and resid 653 through 667 removed outlier: 3.593A pdb=" N LYS D 659 " --> pdb=" O GLU D 655 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Proline residue: D 663 - end of helix Processing helix chain 'D' and resid 671 through 686 removed outlier: 4.031A pdb=" N HIS D 675 " --> pdb=" O LYS D 671 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 684 " --> pdb=" O GLU D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 700 removed outlier: 3.567A pdb=" N GLN D 693 " --> pdb=" O LEU D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 717 removed outlier: 3.502A pdb=" N GLU D 710 " --> pdb=" O PRO D 706 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE D 713 " --> pdb=" O HIS D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 723 removed outlier: 3.597A pdb=" N GLU D 721 " --> pdb=" O ASN D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 742 removed outlier: 3.542A pdb=" N ASN D 738 " --> pdb=" O LYS D 734 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG D 739 " --> pdb=" O GLN D 735 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 740 " --> pdb=" O GLU D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 757 Processing helix chain 'D' and resid 760 through 775 removed outlier: 3.517A pdb=" N TYR D 772 " --> pdb=" O ALA D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 788 Processing helix chain 'D' and resid 797 through 810 Processing helix chain 'D' and resid 816 through 831 removed outlier: 3.918A pdb=" N LEU D 830 " --> pdb=" O ASN D 826 " (cutoff:3.500A) Processing helix chain 'LC' and resid 25 through 30 Processing helix chain 'LC' and resid 33 through 45 removed outlier: 3.609A pdb=" N PHELC 39 " --> pdb=" O ASPLC 35 " (cutoff:3.500A) Processing helix chain 'LC' and resid 116 through 131 removed outlier: 3.734A pdb=" N ILELC 124 " --> pdb=" O LYSLC 120 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYSLC 125 " --> pdb=" O ARGLC 121 " (cutoff:3.500A) Processing helix chain 'LC' and resid 133 through 140 removed outlier: 3.576A pdb=" N VALLC 137 " --> pdb=" O LEULC 133 " (cutoff:3.500A) Processing helix chain 'LC' and resid 156 through 161 Processing helix chain 'LC' and resid 163 through 174 removed outlier: 3.579A pdb=" N ALALC 167 " --> pdb=" O LYSLC 163 " (cutoff:3.500A) Processing helix chain 'LC' and resid 177 through 186 Processing helix chain 'LC' and resid 192 through 198 removed outlier: 3.748A pdb=" N ASNLC 198 " --> pdb=" O LYSLC 195 " (cutoff:3.500A) Processing helix chain 'LC' and resid 216 through 222 removed outlier: 3.773A pdb=" N PHELC 221 " --> pdb=" O ILELC 217 " (cutoff:3.500A) Processing helix chain 'LC' and resid 236 through 241 Processing helix chain 'LC' and resid 254 through 259 removed outlier: 3.543A pdb=" N ARGLC 258 " --> pdb=" O GLULC 254 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYSLC 259 " --> pdb=" O SERLC 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 254 through 259' Processing helix chain 'LC' and resid 259 through 265 Processing helix chain 'LC' and resid 288 through 294 Processing helix chain 'LC' and resid 295 through 300 removed outlier: 3.612A pdb=" N ARGLC 300 " --> pdb=" O PROLC 296 " (cutoff:3.500A) Processing helix chain 'LC' and resid 321 through 329 removed outlier: 3.679A pdb=" N METLC 325 " --> pdb=" O ASNLC 321 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEULC 326 " --> pdb=" O LEULC 322 " (cutoff:3.500A) Processing helix chain 'LC' and resid 331 through 368 removed outlier: 3.573A pdb=" N ALALC 355 " --> pdb=" O VALLC 351 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SERLC 365 " --> pdb=" O LEULC 361 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASPLC 366 " --> pdb=" O GLNLC 362 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLULC 367 " --> pdb=" O ALALC 363 " (cutoff:3.500A) Processing helix chain 'LE' and resid 58 through 66 removed outlier: 3.750A pdb=" N TYRLE 63 " --> pdb=" O ARGLE 59 " (cutoff:3.500A) Processing helix chain 'LE' and resid 132 through 136 Processing helix chain 'LE' and resid 178 through 183 Processing helix chain 'LE' and resid 190 through 192 No H-bonds generated for 'chain 'LE' and resid 190 through 192' Processing helix chain 'LE' and resid 213 through 218 Processing helix chain 'LE' and resid 243 through 264 removed outlier: 3.923A pdb=" N GLNLE 256 " --> pdb=" O ALALE 252 " (cutoff:3.500A) Proline residue: LE 259 - end of helix removed outlier: 3.526A pdb=" N ALALE 263 " --> pdb=" O PROLE 259 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILELE 264 " --> pdb=" O LYSLE 260 " (cutoff:3.500A) Processing helix chain 'LE' and resid 266 through 273 Processing helix chain 'Lk' and resid 7 through 16 Processing helix chain 'Lk' and resid 49 through 59 removed outlier: 3.628A pdb=" N ALALk 53 " --> pdb=" O ASPLk 49 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLNLk 58 " --> pdb=" O GLULk 54 " (cutoff:3.500A) Processing helix chain 'LY' and resid 10 through 20 Processing helix chain 'LY' and resid 22 through 30 Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 75 through 78 Processing helix chain 'LY' and resid 100 through 102 No H-bonds generated for 'chain 'LY' and resid 100 through 102' Processing helix chain 'LY' and resid 112 through 129 removed outlier: 4.118A pdb=" N LYSLY 117 " --> pdb=" O LYSLY 113 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VALLY 128 " --> pdb=" O LYSLY 124 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLYLY 129 " --> pdb=" O SERLY 125 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 10 removed outlier: 3.766A pdb=" N LEULh 9 " --> pdb=" O LYSLh 5 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARGLh 10 " --> pdb=" O ALALh 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lh' and resid 5 through 10' Processing helix chain 'Lh' and resid 13 through 37 removed outlier: 3.653A pdb=" N LEULh 28 " --> pdb=" O LEULh 24 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VALLh 36 " --> pdb=" O ARGLh 32 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THRLh 37 " --> pdb=" O VALLh 33 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 40 through 45 Processing helix chain 'Lh' and resid 45 through 73 removed outlier: 4.266A pdb=" N VALLh 49 " --> pdb=" O SERLh 45 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASNLh 68 " --> pdb=" O THRLh 64 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEULh 69 " --> pdb=" O GLNLh 65 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 90 through 94 removed outlier: 3.564A pdb=" N ARGLh 94 " --> pdb=" O METLh 91 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 96 through 101 removed outlier: 3.743A pdb=" N GLULh 100 " --> pdb=" O ASNLh 96 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASNLh 101 " --> pdb=" O LYSLh 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lh' and resid 96 through 101' Processing helix chain 'Lh' and resid 104 through 114 removed outlier: 3.513A pdb=" N GLNLh 108 " --> pdb=" O THRLh 104 " (cutoff:3.500A) Processing helix chain 'LX' and resid 72 through 76 Processing helix chain 'LX' and resid 83 through 94 removed outlier: 3.565A pdb=" N LYSLX 89 " --> pdb=" O SERLX 85 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILELX 90 " --> pdb=" O ALALX 86 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLULX 91 " --> pdb=" O METLX 87 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASPLX 92 " --> pdb=" O LYSLX 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASNLX 93 " --> pdb=" O LYSLX 89 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASNLX 94 " --> pdb=" O ILELX 90 " (cutoff:3.500A) Processing helix chain 'LX' and resid 105 through 118 Processing helix chain 'LX' and resid 145 through 154 removed outlier: 3.787A pdb=" N VALLX 149 " --> pdb=" O ASPLX 145 " (cutoff:3.500A) Processing helix chain 'LR' and resid 4 through 16 Processing helix chain 'LR' and resid 18 through 20 No H-bonds generated for 'chain 'LR' and resid 18 through 20' Processing helix chain 'LR' and resid 28 through 34 removed outlier: 3.788A pdb=" N ILELR 32 " --> pdb=" O GLULR 28 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 47 Processing helix chain 'LR' and resid 60 through 72 removed outlier: 3.601A pdb=" N ASNLR 66 " --> pdb=" O ARGLR 62 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THRLR 67 " --> pdb=" O CYSLR 63 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEULR 68 " --> pdb=" O ARGLR 64 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALALR 69 " --> pdb=" O LYSLR 65 " (cutoff:3.500A) Processing helix chain 'LR' and resid 77 through 81 removed outlier: 3.717A pdb=" N ARGLR 81 " --> pdb=" O ILELR 78 " (cutoff:3.500A) Processing helix chain 'LR' and resid 84 through 89 Processing helix chain 'LR' and resid 90 through 112 removed outlier: 3.806A pdb=" N THRLR 94 " --> pdb=" O PROLR 90 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N METLR 99 " --> pdb=" O TRPLR 95 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLULR 111 " --> pdb=" O ARGLR 107 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SERLR 112 " --> pdb=" O ARGLR 108 " (cutoff:3.500A) Processing helix chain 'LR' and resid 116 through 129 Processing helix chain 'LR' and resid 134 through 154 removed outlier: 3.608A pdb=" N LEULR 138 " --> pdb=" O ASNLR 134 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYSLR 149 " --> pdb=" O LEULR 145 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALALR 150 " --> pdb=" O LYSLR 146 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 3 through 11 Processing helix chain 'Lr' and resid 31 through 35 removed outlier: 3.854A pdb=" N ARGLr 35 " --> pdb=" O LEULr 32 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 85 through 98 Processing helix chain 'Lr' and resid 106 through 120 removed outlier: 3.521A pdb=" N SERLr 120 " --> pdb=" O ALALr 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 23 Processing helix chain 'B' and resid 26 through 39 removed outlier: 3.799A pdb=" N LEU B 30 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.902A pdb=" N CYS B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 76 removed outlier: 4.007A pdb=" N GLU B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 removed outlier: 3.536A pdb=" N ASP B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 removed outlier: 3.621A pdb=" N LYS B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 127 Processing helix chain 'B' and resid 129 through 144 Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.615A pdb=" N TRP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.785A pdb=" N LYS B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.563A pdb=" N TYR B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.723A pdb=" N LEU B 235 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 Processing helix chain 'B' and resid 257 through 269 removed outlier: 3.729A pdb=" N TYR B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.574A pdb=" N TYR B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Proline residue: B 297 - end of helix removed outlier: 3.632A pdb=" N PHE B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 321 Processing helix chain 'B' and resid 324 through 329 removed outlier: 3.729A pdb=" N LEU B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.926A pdb=" N LYS B 334 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 removed outlier: 3.564A pdb=" N VAL B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 388 removed outlier: 3.749A pdb=" N LEU B 373 " --> pdb=" O PRO B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 404 Processing helix chain 'B' and resid 407 through 420 removed outlier: 4.213A pdb=" N PHE B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 438 Processing helix chain 'B' and resid 441 through 455 removed outlier: 4.021A pdb=" N ASN B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.576A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 484 through 498 removed outlier: 3.726A pdb=" N MET B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 520 removed outlier: 4.136A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 519 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 533 removed outlier: 3.904A pdb=" N PHE B 525 " --> pdb=" O ASP B 521 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET B 530 " --> pdb=" O HIS B 526 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 546 Processing helix chain 'B' and resid 547 through 550 Processing helix chain 'B' and resid 551 through 571 Processing helix chain 'B' and resid 577 through 584 Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 588 through 627 removed outlier: 3.570A pdb=" N GLU B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS B 627 " --> pdb=" O ASN B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 removed outlier: 3.571A pdb=" N LEU B 647 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 668 removed outlier: 3.849A pdb=" N LYS B 659 " --> pdb=" O GLU B 655 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Proline residue: B 663 - end of helix Processing helix chain 'B' and resid 671 through 685 removed outlier: 4.160A pdb=" N HIS B 675 " --> pdb=" O LYS B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 702 removed outlier: 3.834A pdb=" N LEU B 692 " --> pdb=" O PHE B 688 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN B 693 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 701 " --> pdb=" O ARG B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 722 Processing helix chain 'B' and resid 726 through 741 removed outlier: 3.664A pdb=" N VAL B 732 " --> pdb=" O THR B 728 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG B 739 " --> pdb=" O GLN B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 757 Processing helix chain 'B' and resid 760 through 775 Processing helix chain 'B' and resid 778 through 788 removed outlier: 3.649A pdb=" N ALA B 782 " --> pdb=" O SER B 778 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 784 " --> pdb=" O LYS B 780 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 785 " --> pdb=" O ARG B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 810 Processing helix chain 'B' and resid 816 through 831 Processing helix chain 'B' and resid 834 through 838 Processing helix chain 'C' and resid 7 through 22 removed outlier: 4.074A pdb=" N MET C 12 " --> pdb=" O PRO C 8 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS C 16 " --> pdb=" O MET C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.777A pdb=" N TYR C 31 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 82 Processing helix chain 'C' and resid 85 through 103 Processing helix chain 'C' and resid 115 through 125 Processing helix chain 'C' and resid 151 through 178 removed outlier: 4.046A pdb=" N ALA C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'LU' and resid 25 through 31 Processing helix chain 'LU' and resid 35 through 46 removed outlier: 3.772A pdb=" N LEULU 43 " --> pdb=" O PHELU 39 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLNLU 44 " --> pdb=" O GLULU 40 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLULU 45 " --> pdb=" O GLNLU 41 " (cutoff:3.500A) Processing helix chain 'LU' and resid 55 through 58 Processing helix chain 'LU' and resid 79 through 94 removed outlier: 3.547A pdb=" N LEULU 83 " --> pdb=" O SERLU 79 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYSLU 84 " --> pdb=" O LYSLU 80 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 29 through 33 Processing helix chain 'Ld' and resid 37 through 39 No H-bonds generated for 'chain 'Ld' and resid 37 through 39' Processing helix chain 'Ld' and resid 40 through 56 removed outlier: 3.816A pdb=" N ARGLd 50 " --> pdb=" O LEULd 46 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYSLd 51 " --> pdb=" O LYSLd 47 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N METLd 54 " --> pdb=" O ARGLd 50 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYSLd 55 " --> pdb=" O LYSLd 51 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLULd 56 " --> pdb=" O PHELd 52 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 65 through 71 removed outlier: 4.333A pdb=" N ASNLd 69 " --> pdb=" O ASPLd 65 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYSLd 70 " --> pdb=" O THRLd 66 " (cutoff:3.500A) Processing helix chain 'LP' and resid 25 through 37 removed outlier: 3.697A pdb=" N THRLP 29 " --> pdb=" O HISLP 25 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLULP 31 " --> pdb=" O LYSLP 27 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYSLP 37 " --> pdb=" O ALALP 33 " (cutoff:3.500A) Processing helix chain 'LP' and resid 40 through 47 Processing helix chain 'LP' and resid 49 through 54 removed outlier: 4.428A pdb=" N LEULP 53 " --> pdb=" O LYSLP 49 " (cutoff:3.500A) Processing helix chain 'LP' and resid 73 through 77 Processing helix chain 'LP' and resid 84 through 103 removed outlier: 3.542A pdb=" N ALALP 88 " --> pdb=" O PROLP 84 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLULP 89 " --> pdb=" O LYSLP 85 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHELP 90 " --> pdb=" O LYSLP 86 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SERLP 100 " --> pdb=" O LYSLP 96 " (cutoff:3.500A) Processing helix chain 'LP' and resid 108 through 110 No H-bonds generated for 'chain 'LP' and resid 108 through 110' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.673A pdb=" N LYS A 59 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE A 72 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY A 70 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N HIS A 110 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE A 72 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N ARG A 112 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 13.629A pdb=" N SER A 74 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA A 144 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL A 133 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 146 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'LC' and resid 17 through 23 removed outlier: 4.832A pdb=" N LYSLC 20 " --> pdb=" O VALLC 10 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VALLC 153 " --> pdb=" O SERLC 9 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEULC 152 " --> pdb=" O TRPLC 252 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYSLC 208 " --> pdb=" O ILELC 251 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N THRLC 253 " --> pdb=" O CYSLC 208 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ILELC 210 " --> pdb=" O THRLC 253 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILELC 209 " --> pdb=" O LEULC 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'LC' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'LC' and resid 187 through 189 Processing sheet with id=AA5, first strand: chain 'LE' and resid 49 through 51 removed outlier: 3.734A pdb=" N VALLE 51 " --> pdb=" O ILELE 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'LE' and resid 91 through 95 Processing sheet with id=AA7, first strand: chain 'LE' and resid 187 through 189 removed outlier: 4.259A pdb=" N LYSLE 166 " --> pdb=" O LEULE 174 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THRLE 176 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N PHELE 164 " --> pdb=" O THRLE 176 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THRLE 148 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILELE 149 " --> pdb=" O THRLE 197 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILELE 195 " --> pdb=" O ILELE 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Lk' and resid 3 through 5 removed outlier: 4.178A pdb=" N VALLk 46 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VALLk 23 " --> pdb=" O LYSLk 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AB1, first strand: chain 'LY' and resid 79 through 82 removed outlier: 7.425A pdb=" N VALLY 79 " --> pdb=" O VALLY 73 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VALLY 73 " --> pdb=" O VALLY 79 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYRLY 81 " --> pdb=" O VALLY 71 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLULY 54 " --> pdb=" O THRLY 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'LY' and resid 86 through 88 Processing sheet with id=AB3, first strand: chain 'LX' and resid 77 through 80 removed outlier: 3.649A pdb=" N LYSLX 134 " --> pdb=" O VALLX 100 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYSLX 123 " --> pdb=" O ARGLX 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'LR' and resid 22 through 24 removed outlier: 3.599A pdb=" N TRPLR 23 " --> pdb=" O ILELR 51 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILELR 51 " --> pdb=" O TRPLR 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'Lr' and resid 17 through 20 Processing sheet with id=AB6, first strand: chain 'Lr' and resid 49 through 53 Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 5 removed outlier: 6.493A pdb=" N TYR C 43 " --> pdb=" O TYR C 55 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR C 55 " --> pdb=" O TYR C 43 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA C 45 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N VAL C 53 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL C 77 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR C 55 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU C 75 " --> pdb=" O TYR C 55 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU C 57 " --> pdb=" O THR C 73 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 129 through 134 removed outlier: 4.800A pdb=" N ILE C 130 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS C 148 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'LU' and resid 61 through 65 removed outlier: 3.679A pdb=" N ILELU 70 " --> pdb=" O LEULU 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'LU' and resid 48 through 49 Processing sheet with id=AC2, first strand: chain 'Ld' and resid 22 through 28 removed outlier: 4.381A pdb=" N ARGLd 85 " --> pdb=" O VALLd 109 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VALLd 106 " --> pdb=" O ARGLd 63 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'LP' and resid 14 through 22 removed outlier: 5.957A pdb=" N CYSLP 144 " --> pdb=" O ASNLP 21 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HISLP 116 " --> pdb=" O ILELP 149 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THRLP 151 " --> pdb=" O ILELP 114 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILELP 114 " --> pdb=" O THRLP 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'LP' and resid 58 through 59 removed outlier: 3.584A pdb=" N ARGLP 82 " --> pdb=" O VALLP 58 " (cutoff:3.500A) 1542 hydrogen bonds defined for protein. 4506 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 477 hydrogen bonds 820 hydrogen bond angles 0 basepair planarities 180 basepair parallelities 283 stacking parallelities Total time for adding SS restraints: 13.44 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8679 1.33 - 1.45: 13389 1.45 - 1.58: 21839 1.58 - 1.70: 1220 1.70 - 1.82: 242 Bond restraints: 45369 Sorted by residual: bond pdb=" N9 G 14898 " pdb=" C4 G 14898 " ideal model delta sigma weight residual 1.375 1.346 0.029 8.00e-03 1.56e+04 1.34e+01 bond pdb=" N7 G 14872 " pdb=" C5 G 14872 " ideal model delta sigma weight residual 1.388 1.368 0.020 6.00e-03 2.78e+04 1.15e+01 bond pdb=" N1 C 14773 " pdb=" C2 C 14773 " ideal model delta sigma weight residual 1.397 1.364 0.033 1.00e-02 1.00e+04 1.09e+01 bond pdb=" C2 G 14898 " pdb=" N3 G 14898 " ideal model delta sigma weight residual 1.323 1.297 0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C2 C 14773 " pdb=" O2 C 14773 " ideal model delta sigma weight residual 1.240 1.213 0.027 9.00e-03 1.23e+04 9.24e+00 ... (remaining 45364 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 63794 4.91 - 9.81: 243 9.81 - 14.72: 13 14.72 - 19.62: 3 19.62 - 24.53: 1 Bond angle restraints: 64054 Sorted by residual: angle pdb=" CB METLU 34 " pdb=" CG METLU 34 " pdb=" SD METLU 34 " ideal model delta sigma weight residual 112.70 137.23 -24.53 3.00e+00 1.11e-01 6.68e+01 angle pdb=" C1' C 14921 " pdb=" N1 C 14921 " pdb=" C2 C 14921 " ideal model delta sigma weight residual 118.80 127.28 -8.48 1.10e+00 8.26e-01 5.94e+01 angle pdb=" C1' C 1 485 " pdb=" N1 C 1 485 " pdb=" C2 C 1 485 " ideal model delta sigma weight residual 118.80 126.80 -8.00 1.10e+00 8.26e-01 5.29e+01 angle pdb=" C1' C 14733 " pdb=" N1 C 14733 " pdb=" C2 C 14733 " ideal model delta sigma weight residual 118.80 126.78 -7.98 1.10e+00 8.26e-01 5.27e+01 angle pdb=" C1' G 14963 " pdb=" N9 G 14963 " pdb=" C4 G 14963 " ideal model delta sigma weight residual 126.50 135.89 -9.39 1.30e+00 5.92e-01 5.22e+01 ... (remaining 64049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 26931 35.67 - 71.34: 1784 71.34 - 107.01: 239 107.01 - 142.68: 23 142.68 - 178.35: 10 Dihedral angle restraints: 28987 sinusoidal: 18096 harmonic: 10891 Sorted by residual: dihedral pdb=" O4' C 14775 " pdb=" C1' C 14775 " pdb=" N1 C 14775 " pdb=" C2 C 14775 " ideal model delta sinusoidal sigma weight residual 200.00 33.64 166.36 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U 14758 " pdb=" C1' U 14758 " pdb=" N1 U 14758 " pdb=" C2 U 14758 " ideal model delta sinusoidal sigma weight residual 200.00 35.60 164.40 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" O4' C 14928 " pdb=" C1' C 14928 " pdb=" N1 C 14928 " pdb=" C2 C 14928 " ideal model delta sinusoidal sigma weight residual -160.00 -0.59 -159.41 1 1.50e+01 4.44e-03 8.26e+01 ... (remaining 28984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.000: 7527 1.000 - 1.999: 0 1.999 - 2.999: 0 2.999 - 3.999: 0 3.999 - 4.998: 5 Chirality restraints: 7532 Sorted by residual: chirality pdb=" C2 IHP B 901 " pdb=" C1 IHP B 901 " pdb=" C3 IHP B 901 " pdb=" O12 IHP B 901 " both_signs ideal model delta sigma weight residual False -2.52 2.48 -5.00 2.00e-01 2.50e+01 6.25e+02 chirality pdb=" C1 IHP D 900 " pdb=" C2 IHP D 900 " pdb=" C6 IHP D 900 " pdb=" O11 IHP D 900 " both_signs ideal model delta sigma weight residual False 2.32 -2.61 4.93 2.00e-01 2.50e+01 6.07e+02 chirality pdb=" C5 IHP B 901 " pdb=" C4 IHP B 901 " pdb=" C6 IHP B 901 " pdb=" O15 IHP B 901 " both_signs ideal model delta sigma weight residual False -2.42 2.50 -4.92 2.00e-01 2.50e+01 6.05e+02 ... (remaining 7529 not shown) Planarity restraints: 5874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 96 " -0.027 2.00e-02 2.50e+03 5.40e-02 2.91e+01 pdb=" C ARG A 96 " 0.093 2.00e-02 2.50e+03 pdb=" O ARG A 96 " -0.035 2.00e-02 2.50e+03 pdb=" N ALA A 97 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 14731 " -0.057 2.00e-02 2.50e+03 2.59e-02 2.01e+01 pdb=" N9 G 14731 " 0.067 2.00e-02 2.50e+03 pdb=" C8 G 14731 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G 14731 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G 14731 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G 14731 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G 14731 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G 14731 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G 14731 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G 14731 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G 14731 " 0.010 2.00e-02 2.50e+03 pdb=" C4 G 14731 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 14727 " -0.040 2.00e-02 2.50e+03 2.59e-02 1.85e+01 pdb=" N9 A 14727 " 0.071 2.00e-02 2.50e+03 pdb=" C8 A 14727 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A 14727 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A 14727 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 14727 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A 14727 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A 14727 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A 14727 " 0.005 2.00e-02 2.50e+03 pdb=" N3 A 14727 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A 14727 " -0.024 2.00e-02 2.50e+03 ... (remaining 5871 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 730 2.59 - 3.17: 38605 3.17 - 3.74: 81913 3.74 - 4.32: 105117 4.32 - 4.90: 150125 Nonbonded interactions: 376490 Sorted by model distance: nonbonded pdb=" O2 C 1 238 " pdb=" OG SERLY 102 " model vdw 2.012 3.040 nonbonded pdb=" N2 G 14907 " pdb=" O2 C 14914 " model vdw 2.055 2.496 nonbonded pdb=" NH1 ARGLh 32 " pdb=" O LYSLX 78 " model vdw 2.055 3.120 nonbonded pdb=" OG1 THR D 519 " pdb=" OE2 GLU D 545 " model vdw 2.060 3.040 nonbonded pdb=" O6 G 1 493 " pdb=" N1 A 1 660 " model vdw 2.085 2.496 ... (remaining 376485 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' and resid 2 through 178) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 7 through 839 or resid 901)) selection = chain 'D' } 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: 20.490 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: 0.040 Extract box with map and model: 0.960 Check model and map are aligned: 0.160 Set scattering table: 0.160 Process input model: 45.850 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5691 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 45369 Z= 0.294 Angle : 0.926 24.528 64054 Z= 0.611 Chirality : 0.136 4.998 7532 Planarity : 0.006 0.090 5874 Dihedral : 20.641 178.345 21921 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.75 % Favored : 96.05 % Rotamer: Outliers : 0.03 % Allowed : 1.59 % Favored : 98.38 % Cbeta Deviations : 0.03 % 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 (0.13), residues: 3650 helix: -0.07 (0.11), residues: 1898 sheet: -0.91 (0.32), residues: 256 loop : -0.56 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.001 ARGLd 67 TYR 0.049 0.003 TYR B 66 PHE 0.039 0.003 PHE D 679 TRP 0.052 0.003 TRPLR 95 HIS 0.015 0.002 HIS B 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.29 (45369) covalent geometry : angle 0.92638 / 0.61 (64054) hydrogen bonds : bond 0.22295 / 14.87 ( 2019) hydrogen bonds : angle 7.19443 / 5.12 ( 5326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 565 time to evaluate : 1.333 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: 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: 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: D 266 LYS cc_start: 0.3945 (mtmt) cc_final: 0.3670 (tmtt) REVERT: D 273 MET cc_start: 0.2987 (tmm) cc_final: 0.1770 (mtt) REVERT: D 316 MET cc_start: -0.2733 (tpp) cc_final: -0.3446 (tpt) REVERT: D 498 MET cc_start: 0.4935 (pmm) cc_final: 0.4638 (pmm) REVERT: D 770 MET cc_start: 0.1958 (ttt) cc_final: 0.1574 (ttt) REVERT: LC 97 ARG cc_start: 0.8621 (ttt-90) cc_final: 0.6953 (ptt180) REVERT: LC 102 PHE cc_start: 0.8484 (t80) cc_final: 0.7076 (p90) REVERT: LC 105 THR cc_start: 0.8906 (p) cc_final: 0.8612 (p) REVERT: LC 120 LYS cc_start: 0.9624 (mtmt) cc_final: 0.9252 (tttt) REVERT: LC 211 TYR cc_start: 0.9099 (p90) cc_final: 0.8862 (p90) REVERT: LC 250 CYS cc_start: 0.8985 (p) cc_final: 0.8679 (p) REVERT: LC 286 ASN cc_start: 0.9345 (t0) cc_final: 0.9108 (t0) REVERT: LC 331 TYR cc_start: 0.8621 (t80) cc_final: 0.8070 (m-10) REVERT: LE 207 LYS cc_start: 0.9065 (mmpt) cc_final: 0.8604 (tppt) REVERT: LE 275 PHE cc_start: 0.9231 (t80) cc_final: 0.8988 (t80) REVERT: Lk 30 ASP cc_start: 0.9178 (p0) cc_final: 0.8972 (p0) REVERT: LY 37 GLU cc_start: 0.9003 (pm20) cc_final: 0.8242 (pm20) REVERT: LY 38 LEU cc_start: 0.9471 (mt) cc_final: 0.8908 (mt) REVERT: LY 43 ASN cc_start: 0.9516 (t0) cc_final: 0.9158 (t0) REVERT: LY 47 MET cc_start: 0.9269 (tpp) cc_final: 0.8661 (tpp) REVERT: Lh 30 GLN cc_start: 0.9380 (tp-100) cc_final: 0.9174 (tp-100) REVERT: LX 46 PHE cc_start: 0.8097 (t80) cc_final: 0.6819 (m-80) REVERT: LX 88 LYS cc_start: 0.9569 (mtmm) cc_final: 0.8985 (mttm) REVERT: LX 116 LEU cc_start: 0.9398 (tp) cc_final: 0.9108 (tp) REVERT: LX 117 TYR cc_start: 0.9017 (m-10) cc_final: 0.8764 (m-10) REVERT: LX 134 LYS cc_start: 0.7698 (tttt) cc_final: 0.7447 (tptt) REVERT: LX 144 TYR cc_start: 0.8799 (m-80) cc_final: 0.8259 (m-10) REVERT: LR 10 LEU cc_start: 0.9516 (mt) cc_final: 0.9202 (tp) REVERT: LR 25 ASP cc_start: 0.8895 (t70) cc_final: 0.8393 (t0) REVERT: LR 28 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8877 (mm-30) REVERT: LR 52 ARG cc_start: 0.8903 (ttm-80) cc_final: 0.8438 (ttm-80) REVERT: Lr 6 GLN cc_start: 0.9297 (mt0) cc_final: 0.9019 (mt0) REVERT: Lr 33 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7628 (mmmt) REVERT: Lr 40 TYR cc_start: 0.8989 (m-10) cc_final: 0.8780 (m-80) REVERT: Lr 41 ASN cc_start: 0.8233 (m-40) cc_final: 0.7646 (t0) REVERT: Lr 47 LYS cc_start: 0.9100 (tttt) cc_final: 0.8856 (tmtt) REVERT: Lr 56 ASP cc_start: 0.9169 (p0) cc_final: 0.8711 (p0) REVERT: Lr 58 LYS cc_start: 0.8860 (tppt) cc_final: 0.8456 (tppt) REVERT: Lr 79 ARG cc_start: 0.9245 (ttm-80) cc_final: 0.8814 (ttm-80) REVERT: Lr 83 ASN cc_start: 0.8684 (t0) cc_final: 0.7946 (t0) REVERT: B 166 MET cc_start: -0.0401 (tmm) cc_final: -0.2303 (pmm) REVERT: C 14 MET cc_start: 0.5473 (mmt) cc_final: 0.5007 (mmt) REVERT: C 60 MET cc_start: -0.0873 (mmm) cc_final: -0.1675 (mmp) REVERT: C 98 MET cc_start: -0.4464 (tpt) cc_final: -0.5593 (mtt) REVERT: LU 19 LEU cc_start: 0.8880 (pp) cc_final: 0.8418 (pp) REVERT: LU 21 PHE cc_start: 0.9340 (m-80) cc_final: 0.8886 (m-80) REVERT: Ld 44 ARG cc_start: 0.9068 (tpt90) cc_final: 0.8797 (tpt90) REVERT: Ld 47 LYS cc_start: 0.9284 (mptt) cc_final: 0.8907 (mptt) REVERT: Ld 48 GLU cc_start: 0.9049 (tp30) cc_final: 0.8572 (tp30) REVERT: Ld 50 ARG cc_start: 0.9269 (mmt180) cc_final: 0.8596 (mmt180) REVERT: LP 7 ASP cc_start: 0.8579 (t0) cc_final: 0.8375 (t0) REVERT: LP 31 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8447 (mm-30) REVERT: LP 47 TYR cc_start: 0.8577 (t80) cc_final: 0.8273 (t80) REVERT: LP 56 GLN cc_start: 0.7371 (tp-100) cc_final: 0.7110 (mm-40) REVERT: LP 112 LEU cc_start: 0.9503 (mm) cc_final: 0.8507 (mm) REVERT: LP 152 GLU cc_start: 0.8687 (tp30) cc_final: 0.8104 (tp30) outliers start: 1 outliers final: 0 residues processed: 565 average time/residue: 0.2837 time to fit residues: 257.8406 Evaluate side-chains 456 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 0.0000 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 9.9990 overall best weight: 2.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 ASN ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 HIS A 153 GLN D 75 ASN D 483 GLN D 571 ASN ** D 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 212 ASN LC 299 GLN LE 279 ASN ** LX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 36 ASN ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN B 435 GLN B 478 ASN B 603 GLN B 614 ASN B 621 GLN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ld 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 101 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.100153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.066522 restraints weight = 288541.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.066143 restraints weight = 224250.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.066169 restraints weight = 189903.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.066237 restraints weight = 174660.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.066237 restraints weight = 171439.837| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 45369 Z= 0.193 Angle : 0.748 24.358 64054 Z= 0.402 Chirality : 0.046 1.180 7532 Planarity : 0.006 0.081 5874 Dihedral : 22.967 177.586 13912 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.88 % Rotamer: Outliers : 1.56 % Allowed : 9.66 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 3650 helix: 0.08 (0.11), residues: 2048 sheet: -0.89 (0.31), residues: 253 loop : -0.66 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGLY 17 TYR 0.037 0.002 TYR B 21 PHE 0.028 0.002 PHE D 716 TRP 0.038 0.003 TRP B 83 HIS 0.019 0.002 HIS D 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 (45369) covalent geometry : angle 0.74763 / 0.40 (64054) hydrogen bonds : bond 0.07634 / 5.13 ( 2019) hydrogen bonds : angle 5.69175 / 4.04 ( 5326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 520 time to evaluate : 1.527 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: 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: 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: symmetry clash REVERT: D 20 CYS cc_start: 0.3119 (m) cc_final: 0.2342 (m) REVERT: D 273 MET cc_start: 0.4846 (tmm) cc_final: 0.4022 (mtt) REVERT: D 343 GLU cc_start: 0.3665 (OUTLIER) cc_final: 0.3314 (pp20) REVERT: D 485 MET cc_start: 0.1102 (tmm) cc_final: 0.0568 (tmm) REVERT: D 770 MET cc_start: 0.2853 (ttt) cc_final: 0.2621 (ttt) REVERT: LC 97 ARG cc_start: 0.8566 (ttt-90) cc_final: 0.6770 (ptt180) REVERT: LC 102 PHE cc_start: 0.8667 (t80) cc_final: 0.7049 (p90) REVERT: LC 120 LYS cc_start: 0.9621 (mtmt) cc_final: 0.9216 (tttt) REVERT: LC 211 TYR cc_start: 0.9056 (p90) cc_final: 0.8699 (p90) REVERT: LC 250 CYS cc_start: 0.9142 (p) cc_final: 0.8906 (p) REVERT: LC 286 ASN cc_start: 0.9478 (t0) cc_final: 0.9261 (t0) REVERT: LE 119 GLU cc_start: 0.3365 (OUTLIER) cc_final: 0.2945 (pm20) REVERT: LE 120 ASP cc_start: 0.8316 (t0) cc_final: 0.7966 (m-30) REVERT: LE 207 LYS cc_start: 0.8832 (mmpt) cc_final: 0.8514 (tppt) REVERT: LE 275 PHE cc_start: 0.8937 (t80) cc_final: 0.8634 (t80) REVERT: Lk 30 ASP cc_start: 0.9009 (p0) cc_final: 0.8757 (p0) REVERT: LY 37 GLU cc_start: 0.8762 (pm20) cc_final: 0.8176 (pm20) REVERT: LY 38 LEU cc_start: 0.9438 (mt) cc_final: 0.8822 (mt) REVERT: LY 43 ASN cc_start: 0.9249 (t0) cc_final: 0.8929 (t0) REVERT: LY 47 MET cc_start: 0.9130 (tpp) cc_final: 0.8306 (tpp) REVERT: Lh 30 GLN cc_start: 0.9177 (tp-100) cc_final: 0.8963 (tp-100) REVERT: LX 46 PHE cc_start: 0.8047 (t80) cc_final: 0.6749 (m-80) REVERT: LX 116 LEU cc_start: 0.9424 (tp) cc_final: 0.9022 (tp) REVERT: LX 117 TYR cc_start: 0.8732 (m-10) cc_final: 0.8507 (m-10) REVERT: LX 134 LYS cc_start: 0.7758 (tttt) cc_final: 0.7493 (tptt) REVERT: LX 144 TYR cc_start: 0.8717 (m-80) cc_final: 0.8219 (m-10) REVERT: LR 10 LEU cc_start: 0.9531 (mt) cc_final: 0.9221 (tp) REVERT: LR 25 ASP cc_start: 0.8809 (t70) cc_final: 0.8323 (t0) REVERT: LR 28 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8918 (mm-30) REVERT: LR 34 ASN cc_start: 0.8778 (m110) cc_final: 0.8532 (m110) REVERT: LR 52 ARG cc_start: 0.8973 (ttm-80) cc_final: 0.8660 (ttm-80) REVERT: Lr 33 LYS cc_start: 0.8423 (mtmt) cc_final: 0.7756 (mmmt) REVERT: Lr 41 ASN cc_start: 0.8401 (m-40) cc_final: 0.8056 (t0) REVERT: Lr 56 ASP cc_start: 0.9039 (p0) cc_final: 0.8608 (p0) REVERT: Lr 58 LYS cc_start: 0.8789 (tppt) cc_final: 0.8462 (tppt) REVERT: Lr 79 ARG cc_start: 0.8986 (ttm-80) cc_final: 0.8551 (ttm-80) REVERT: Lr 83 ASN cc_start: 0.8454 (t0) cc_final: 0.7605 (t0) REVERT: B 119 ASP cc_start: 0.7388 (m-30) cc_final: 0.7163 (t0) REVERT: C 14 MET cc_start: 0.6399 (mmt) cc_final: 0.5925 (mmt) REVERT: C 28 MET cc_start: 0.6622 (tpt) cc_final: 0.5174 (ptt) REVERT: C 60 MET cc_start: 0.4738 (mmm) cc_final: 0.3770 (mmm) REVERT: C 69 HIS cc_start: 0.2477 (OUTLIER) cc_final: 0.1210 (t-90) REVERT: C 98 MET cc_start: -0.4911 (tpt) cc_final: -0.6177 (mtt) REVERT: LU 21 PHE cc_start: 0.9126 (m-80) cc_final: 0.8888 (m-10) REVERT: LU 30 GLU cc_start: 0.9493 (mm-30) cc_final: 0.8991 (pp20) REVERT: LU 83 LEU cc_start: 0.9187 (mt) cc_final: 0.8892 (mp) REVERT: LU 98 ASP cc_start: 0.9321 (p0) cc_final: 0.9030 (p0) REVERT: Ld 44 ARG cc_start: 0.9046 (tpt90) cc_final: 0.8774 (tpt90) REVERT: Ld 47 LYS cc_start: 0.9386 (mptt) cc_final: 0.9053 (mptt) REVERT: Ld 48 GLU cc_start: 0.9330 (tp30) cc_final: 0.8778 (tp30) REVERT: Ld 50 ARG cc_start: 0.9426 (mmt180) cc_final: 0.8725 (mmt180) REVERT: Ld 54 MET cc_start: 0.9508 (mmm) cc_final: 0.9283 (mmm) REVERT: LP 3 ARG cc_start: 0.8015 (tpm170) cc_final: 0.7293 (tmt170) REVERT: LP 7 ASP cc_start: 0.8622 (t0) cc_final: 0.8382 (t0) REVERT: LP 26 PHE cc_start: 0.9183 (t80) cc_final: 0.8616 (t80) REVERT: LP 31 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8270 (mm-30) REVERT: LP 36 ILE cc_start: 0.9630 (pt) cc_final: 0.9373 (tp) REVERT: LP 39 MET cc_start: 0.8188 (mpp) cc_final: 0.7773 (mpp) REVERT: LP 47 TYR cc_start: 0.8486 (t80) cc_final: 0.8256 (t80) REVERT: LP 60 PHE cc_start: 0.9380 (m-80) cc_final: 0.8912 (m-80) REVERT: LP 76 TRP cc_start: 0.8458 (m100) cc_final: 0.7591 (m100) REVERT: LP 112 LEU cc_start: 0.9437 (mm) cc_final: 0.8774 (mm) REVERT: LP 152 GLU cc_start: 0.8609 (tp30) cc_final: 0.8024 (tp30) outliers start: 51 outliers final: 26 residues processed: 536 average time/residue: 0.2802 time to fit residues: 242.3672 Evaluate side-chains 478 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 449 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain LC residue 361 LEU Chi-restraints excluded: chain LE residue 119 GLU Chi-restraints excluded: chain LE residue 200 LYS Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain LX residue 101 ASP Chi-restraints excluded: chain LX residue 118 ASP Chi-restraints excluded: chain LX residue 121 VAL Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LR residue 22 VAL Chi-restraints excluded: chain Lr residue 36 ASN Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain Ld residue 27 ILE Chi-restraints excluded: chain Ld residue 49 ILE Chi-restraints excluded: chain Ld residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 157 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 275 optimal weight: 6.9990 chunk 407 optimal weight: 3.9990 chunk 413 optimal weight: 5.9990 chunk 310 optimal weight: 50.0000 chunk 280 optimal weight: 0.0570 chunk 121 optimal weight: 20.0000 chunk 401 optimal weight: 6.9990 chunk 339 optimal weight: 20.0000 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 HIS ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 276 ASN LC 317 ASN ** LX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 6 GLN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 ASN ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ld 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 34 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.098587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.065546 restraints weight = 292804.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.067372 restraints weight = 227086.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.065498 restraints weight = 183109.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.065693 restraints weight = 193507.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.065709 restraints weight = 170614.642| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 45369 Z= 0.210 Angle : 0.692 13.933 64054 Z= 0.375 Chirality : 0.042 0.362 7532 Planarity : 0.005 0.061 5874 Dihedral : 22.996 177.386 13912 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 2.24 % Allowed : 12.35 % Favored : 85.41 % 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: -0.48 (0.13), residues: 3650 helix: 0.11 (0.11), residues: 2044 sheet: -0.90 (0.31), residues: 261 loop : -0.65 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 91 TYR 0.046 0.002 TYRLC 331 PHE 0.023 0.002 PHELC 39 TRP 0.032 0.002 TRPLR 95 HIS 0.016 0.002 HIS D 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 (45369) covalent geometry : angle 0.69194 / 0.38 (64054) hydrogen bonds : bond 0.07496 / 5.05 ( 2019) hydrogen bonds : angle 5.45722 / 3.87 ( 5326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 476 time to evaluate : 1.364 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: 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: 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: D 20 CYS cc_start: 0.2987 (m) cc_final: 0.2644 (m) REVERT: D 273 MET cc_start: 0.5001 (tmm) cc_final: 0.4013 (mtt) REVERT: D 316 MET cc_start: -0.5570 (OUTLIER) cc_final: -0.6130 (tpt) REVERT: D 343 GLU cc_start: 0.3535 (OUTLIER) cc_final: 0.3165 (pp20) REVERT: D 485 MET cc_start: -0.0381 (tmm) cc_final: -0.0918 (tmm) REVERT: LC 52 TYR cc_start: -0.1122 (OUTLIER) cc_final: -0.1827 (m-10) REVERT: LC 102 PHE cc_start: 0.8703 (t80) cc_final: 0.7088 (p90) REVERT: LC 120 LYS cc_start: 0.9589 (mtmt) cc_final: 0.9241 (tttt) REVERT: LC 227 ILE cc_start: 0.9343 (mt) cc_final: 0.9090 (mt) REVERT: LC 250 CYS cc_start: 0.9232 (p) cc_final: 0.9026 (p) REVERT: LC 288 ASP cc_start: 0.9121 (t0) cc_final: 0.8844 (t0) REVERT: LE 119 GLU cc_start: 0.2985 (OUTLIER) cc_final: 0.2701 (pm20) REVERT: LE 207 LYS cc_start: 0.8744 (mmpt) cc_final: 0.8472 (tppt) REVERT: LE 275 PHE cc_start: 0.9089 (t80) cc_final: 0.8828 (t80) REVERT: LE 282 TYR cc_start: 0.9195 (m-10) cc_final: 0.8991 (m-10) REVERT: Lk 30 ASP cc_start: 0.9055 (p0) cc_final: 0.8767 (p0) REVERT: LY 30 MET cc_start: 0.9341 (mmm) cc_final: 0.8797 (mmt) REVERT: LY 37 GLU cc_start: 0.8898 (pm20) cc_final: 0.8308 (pm20) REVERT: LY 38 LEU cc_start: 0.9478 (mt) cc_final: 0.8939 (mt) REVERT: LY 43 ASN cc_start: 0.9304 (t0) cc_final: 0.9001 (t0) REVERT: Lh 18 LEU cc_start: 0.9394 (mt) cc_final: 0.9155 (mt) REVERT: Lh 35 LYS cc_start: 0.9355 (ptmm) cc_final: 0.8989 (ptmm) REVERT: LX 46 PHE cc_start: 0.7941 (t80) cc_final: 0.6701 (m-80) REVERT: LX 76 ILE cc_start: 0.9418 (mt) cc_final: 0.9154 (mm) REVERT: LX 79 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7806 (t80) REVERT: LX 88 LYS cc_start: 0.9485 (mtmm) cc_final: 0.9069 (mttm) REVERT: LX 116 LEU cc_start: 0.9445 (tp) cc_final: 0.9060 (tp) REVERT: LX 117 TYR cc_start: 0.8809 (m-10) cc_final: 0.8510 (m-10) REVERT: LX 134 LYS cc_start: 0.7840 (tttt) cc_final: 0.7544 (tptt) REVERT: LR 10 LEU cc_start: 0.9555 (mt) cc_final: 0.9239 (tp) REVERT: LR 34 ASN cc_start: 0.8875 (m110) cc_final: 0.8625 (m-40) REVERT: LR 38 ARG cc_start: 0.9565 (mtt-85) cc_final: 0.8941 (mtp85) REVERT: LR 51 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8915 (mp) REVERT: LR 52 ARG cc_start: 0.8997 (ttm-80) cc_final: 0.8771 (ttm-80) REVERT: LR 133 LYS cc_start: 0.8710 (mmtm) cc_final: 0.8399 (mmtm) REVERT: Lr 33 LYS cc_start: 0.8334 (mtmt) cc_final: 0.7745 (mmmt) REVERT: Lr 41 ASN cc_start: 0.8421 (m-40) cc_final: 0.8128 (t0) REVERT: Lr 47 LYS cc_start: 0.8834 (tttt) cc_final: 0.8493 (tmtt) REVERT: Lr 52 GLU cc_start: 0.8427 (mp0) cc_final: 0.7841 (mp0) REVERT: Lr 56 ASP cc_start: 0.8989 (p0) cc_final: 0.8545 (p0) REVERT: Lr 58 LYS cc_start: 0.8825 (tppt) cc_final: 0.8508 (tppt) REVERT: Lr 79 ARG cc_start: 0.9022 (ttm-80) cc_final: 0.8256 (ttm-80) REVERT: Lr 83 ASN cc_start: 0.8621 (t0) cc_final: 0.7952 (t0) REVERT: C 28 MET cc_start: 0.6959 (tpt) cc_final: 0.5886 (ptt) REVERT: C 60 MET cc_start: 0.5058 (mmm) cc_final: 0.4360 (mmm) REVERT: C 69 HIS cc_start: 0.3222 (t70) cc_final: 0.1929 (t-90) REVERT: C 98 MET cc_start: -0.4637 (tpt) cc_final: -0.6086 (mtt) REVERT: LU 21 PHE cc_start: 0.9093 (m-80) cc_final: 0.8584 (m-80) REVERT: Ld 44 ARG cc_start: 0.9083 (tpt90) cc_final: 0.8663 (tpt90) REVERT: Ld 47 LYS cc_start: 0.9421 (mptt) cc_final: 0.8910 (mmmt) REVERT: Ld 48 GLU cc_start: 0.9340 (tp30) cc_final: 0.8331 (tp30) REVERT: Ld 50 ARG cc_start: 0.9489 (mtt180) cc_final: 0.8925 (mmt-90) REVERT: LP 7 ASP cc_start: 0.8602 (t0) cc_final: 0.8350 (t0) REVERT: LP 31 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8129 (mm-30) REVERT: LP 34 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7465 (mm110) REVERT: LP 60 PHE cc_start: 0.9531 (m-80) cc_final: 0.8982 (m-80) REVERT: LP 152 GLU cc_start: 0.8415 (tp30) cc_final: 0.8164 (tp30) outliers start: 73 outliers final: 48 residues processed: 505 average time/residue: 0.2575 time to fit residues: 210.8648 Evaluate side-chains 488 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 433 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain LC residue 52 TYR Chi-restraints excluded: chain LC residue 57 LEU Chi-restraints excluded: chain LC residue 62 THR Chi-restraints excluded: chain LC residue 125 CYS Chi-restraints excluded: chain LC residue 235 LEU Chi-restraints excluded: chain LC residue 285 ILE Chi-restraints excluded: chain LC residue 361 LEU Chi-restraints excluded: chain LE residue 119 GLU Chi-restraints excluded: chain LE residue 143 SER Chi-restraints excluded: chain LE residue 200 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain LY residue 12 SER Chi-restraints excluded: chain LY residue 52 ASP Chi-restraints excluded: chain LY residue 67 ILE Chi-restraints excluded: chain LY residue 106 ILE Chi-restraints excluded: chain Lh residue 14 LYS Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain LX residue 79 PHE Chi-restraints excluded: chain LX residue 84 GLU Chi-restraints excluded: chain LX residue 101 ASP Chi-restraints excluded: chain LX residue 121 VAL Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LR residue 22 VAL Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LR residue 99 MET Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain Ld residue 27 ILE Chi-restraints excluded: chain Ld residue 49 ILE Chi-restraints excluded: chain Ld residue 72 VAL Chi-restraints excluded: chain Ld residue 80 VAL Chi-restraints excluded: chain Ld residue 84 ILE Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain LP residue 34 GLN Chi-restraints excluded: chain LP residue 51 VAL Chi-restraints excluded: chain LP residue 91 LEU Chi-restraints excluded: chain LP residue 113 VAL Chi-restraints excluded: chain LP residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 190 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 392 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 416 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 321 ASN ** LY 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 40 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 145 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.096535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.064197 restraints weight = 296072.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.064624 restraints weight = 234756.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.066214 restraints weight = 204512.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.065135 restraints weight = 158434.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.064732 restraints weight = 166365.878| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 45369 Z= 0.261 Angle : 0.736 13.835 64054 Z= 0.399 Chirality : 0.043 0.363 7532 Planarity : 0.006 0.059 5874 Dihedral : 23.229 177.026 13912 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 25.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.58 % Rotamer: Outliers : 3.56 % Allowed : 13.67 % Favored : 82.77 % 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: -0.73 (0.13), residues: 3650 helix: -0.06 (0.11), residues: 2059 sheet: -1.12 (0.31), residues: 264 loop : -0.80 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 91 TYR 0.047 0.002 TYRLC 331 PHE 0.027 0.002 PHELC 39 TRP 0.038 0.003 TRPLR 95 HIS 0.010 0.002 HIS D 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.26 (45369) covalent geometry : angle 0.73578 / 0.40 (64054) hydrogen bonds : bond 0.08228 / 5.60 ( 2019) hydrogen bonds : angle 5.41848 / 3.86 ( 5326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 455 time to evaluate : 1.433 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 CYS cc_start: 0.3086 (m) cc_final: 0.2811 (m) REVERT: D 316 MET cc_start: -0.5487 (OUTLIER) cc_final: -0.6053 (tpt) REVERT: D 343 GLU cc_start: 0.3823 (OUTLIER) cc_final: 0.3452 (pp20) REVERT: D 485 MET cc_start: -0.0276 (tmm) cc_final: -0.0715 (tmm) REVERT: LC 52 TYR cc_start: -0.0331 (OUTLIER) cc_final: -0.1203 (m-10) REVERT: LC 102 PHE cc_start: 0.8853 (t80) cc_final: 0.7099 (p90) REVERT: LC 156 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: LC 315 LYS cc_start: 0.9290 (tttm) cc_final: 0.9047 (tptm) REVERT: LC 325 MET cc_start: 0.8720 (mmt) cc_final: 0.8308 (mmt) REVERT: LE 282 TYR cc_start: 0.9319 (m-10) cc_final: 0.9095 (m-10) REVERT: Lk 30 ASP cc_start: 0.9196 (p0) cc_final: 0.8906 (p0) REVERT: LY 30 MET cc_start: 0.9410 (mmm) cc_final: 0.8825 (mmt) REVERT: LY 37 GLU cc_start: 0.8923 (pm20) cc_final: 0.8462 (pm20) REVERT: LY 38 LEU cc_start: 0.9531 (mt) cc_final: 0.8783 (mt) REVERT: LY 43 ASN cc_start: 0.9323 (t0) cc_final: 0.9051 (t0) REVERT: LY 67 ILE cc_start: 0.9536 (OUTLIER) cc_final: 0.9291 (tp) REVERT: Lh 18 LEU cc_start: 0.9427 (mt) cc_final: 0.9218 (mt) REVERT: Lh 32 ARG cc_start: 0.9435 (ttm110) cc_final: 0.9004 (ptp90) REVERT: Lh 35 LYS cc_start: 0.9460 (ptmm) cc_final: 0.8840 (tppt) REVERT: LX 46 PHE cc_start: 0.8036 (t80) cc_final: 0.6785 (m-80) REVERT: LX 116 LEU cc_start: 0.9540 (tp) cc_final: 0.9086 (tp) REVERT: LX 117 TYR cc_start: 0.8935 (m-10) cc_final: 0.8621 (m-10) REVERT: LX 134 LYS cc_start: 0.7917 (tttt) cc_final: 0.7623 (tptt) REVERT: LR 10 LEU cc_start: 0.9563 (mt) cc_final: 0.9300 (tp) REVERT: LR 34 ASN cc_start: 0.8957 (m110) cc_final: 0.8708 (m-40) REVERT: LR 38 ARG cc_start: 0.9541 (mtt-85) cc_final: 0.8806 (mtt-85) REVERT: LR 51 ILE cc_start: 0.9383 (pt) cc_final: 0.9007 (mp) REVERT: LR 52 ARG cc_start: 0.9073 (ttm-80) cc_final: 0.8820 (ttm-80) REVERT: LR 76 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7251 (tmm) REVERT: LR 99 MET cc_start: 0.2395 (OUTLIER) cc_final: 0.2061 (ttt) REVERT: Lr 6 GLN cc_start: 0.9570 (mp10) cc_final: 0.9363 (mp10) REVERT: Lr 33 LYS cc_start: 0.8646 (mtmt) cc_final: 0.8189 (mmmt) REVERT: Lr 47 LYS cc_start: 0.8648 (tttt) cc_final: 0.8338 (tttt) REVERT: Lr 56 ASP cc_start: 0.8955 (p0) cc_final: 0.8538 (p0) REVERT: Lr 58 LYS cc_start: 0.8905 (tppt) cc_final: 0.8563 (tppt) REVERT: Lr 65 LYS cc_start: 0.9425 (tppt) cc_final: 0.8959 (ttmm) REVERT: Lr 83 ASN cc_start: 0.8872 (t0) cc_final: 0.8067 (t0) REVERT: B 166 MET cc_start: 0.0053 (tmm) cc_final: -0.1021 (tpp) REVERT: B 171 LEU cc_start: 0.5965 (mm) cc_final: 0.5700 (mt) REVERT: B 618 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7471 (tm-30) REVERT: B 625 LYS cc_start: 0.8139 (pptt) cc_final: 0.7911 (pttp) REVERT: C 28 MET cc_start: 0.7008 (tpt) cc_final: 0.5731 (ptt) REVERT: C 60 MET cc_start: 0.5165 (mmm) cc_final: 0.4430 (mmm) REVERT: C 69 HIS cc_start: 0.2955 (t70) cc_final: 0.1559 (t-90) REVERT: C 98 MET cc_start: -0.4621 (tpt) cc_final: -0.6131 (mtt) REVERT: Ld 22 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9277 (t) REVERT: Ld 44 ARG cc_start: 0.9308 (tpt90) cc_final: 0.8828 (tpt90) REVERT: Ld 50 ARG cc_start: 0.9454 (mtt180) cc_final: 0.8933 (mmt180) REVERT: Ld 115 LYS cc_start: 0.8916 (tptt) cc_final: 0.8560 (tptp) REVERT: LP 7 ASP cc_start: 0.8677 (t0) cc_final: 0.8437 (t0) REVERT: LP 31 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8341 (mm-30) REVERT: LP 34 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7987 (mt0) REVERT: LP 60 PHE cc_start: 0.9649 (m-80) cc_final: 0.9095 (m-80) outliers start: 116 outliers final: 71 residues processed: 518 average time/residue: 0.2755 time to fit residues: 231.4929 Evaluate side-chains 500 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 421 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 770 MET Chi-restraints excluded: chain LC residue 52 TYR Chi-restraints excluded: chain LC residue 57 LEU Chi-restraints excluded: chain LC residue 125 CYS Chi-restraints excluded: chain LC residue 144 ILE Chi-restraints excluded: chain LC residue 152 LEU Chi-restraints excluded: chain LC residue 156 ASP Chi-restraints excluded: chain LC residue 235 LEU Chi-restraints excluded: chain LC residue 251 ILE Chi-restraints excluded: chain LC residue 285 ILE Chi-restraints excluded: chain LC residue 361 LEU Chi-restraints excluded: chain LE residue 143 SER Chi-restraints excluded: chain LE residue 200 LYS Chi-restraints excluded: chain LE residue 243 THR Chi-restraints excluded: chain Lk residue 9 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 67 ILE Chi-restraints excluded: chain LY residue 106 ILE Chi-restraints excluded: chain LY residue 109 LEU Chi-restraints excluded: chain Lh residue 14 LYS Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Lh residue 48 ARG Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain LX residue 84 GLU Chi-restraints excluded: chain LX residue 96 LEU Chi-restraints excluded: chain LX residue 100 VAL Chi-restraints excluded: chain LX residue 101 ASP Chi-restraints excluded: chain LX residue 118 ASP Chi-restraints excluded: chain LX residue 121 VAL Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LR residue 22 VAL Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 76 MET Chi-restraints excluded: chain LR residue 99 MET Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain Lr residue 23 GLN Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 81 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain C residue 71 HIS Chi-restraints excluded: chain LU residue 76 VAL Chi-restraints excluded: chain Ld residue 22 THR Chi-restraints excluded: chain Ld residue 27 ILE Chi-restraints excluded: chain Ld residue 49 ILE Chi-restraints excluded: chain Ld residue 55 LYS Chi-restraints excluded: chain Ld residue 72 VAL Chi-restraints excluded: chain Ld residue 80 VAL Chi-restraints excluded: chain Ld residue 84 ILE Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain LP residue 22 LEU Chi-restraints excluded: chain LP residue 51 VAL Chi-restraints excluded: chain LP residue 91 LEU Chi-restraints excluded: chain LP residue 97 ASN Chi-restraints excluded: chain LP residue 113 VAL Chi-restraints excluded: chain LP residue 119 VAL Chi-restraints excluded: chain LP residue 142 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 189 optimal weight: 4.9990 chunk 267 optimal weight: 0.5980 chunk 233 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 341 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 231 optimal weight: 7.9990 chunk 334 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 ASN ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 828 HIS ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.097398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.064999 restraints weight = 295393.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.066337 restraints weight = 231566.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.065259 restraints weight = 187455.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.065441 restraints weight = 180160.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.065284 restraints weight = 181963.373| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 45369 Z= 0.192 Angle : 0.676 17.021 64054 Z= 0.363 Chirality : 0.041 0.364 7532 Planarity : 0.005 0.057 5874 Dihedral : 23.246 177.251 13912 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.41 % Rotamer: Outliers : 3.28 % Allowed : 15.70 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 3650 helix: 0.05 (0.11), residues: 2057 sheet: -1.19 (0.31), residues: 264 loop : -0.78 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGLd 67 TYR 0.035 0.002 TYRLC 331 PHE 0.029 0.002 PHELC 39 TRP 0.025 0.002 TRPLR 95 HIS 0.008 0.002 HIS D 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (45369) covalent geometry : angle 0.67573 / 0.36 (64054) hydrogen bonds : bond 0.07002 / 4.73 ( 2019) hydrogen bonds : angle 5.27295 / 3.74 ( 5326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 450 time to evaluate : 1.700 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: 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: 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: symmetry clash REVERT: A 14 MET cc_start: 0.3932 (mmp) cc_final: 0.3330 (mmm) REVERT: D 156 ILE cc_start: 0.6028 (OUTLIER) cc_final: 0.5595 (mm) REVERT: D 273 MET cc_start: 0.4092 (tmm) cc_final: 0.2514 (mtt) REVERT: D 316 MET cc_start: -0.5519 (OUTLIER) cc_final: -0.6046 (tpt) REVERT: D 343 GLU cc_start: 0.3911 (OUTLIER) cc_final: 0.3584 (pp20) REVERT: D 770 MET cc_start: 0.2474 (ttt) cc_final: 0.2223 (ptm) REVERT: LC 33 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.8315 (mmp-170) REVERT: LC 52 TYR cc_start: -0.1240 (OUTLIER) cc_final: -0.2179 (m-10) REVERT: LC 102 PHE cc_start: 0.8891 (t80) cc_final: 0.7144 (p90) REVERT: LC 156 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: LC 211 TYR cc_start: 0.9112 (p90) cc_final: 0.8421 (p90) REVERT: LC 325 MET cc_start: 0.8644 (mmp) cc_final: 0.8393 (mmt) REVERT: LC 331 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.5790 (m-10) REVERT: LE 115 TYR cc_start: 0.8808 (t80) cc_final: 0.8428 (t80) REVERT: LE 119 GLU cc_start: 0.5654 (pm20) cc_final: 0.5200 (pm20) REVERT: LE 282 TYR cc_start: 0.9326 (m-10) cc_final: 0.9044 (m-10) REVERT: Lk 30 ASP cc_start: 0.9141 (p0) cc_final: 0.8837 (p0) REVERT: LY 37 GLU cc_start: 0.8991 (pm20) cc_final: 0.8495 (pm20) REVERT: LY 38 LEU cc_start: 0.9389 (mt) cc_final: 0.8940 (mt) REVERT: LY 43 ASN cc_start: 0.9296 (t0) cc_final: 0.9008 (t0) REVERT: LY 67 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9256 (tp) REVERT: Lh 35 LYS cc_start: 0.9461 (ptmm) cc_final: 0.8853 (tppt) REVERT: LX 46 PHE cc_start: 0.8063 (t80) cc_final: 0.6769 (m-80) REVERT: LX 76 ILE cc_start: 0.9499 (mt) cc_final: 0.9250 (mm) REVERT: LX 88 LYS cc_start: 0.9512 (mtmm) cc_final: 0.9071 (mttm) REVERT: LX 116 LEU cc_start: 0.9518 (tp) cc_final: 0.9026 (tp) REVERT: LX 117 TYR cc_start: 0.8894 (m-10) cc_final: 0.8549 (m-10) REVERT: LX 134 LYS cc_start: 0.7880 (tttt) cc_final: 0.7599 (tptt) REVERT: LR 10 LEU cc_start: 0.9517 (mt) cc_final: 0.9248 (tp) REVERT: LR 34 ASN cc_start: 0.8960 (m110) cc_final: 0.8690 (m110) REVERT: LR 38 ARG cc_start: 0.9520 (mtt-85) cc_final: 0.8803 (mtt-85) REVERT: LR 51 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9073 (mp) REVERT: LR 52 ARG cc_start: 0.9099 (ttm-80) cc_final: 0.8795 (ttm-80) REVERT: LR 76 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7167 (tmm) REVERT: LR 99 MET cc_start: 0.2299 (OUTLIER) cc_final: 0.1899 (ttt) REVERT: LR 119 MET cc_start: 0.8757 (pmm) cc_final: 0.8480 (pmm) REVERT: Lr 33 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8033 (mmmt) REVERT: Lr 47 LYS cc_start: 0.8693 (tttt) cc_final: 0.8417 (tttt) REVERT: Lr 56 ASP cc_start: 0.8968 (p0) cc_final: 0.8572 (p0) REVERT: Lr 58 LYS cc_start: 0.8867 (tppt) cc_final: 0.8543 (tppt) REVERT: Lr 65 LYS cc_start: 0.9413 (tppt) cc_final: 0.9002 (ttmm) REVERT: Lr 83 ASN cc_start: 0.8837 (t0) cc_final: 0.8043 (t0) REVERT: B 618 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7493 (tm-30) REVERT: B 625 LYS cc_start: 0.8103 (pptt) cc_final: 0.7903 (pttp) REVERT: C 18 ASN cc_start: 0.6859 (OUTLIER) cc_final: 0.6562 (p0) REVERT: C 28 MET cc_start: 0.6990 (tpt) cc_final: 0.6001 (ptt) REVERT: C 60 MET cc_start: 0.5257 (mmm) cc_final: 0.4570 (mmm) REVERT: C 69 HIS cc_start: 0.3263 (t70) cc_final: 0.1883 (t-90) REVERT: C 98 MET cc_start: -0.4504 (tpt) cc_final: -0.6103 (mtt) REVERT: LU 21 PHE cc_start: 0.9029 (m-80) cc_final: 0.8392 (m-80) REVERT: LU 30 GLU cc_start: 0.9414 (mm-30) cc_final: 0.8828 (pp20) REVERT: LU 34 MET cc_start: 0.8051 (ppp) cc_final: 0.7258 (ppp) REVERT: LU 78 PHE cc_start: 0.7851 (t80) cc_final: 0.7423 (t80) REVERT: Ld 44 ARG cc_start: 0.9351 (tpt90) cc_final: 0.8989 (tpt90) REVERT: Ld 48 GLU cc_start: 0.9225 (tm-30) cc_final: 0.9012 (tm-30) REVERT: Ld 50 ARG cc_start: 0.9407 (mtt180) cc_final: 0.8848 (mmt-90) REVERT: LP 7 ASP cc_start: 0.8740 (t0) cc_final: 0.8508 (t0) REVERT: LP 31 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8265 (mm-30) REVERT: LP 152 GLU cc_start: 0.8276 (tp30) cc_final: 0.7791 (tp30) outliers start: 107 outliers final: 67 residues processed: 507 average time/residue: 0.2685 time to fit residues: 220.1983 Evaluate side-chains 501 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 423 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain LC residue 52 TYR Chi-restraints excluded: chain LC residue 57 LEU Chi-restraints excluded: chain LC residue 62 THR Chi-restraints excluded: chain LC residue 125 CYS Chi-restraints excluded: chain LC residue 152 LEU Chi-restraints excluded: chain LC residue 156 ASP Chi-restraints excluded: chain LC residue 230 LEU Chi-restraints excluded: chain LC residue 235 LEU Chi-restraints excluded: chain LC residue 251 ILE Chi-restraints excluded: chain LC residue 285 ILE Chi-restraints excluded: chain LC residue 309 ILE Chi-restraints excluded: chain LC residue 331 TYR Chi-restraints excluded: chain LC residue 361 LEU Chi-restraints excluded: chain LE residue 118 THR Chi-restraints excluded: chain LE residue 200 LYS Chi-restraints excluded: chain LE residue 243 THR Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain LY residue 41 LYS Chi-restraints excluded: chain LY residue 52 ASP Chi-restraints excluded: chain LY residue 67 ILE Chi-restraints excluded: chain LY residue 106 ILE Chi-restraints excluded: chain LY residue 109 LEU Chi-restraints excluded: chain Lh residue 14 LYS Chi-restraints excluded: chain Lh residue 48 ARG Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain LX residue 73 HIS Chi-restraints excluded: chain LX residue 84 GLU Chi-restraints excluded: chain LX residue 101 ASP Chi-restraints excluded: chain LX residue 118 ASP Chi-restraints excluded: chain LX residue 121 VAL Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 76 MET Chi-restraints excluded: chain LR residue 99 MET Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 23 GLN Chi-restraints excluded: chain Lr residue 36 ASN Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 62 VAL Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain Ld residue 27 ILE Chi-restraints excluded: chain Ld residue 49 ILE Chi-restraints excluded: chain Ld residue 55 LYS Chi-restraints excluded: chain Ld residue 67 ARG Chi-restraints excluded: chain Ld residue 72 VAL Chi-restraints excluded: chain Ld residue 80 VAL Chi-restraints excluded: chain Ld residue 84 ILE Chi-restraints excluded: chain Ld residue 102 LEU Chi-restraints excluded: chain Ld residue 103 TYR Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain LP residue 22 LEU Chi-restraints excluded: chain LP residue 48 LEU Chi-restraints excluded: chain LP residue 51 VAL Chi-restraints excluded: chain LP residue 113 VAL Chi-restraints excluded: chain LP residue 119 VAL Chi-restraints excluded: chain LP residue 142 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 244 optimal weight: 0.0070 chunk 212 optimal weight: 9.9990 chunk 306 optimal weight: 30.0000 chunk 220 optimal weight: 7.9990 chunk 333 optimal weight: 7.9990 chunk 115 optimal weight: 30.0000 chunk 247 optimal weight: 10.0000 chunk 316 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 360 optimal weight: 1.9990 overall best weight: 5.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 256 GLN ** LX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.096689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.064795 restraints weight = 294757.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.064354 restraints weight = 240108.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.064642 restraints weight = 198616.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.064523 restraints weight = 179191.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.064529 restraints weight = 185251.856| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45369 Z= 0.207 Angle : 0.691 17.696 64054 Z= 0.372 Chirality : 0.042 0.534 7532 Planarity : 0.005 0.057 5874 Dihedral : 23.268 177.215 13912 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 23.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 3.74 % Allowed : 16.49 % Favored : 79.77 % 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: -0.62 (0.13), residues: 3650 helix: 0.05 (0.11), residues: 2040 sheet: -1.22 (0.32), residues: 255 loop : -0.77 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGLC 336 TYR 0.024 0.002 TYRLE 69 PHE 0.017 0.002 PHELd 114 TRP 0.028 0.002 TRPLR 95 HIS 0.008 0.002 HIS C 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.21 (45369) covalent geometry : angle 0.69070 / 0.37 (64054) hydrogen bonds : bond 0.07221 / 4.89 ( 2019) hydrogen bonds : angle 5.23117 / 3.72 ( 5326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 441 time to evaluate : 1.340 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.4503 (mmp) cc_final: 0.3753 (mmm) REVERT: D 20 CYS cc_start: 0.3096 (m) cc_final: 0.2675 (m) REVERT: D 156 ILE cc_start: 0.5811 (OUTLIER) cc_final: 0.5409 (mm) REVERT: D 316 MET cc_start: -0.5518 (OUTLIER) cc_final: -0.6046 (tpt) REVERT: D 343 GLU cc_start: 0.3852 (OUTLIER) cc_final: 0.3521 (pp20) REVERT: LC 102 PHE cc_start: 0.8679 (t80) cc_final: 0.6952 (p90) REVERT: LC 156 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: LC 315 LYS cc_start: 0.9272 (tttm) cc_final: 0.9044 (tptm) REVERT: LC 325 MET cc_start: 0.8725 (mmp) cc_final: 0.8431 (mmt) REVERT: LC 331 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.6524 (m-10) REVERT: LC 335 MET cc_start: 0.8867 (mpp) cc_final: 0.8557 (mpp) REVERT: LE 115 TYR cc_start: 0.8819 (t80) cc_final: 0.8471 (t80) REVERT: LE 119 GLU cc_start: 0.5486 (pm20) cc_final: 0.5227 (mp0) REVERT: Lk 30 ASP cc_start: 0.9187 (p0) cc_final: 0.8858 (p0) REVERT: LY 37 GLU cc_start: 0.9015 (pm20) cc_final: 0.8563 (pm20) REVERT: LY 38 LEU cc_start: 0.9407 (mt) cc_final: 0.8938 (mt) REVERT: LY 43 ASN cc_start: 0.9314 (t0) cc_final: 0.9045 (t0) REVERT: LY 67 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9262 (tp) REVERT: Lh 32 ARG cc_start: 0.9558 (ttm110) cc_final: 0.9302 (ttm110) REVERT: Lh 35 LYS cc_start: 0.9516 (ptmm) cc_final: 0.8922 (tppt) REVERT: Lh 48 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7395 (mpt180) REVERT: LX 76 ILE cc_start: 0.9571 (mt) cc_final: 0.9371 (mm) REVERT: LX 88 LYS cc_start: 0.9489 (mtmm) cc_final: 0.9080 (mttm) REVERT: LX 116 LEU cc_start: 0.9553 (tp) cc_final: 0.9091 (tp) REVERT: LX 117 TYR cc_start: 0.8960 (m-10) cc_final: 0.8609 (m-10) REVERT: LX 134 LYS cc_start: 0.7879 (tttt) cc_final: 0.7538 (tppt) REVERT: LR 10 LEU cc_start: 0.9521 (mt) cc_final: 0.9270 (tp) REVERT: LR 34 ASN cc_start: 0.9029 (m110) cc_final: 0.8773 (m110) REVERT: LR 38 ARG cc_start: 0.9507 (mtt-85) cc_final: 0.8837 (mtt-85) REVERT: LR 51 ILE cc_start: 0.9451 (pt) cc_final: 0.9111 (mp) REVERT: LR 52 ARG cc_start: 0.9132 (ttm-80) cc_final: 0.8881 (ttm-80) REVERT: LR 76 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7268 (tmm) REVERT: LR 96 MET cc_start: 0.3457 (mmt) cc_final: 0.3033 (mmt) REVERT: LR 119 MET cc_start: 0.8810 (pmm) cc_final: 0.8578 (pmm) REVERT: Lr 33 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8034 (mmmt) REVERT: Lr 41 ASN cc_start: 0.8980 (t0) cc_final: 0.8751 (t0) REVERT: Lr 52 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8570 (mp0) REVERT: Lr 56 ASP cc_start: 0.9000 (p0) cc_final: 0.8621 (p0) REVERT: Lr 58 LYS cc_start: 0.8939 (tppt) cc_final: 0.8630 (tppt) REVERT: Lr 65 LYS cc_start: 0.9436 (tppt) cc_final: 0.8988 (ttmm) REVERT: Lr 83 ASN cc_start: 0.8841 (t0) cc_final: 0.8093 (t0) REVERT: B 32 PHE cc_start: 0.7872 (m-80) cc_final: 0.7643 (m-80) REVERT: B 166 MET cc_start: -0.1450 (tmm) cc_final: -0.2257 (tpp) REVERT: C 18 ASN cc_start: 0.6424 (OUTLIER) cc_final: 0.5996 (p0) REVERT: C 28 MET cc_start: 0.6864 (tpt) cc_final: 0.6001 (ptt) REVERT: C 60 MET cc_start: 0.5114 (mmm) cc_final: 0.4255 (mmm) REVERT: C 69 HIS cc_start: 0.2970 (t70) cc_final: 0.1530 (t-90) REVERT: C 98 MET cc_start: -0.4333 (tpt) cc_final: -0.6058 (mtt) REVERT: LU 21 PHE cc_start: 0.9050 (m-80) cc_final: 0.8601 (m-80) REVERT: LU 30 GLU cc_start: 0.9429 (mm-30) cc_final: 0.8805 (pp20) REVERT: LU 34 MET cc_start: 0.8156 (ppp) cc_final: 0.7550 (ppp) REVERT: Ld 22 THR cc_start: 0.9527 (OUTLIER) cc_final: 0.9317 (t) REVERT: Ld 44 ARG cc_start: 0.9399 (tpt90) cc_final: 0.9173 (tpt90) REVERT: Ld 47 LYS cc_start: 0.9321 (mptt) cc_final: 0.9055 (mptt) REVERT: Ld 48 GLU cc_start: 0.9277 (tm-30) cc_final: 0.9014 (tm-30) REVERT: Ld 50 ARG cc_start: 0.9419 (mtt180) cc_final: 0.8899 (mmt180) REVERT: LP 7 ASP cc_start: 0.8802 (t0) cc_final: 0.8590 (t0) REVERT: LP 31 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8169 (mm-30) REVERT: LP 115 GLU cc_start: 0.9134 (pm20) cc_final: 0.8851 (pm20) outliers start: 122 outliers final: 78 residues processed: 510 average time/residue: 0.2587 time to fit residues: 213.7675 Evaluate side-chains 507 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 419 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 411 PHE Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain LC residue 52 TYR Chi-restraints excluded: chain LC residue 57 LEU Chi-restraints excluded: chain LC residue 62 THR Chi-restraints excluded: chain LC residue 125 CYS Chi-restraints excluded: chain LC residue 144 ILE Chi-restraints excluded: chain LC residue 156 ASP Chi-restraints excluded: chain LC residue 235 LEU Chi-restraints excluded: chain LC residue 251 ILE Chi-restraints excluded: chain LC residue 285 ILE Chi-restraints excluded: chain LC residue 309 ILE Chi-restraints excluded: chain LC residue 317 ASN Chi-restraints excluded: chain LC residue 331 TYR Chi-restraints excluded: chain LC residue 361 LEU Chi-restraints excluded: chain LE residue 118 THR Chi-restraints excluded: chain LE residue 200 LYS Chi-restraints excluded: chain LE residue 243 THR Chi-restraints excluded: chain Lk residue 9 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 41 LYS Chi-restraints excluded: chain LY residue 67 ILE Chi-restraints excluded: chain LY residue 102 SER Chi-restraints excluded: chain LY residue 106 ILE Chi-restraints excluded: chain Lh residue 4 ILE Chi-restraints excluded: chain Lh residue 18 LEU Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Lh residue 48 ARG Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain LX residue 84 GLU Chi-restraints excluded: chain LX residue 96 LEU Chi-restraints excluded: chain LX residue 101 ASP Chi-restraints excluded: chain LX residue 118 ASP Chi-restraints excluded: chain LX residue 121 VAL Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 76 MET Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 62 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain LU residue 76 VAL Chi-restraints excluded: chain Ld residue 22 THR Chi-restraints excluded: chain Ld residue 27 ILE Chi-restraints excluded: chain Ld residue 49 ILE Chi-restraints excluded: chain Ld residue 55 LYS Chi-restraints excluded: chain Ld residue 67 ARG Chi-restraints excluded: chain Ld residue 72 VAL Chi-restraints excluded: chain Ld residue 80 VAL Chi-restraints excluded: chain Ld residue 84 ILE Chi-restraints excluded: chain Ld residue 102 LEU Chi-restraints excluded: chain Ld residue 103 TYR Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain LP residue 22 LEU Chi-restraints excluded: chain LP residue 34 GLN Chi-restraints excluded: chain LP residue 48 LEU Chi-restraints excluded: chain LP residue 90 PHE Chi-restraints excluded: chain LP residue 113 VAL Chi-restraints excluded: chain LP residue 119 VAL Chi-restraints excluded: chain LP residue 142 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 80 optimal weight: 0.0270 chunk 281 optimal weight: 5.9990 chunk 272 optimal weight: 0.9990 chunk 302 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 134 optimal weight: 30.0000 chunk 10 optimal weight: 50.0000 chunk 337 optimal weight: 3.9990 chunk 372 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 256 GLN ** LX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 36 ASN Lr 45 HIS ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.097562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.065358 restraints weight = 294543.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.066643 restraints weight = 231570.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.065636 restraints weight = 202049.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.065716 restraints weight = 190063.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.065712 restraints weight = 184153.495| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 45369 Z= 0.169 Angle : 0.669 15.784 64054 Z= 0.357 Chirality : 0.041 0.376 7532 Planarity : 0.005 0.057 5874 Dihedral : 23.235 177.472 13912 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 3.19 % Allowed : 18.27 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3650 helix: 0.13 (0.11), residues: 2049 sheet: -1.20 (0.32), residues: 261 loop : -0.72 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGLC 71 TYR 0.033 0.002 TYRLC 331 PHE 0.031 0.002 PHELC 39 TRP 0.020 0.002 TRPLR 95 HIS 0.007 0.002 HIS C 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (45369) covalent geometry : angle 0.66867 / 0.36 (64054) hydrogen bonds : bond 0.06525 / 4.39 ( 2019) hydrogen bonds : angle 5.13859 / 3.65 ( 5326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 444 time to evaluate : 1.389 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: 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: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.4486 (mmp) cc_final: 0.3689 (mmm) REVERT: D 156 ILE cc_start: 0.5969 (OUTLIER) cc_final: 0.5577 (mm) REVERT: D 316 MET cc_start: -0.5527 (OUTLIER) cc_final: -0.6004 (tpt) REVERT: D 343 GLU cc_start: 0.4016 (OUTLIER) cc_final: 0.3718 (pp20) REVERT: LC 102 PHE cc_start: 0.8540 (t80) cc_final: 0.6889 (p90) REVERT: LC 156 ASP cc_start: 0.7698 (m-30) cc_final: 0.7408 (m-30) REVERT: LC 211 TYR cc_start: 0.9124 (p90) cc_final: 0.8484 (p90) REVERT: LC 315 LYS cc_start: 0.9221 (tttm) cc_final: 0.8996 (tptm) REVERT: LC 325 MET cc_start: 0.8654 (mmp) cc_final: 0.8354 (mmt) REVERT: LC 331 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.6702 (m-10) REVERT: LE 115 TYR cc_start: 0.8805 (t80) cc_final: 0.8473 (t80) REVERT: LE 119 GLU cc_start: 0.5447 (pm20) cc_final: 0.5210 (mp0) REVERT: Lk 30 ASP cc_start: 0.9119 (p0) cc_final: 0.8790 (p0) REVERT: LY 37 GLU cc_start: 0.9060 (pm20) cc_final: 0.8601 (pm20) REVERT: LY 38 LEU cc_start: 0.9402 (mt) cc_final: 0.9022 (mt) REVERT: LY 43 ASN cc_start: 0.9270 (t0) cc_final: 0.8954 (t0) REVERT: LY 67 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9236 (tp) REVERT: LY 80 ILE cc_start: 0.9534 (mp) cc_final: 0.9316 (tp) REVERT: Lh 32 ARG cc_start: 0.9411 (ttm110) cc_final: 0.9114 (ttm110) REVERT: Lh 35 LYS cc_start: 0.9511 (ptmm) cc_final: 0.8966 (tppt) REVERT: Lh 48 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7369 (mpt180) REVERT: LX 116 LEU cc_start: 0.9515 (tp) cc_final: 0.9062 (tp) REVERT: LX 117 TYR cc_start: 0.8943 (m-10) cc_final: 0.8588 (m-10) REVERT: LX 134 LYS cc_start: 0.7900 (tttt) cc_final: 0.7669 (tptt) REVERT: LR 10 LEU cc_start: 0.9494 (mt) cc_final: 0.9245 (tp) REVERT: LR 34 ASN cc_start: 0.9034 (m110) cc_final: 0.8806 (m110) REVERT: LR 38 ARG cc_start: 0.9486 (mtt-85) cc_final: 0.8831 (mtt-85) REVERT: LR 51 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9060 (mp) REVERT: LR 52 ARG cc_start: 0.9164 (ttm-80) cc_final: 0.8791 (ttm-80) REVERT: LR 76 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7189 (tmm) REVERT: LR 96 MET cc_start: 0.3185 (mmt) cc_final: 0.2930 (mmt) REVERT: Lr 33 LYS cc_start: 0.8550 (mtmt) cc_final: 0.7993 (mmmt) REVERT: Lr 41 ASN cc_start: 0.8973 (t0) cc_final: 0.8697 (t0) REVERT: Lr 44 ILE cc_start: 0.9531 (pp) cc_final: 0.9311 (pp) REVERT: Lr 56 ASP cc_start: 0.9035 (p0) cc_final: 0.8665 (p0) REVERT: Lr 58 LYS cc_start: 0.8955 (tppt) cc_final: 0.8675 (tppt) REVERT: Lr 65 LYS cc_start: 0.9413 (tppt) cc_final: 0.8937 (ttmm) REVERT: Lr 83 ASN cc_start: 0.8826 (t0) cc_final: 0.8040 (t0) REVERT: B 166 MET cc_start: -0.0465 (tmm) cc_final: -0.1180 (tpp) REVERT: C 18 ASN cc_start: 0.7032 (OUTLIER) cc_final: 0.6466 (p0) REVERT: C 60 MET cc_start: 0.5274 (mmm) cc_final: 0.4602 (mmm) REVERT: C 69 HIS cc_start: 0.3354 (t70) cc_final: 0.1936 (t-90) REVERT: C 98 MET cc_start: -0.4331 (tpt) cc_final: -0.6184 (mtt) REVERT: LU 21 PHE cc_start: 0.8947 (m-80) cc_final: 0.8485 (m-80) REVERT: LU 30 GLU cc_start: 0.9374 (mm-30) cc_final: 0.8750 (pp20) REVERT: LU 34 MET cc_start: 0.7984 (ppp) cc_final: 0.7441 (ppp) REVERT: Ld 44 ARG cc_start: 0.9360 (tpt90) cc_final: 0.9136 (tpt90) REVERT: Ld 47 LYS cc_start: 0.9338 (mptt) cc_final: 0.9044 (mptt) REVERT: Ld 48 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8991 (tm-30) REVERT: Ld 50 ARG cc_start: 0.9413 (mtt180) cc_final: 0.9125 (mtt-85) REVERT: LP 7 ASP cc_start: 0.8731 (t0) cc_final: 0.8526 (t0) REVERT: LP 31 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8128 (mm-30) REVERT: LP 34 GLN cc_start: 0.7022 (mm-40) cc_final: 0.6542 (mt0) REVERT: LP 115 GLU cc_start: 0.9128 (pm20) cc_final: 0.8904 (pm20) outliers start: 104 outliers final: 69 residues processed: 498 average time/residue: 0.2521 time to fit residues: 203.6274 Evaluate side-chains 498 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 420 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 411 PHE Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain LC residue 52 TYR Chi-restraints excluded: chain LC residue 57 LEU Chi-restraints excluded: chain LC residue 62 THR Chi-restraints excluded: chain LC residue 125 CYS Chi-restraints excluded: chain LC residue 144 ILE Chi-restraints excluded: chain LC residue 235 LEU Chi-restraints excluded: chain LC residue 285 ILE Chi-restraints excluded: chain LC residue 309 ILE Chi-restraints excluded: chain LC residue 317 ASN Chi-restraints excluded: chain LC residue 331 TYR Chi-restraints excluded: chain LC residue 361 LEU Chi-restraints excluded: chain LE residue 118 THR Chi-restraints excluded: chain LE residue 200 LYS Chi-restraints excluded: chain LE residue 243 THR Chi-restraints excluded: chain Lk residue 9 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 12 SER Chi-restraints excluded: chain LY residue 67 ILE Chi-restraints excluded: chain LY residue 106 ILE Chi-restraints excluded: chain Lh residue 4 ILE Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Lh residue 48 ARG Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain LX residue 101 ASP Chi-restraints excluded: chain LX residue 118 ASP Chi-restraints excluded: chain LX residue 121 VAL Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 76 MET Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 62 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain Ld residue 27 ILE Chi-restraints excluded: chain Ld residue 55 LYS Chi-restraints excluded: chain Ld residue 67 ARG Chi-restraints excluded: chain Ld residue 80 VAL Chi-restraints excluded: chain Ld residue 84 ILE Chi-restraints excluded: chain Ld residue 102 LEU Chi-restraints excluded: chain Ld residue 103 TYR Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain LP residue 22 LEU Chi-restraints excluded: chain LP residue 48 LEU Chi-restraints excluded: chain LP residue 90 PHE Chi-restraints excluded: chain LP residue 113 VAL Chi-restraints excluded: chain LP residue 114 ILE Chi-restraints excluded: chain LP residue 142 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 112 optimal weight: 30.0000 chunk 382 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 323 optimal weight: 20.0000 chunk 249 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 314 optimal weight: 40.0000 chunk 44 optimal weight: 20.0000 overall best weight: 4.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 36 ASN Lr 100 ASN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 50 ASN ** LP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.096931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.065292 restraints weight = 295818.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.066003 restraints weight = 228558.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.065016 restraints weight = 190414.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.065334 restraints weight = 183487.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.065136 restraints weight = 174656.605| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 45369 Z= 0.199 Angle : 0.700 15.375 64054 Z= 0.373 Chirality : 0.042 0.386 7532 Planarity : 0.005 0.058 5874 Dihedral : 23.242 177.499 13912 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 3.34 % Allowed : 18.61 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3650 helix: 0.04 (0.11), residues: 2059 sheet: -1.18 (0.32), residues: 260 loop : -0.78 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGLd 67 TYR 0.033 0.002 TYR B 21 PHE 0.024 0.002 PHELX 46 TRP 0.026 0.002 TRPLR 95 HIS 0.007 0.002 HISLE 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.20 (45369) covalent geometry : angle 0.69988 / 0.37 (64054) hydrogen bonds : bond 0.06910 / 4.67 ( 2019) hydrogen bonds : angle 5.16266 / 3.67 ( 5326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 435 time to evaluate : 1.147 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.4651 (mmp) cc_final: 0.3848 (mmm) REVERT: D 316 MET cc_start: -0.5414 (OUTLIER) cc_final: -0.5961 (tpt) REVERT: D 343 GLU cc_start: 0.4126 (OUTLIER) cc_final: 0.3814 (pp20) REVERT: D 770 MET cc_start: 0.2014 (ttt) cc_final: 0.0983 (tmm) REVERT: LC 102 PHE cc_start: 0.8463 (t80) cc_final: 0.6839 (p90) REVERT: LC 156 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: LC 211 TYR cc_start: 0.9120 (p90) cc_final: 0.8509 (p90) REVERT: LC 325 MET cc_start: 0.8641 (mmp) cc_final: 0.8327 (mmt) REVERT: LC 331 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7139 (m-10) REVERT: LE 115 TYR cc_start: 0.8763 (t80) cc_final: 0.8435 (t80) REVERT: LE 120 ASP cc_start: 0.8725 (t0) cc_final: 0.8431 (m-30) REVERT: LE 282 TYR cc_start: 0.9388 (m-80) cc_final: 0.8858 (m-10) REVERT: Lk 30 ASP cc_start: 0.9204 (p0) cc_final: 0.8880 (p0) REVERT: LY 37 GLU cc_start: 0.9099 (pm20) cc_final: 0.8635 (pm20) REVERT: LY 38 LEU cc_start: 0.9479 (mt) cc_final: 0.9040 (mt) REVERT: LY 43 ASN cc_start: 0.9195 (t0) cc_final: 0.8924 (t0) REVERT: LY 67 ILE cc_start: 0.9525 (OUTLIER) cc_final: 0.9259 (tp) REVERT: LY 80 ILE cc_start: 0.9554 (mp) cc_final: 0.9315 (tp) REVERT: Lh 32 ARG cc_start: 0.9502 (ttm110) cc_final: 0.9230 (ttm110) REVERT: Lh 35 LYS cc_start: 0.9548 (ptmm) cc_final: 0.9068 (tppt) REVERT: Lh 48 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7406 (mpt180) REVERT: LX 114 LYS cc_start: 0.9535 (mmtp) cc_final: 0.9253 (mmmt) REVERT: LX 116 LEU cc_start: 0.9560 (tp) cc_final: 0.9110 (tp) REVERT: LX 117 TYR cc_start: 0.8945 (m-10) cc_final: 0.8594 (m-10) REVERT: LX 134 LYS cc_start: 0.7891 (tttt) cc_final: 0.7656 (tptt) REVERT: LX 139 ARG cc_start: 0.8994 (tpt-90) cc_final: 0.8475 (tpt-90) REVERT: LR 10 LEU cc_start: 0.9483 (mt) cc_final: 0.9257 (tp) REVERT: LR 34 ASN cc_start: 0.9053 (m110) cc_final: 0.8827 (m110) REVERT: LR 38 ARG cc_start: 0.9473 (mtt-85) cc_final: 0.8826 (mtt-85) REVERT: LR 51 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9105 (mp) REVERT: LR 52 ARG cc_start: 0.9136 (ttm-80) cc_final: 0.8706 (ttm-80) REVERT: LR 76 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7261 (tmm) REVERT: LR 96 MET cc_start: 0.3557 (mmt) cc_final: 0.3295 (mmt) REVERT: LR 134 ASN cc_start: 0.9229 (m-40) cc_final: 0.8978 (m110) REVERT: Lr 33 LYS cc_start: 0.8560 (mtmt) cc_final: 0.7991 (mmmt) REVERT: Lr 41 ASN cc_start: 0.9009 (t0) cc_final: 0.8564 (t0) REVERT: Lr 44 ILE cc_start: 0.9514 (pp) cc_final: 0.9210 (pp) REVERT: Lr 56 ASP cc_start: 0.8990 (p0) cc_final: 0.8596 (p0) REVERT: Lr 58 LYS cc_start: 0.8942 (tppt) cc_final: 0.8664 (tppt) REVERT: Lr 65 LYS cc_start: 0.9445 (tppt) cc_final: 0.8990 (ttmm) REVERT: Lr 83 ASN cc_start: 0.8885 (t0) cc_final: 0.8046 (t0) REVERT: B 96 TYR cc_start: 0.7441 (m-80) cc_final: 0.7110 (m-80) REVERT: B 166 MET cc_start: -0.0755 (tmm) cc_final: -0.1570 (tpp) REVERT: B 618 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 12 MET cc_start: 0.5761 (ppp) cc_final: 0.5428 (ptt) REVERT: C 18 ASN cc_start: 0.7094 (OUTLIER) cc_final: 0.6511 (p0) REVERT: C 60 MET cc_start: 0.5143 (mmm) cc_final: 0.4410 (mmm) REVERT: C 69 HIS cc_start: 0.3251 (t70) cc_final: 0.1706 (t-90) REVERT: C 98 MET cc_start: -0.4186 (tpt) cc_final: -0.6036 (mtt) REVERT: LU 21 PHE cc_start: 0.8961 (m-80) cc_final: 0.8531 (m-80) REVERT: LU 30 GLU cc_start: 0.9398 (mm-30) cc_final: 0.8800 (pp20) REVERT: LU 34 MET cc_start: 0.8039 (ppp) cc_final: 0.7556 (ppp) REVERT: Ld 44 ARG cc_start: 0.9408 (tpt90) cc_final: 0.9032 (tpt90) REVERT: Ld 48 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8999 (tm-30) REVERT: Ld 50 ARG cc_start: 0.9401 (mtt180) cc_final: 0.9086 (mtt-85) REVERT: LP 7 ASP cc_start: 0.8654 (t0) cc_final: 0.8430 (t0) REVERT: LP 31 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8180 (mm-30) REVERT: LP 60 PHE cc_start: 0.9582 (m-80) cc_final: 0.9113 (m-80) outliers start: 109 outliers final: 80 residues processed: 495 average time/residue: 0.2538 time to fit residues: 203.8648 Evaluate side-chains 501 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 412 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 411 PHE Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain LC residue 44 LEU Chi-restraints excluded: chain LC residue 52 TYR Chi-restraints excluded: chain LC residue 57 LEU Chi-restraints excluded: chain LC residue 62 THR Chi-restraints excluded: chain LC residue 125 CYS Chi-restraints excluded: chain LC residue 144 ILE Chi-restraints excluded: chain LC residue 156 ASP Chi-restraints excluded: chain LC residue 235 LEU Chi-restraints excluded: chain LC residue 285 ILE Chi-restraints excluded: chain LC residue 309 ILE Chi-restraints excluded: chain LC residue 317 ASN Chi-restraints excluded: chain LC residue 331 TYR Chi-restraints excluded: chain LC residue 361 LEU Chi-restraints excluded: chain LE residue 118 THR Chi-restraints excluded: chain LE residue 200 LYS Chi-restraints excluded: chain LE residue 243 THR Chi-restraints excluded: chain Lk residue 9 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 52 ASP Chi-restraints excluded: chain LY residue 67 ILE Chi-restraints excluded: chain LY residue 106 ILE Chi-restraints excluded: chain Lh residue 4 ILE Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Lh residue 48 ARG Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain LX residue 96 LEU Chi-restraints excluded: chain LX residue 101 ASP Chi-restraints excluded: chain LX residue 118 ASP Chi-restraints excluded: chain LX residue 121 VAL Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 76 MET Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 36 ASN Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 62 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 81 THR Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain Ld residue 27 ILE Chi-restraints excluded: chain Ld residue 55 LYS Chi-restraints excluded: chain Ld residue 67 ARG Chi-restraints excluded: chain Ld residue 80 VAL Chi-restraints excluded: chain Ld residue 84 ILE Chi-restraints excluded: chain Ld residue 102 LEU Chi-restraints excluded: chain Ld residue 103 TYR Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain LP residue 22 LEU Chi-restraints excluded: chain LP residue 48 LEU Chi-restraints excluded: chain LP residue 90 PHE Chi-restraints excluded: chain LP residue 97 ASN Chi-restraints excluded: chain LP residue 113 VAL Chi-restraints excluded: chain LP residue 119 VAL Chi-restraints excluded: chain LP residue 142 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 239 optimal weight: 2.9990 chunk 409 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 386 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 404 optimal weight: 8.9990 chunk 257 optimal weight: 5.9990 chunk 344 optimal weight: 30.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 GLN ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 120 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.097295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.065300 restraints weight = 296758.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.066248 restraints weight = 243199.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.065333 restraints weight = 194111.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.065481 restraints weight = 181002.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.065424 restraints weight = 185051.338| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 45369 Z= 0.183 Angle : 0.702 16.654 64054 Z= 0.374 Chirality : 0.041 0.386 7532 Planarity : 0.005 0.079 5874 Dihedral : 23.229 177.693 13912 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.70 % Rotamer: Outliers : 3.16 % Allowed : 19.28 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3650 helix: 0.03 (0.11), residues: 2049 sheet: -1.19 (0.32), residues: 259 loop : -0.77 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGLR 151 TYR 0.029 0.002 TYRLC 331 PHE 0.033 0.002 PHELC 39 TRP 0.022 0.002 TRPLR 95 HIS 0.008 0.002 HIS C 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (45369) covalent geometry : angle 0.70222 / 0.37 (64054) hydrogen bonds : bond 0.06585 / 4.44 ( 2019) hydrogen bonds : angle 5.17210 / 3.68 ( 5326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 427 time to evaluate : 1.453 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: 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: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.4811 (mmp) cc_final: 0.4066 (mmm) REVERT: D 316 MET cc_start: -0.5668 (OUTLIER) cc_final: -0.6098 (tpt) REVERT: D 343 GLU cc_start: 0.4078 (OUTLIER) cc_final: 0.3785 (pp20) REVERT: LC 65 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8777 (mp0) REVERT: LC 102 PHE cc_start: 0.8323 (t80) cc_final: 0.6748 (p90) REVERT: LC 156 ASP cc_start: 0.7780 (m-30) cc_final: 0.7488 (m-30) REVERT: LC 211 TYR cc_start: 0.9085 (p90) cc_final: 0.8483 (p90) REVERT: LC 250 CYS cc_start: 0.9349 (p) cc_final: 0.8979 (p) REVERT: LC 325 MET cc_start: 0.8593 (mmp) cc_final: 0.8292 (mmt) REVERT: LC 331 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7196 (m-10) REVERT: LE 115 TYR cc_start: 0.8750 (t80) cc_final: 0.8469 (t80) REVERT: LE 120 ASP cc_start: 0.8647 (t0) cc_final: 0.8443 (m-30) REVERT: Lk 30 ASP cc_start: 0.9170 (p0) cc_final: 0.8843 (p0) REVERT: LY 37 GLU cc_start: 0.9090 (pm20) cc_final: 0.8621 (pm20) REVERT: LY 38 LEU cc_start: 0.9485 (mt) cc_final: 0.9056 (mt) REVERT: LY 43 ASN cc_start: 0.9169 (t0) cc_final: 0.8895 (t0) REVERT: LY 52 ASP cc_start: 0.9432 (OUTLIER) cc_final: 0.8704 (p0) REVERT: LY 67 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9230 (tp) REVERT: LY 80 ILE cc_start: 0.9578 (mp) cc_final: 0.9310 (tp) REVERT: Lh 32 ARG cc_start: 0.9485 (ttm110) cc_final: 0.9210 (ttm110) REVERT: Lh 35 LYS cc_start: 0.9524 (ptmm) cc_final: 0.9038 (tppt) REVERT: Lh 48 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7403 (mpt180) REVERT: LX 114 LYS cc_start: 0.9524 (mmtp) cc_final: 0.9237 (mmmt) REVERT: LX 116 LEU cc_start: 0.9537 (tp) cc_final: 0.9086 (tp) REVERT: LX 117 TYR cc_start: 0.8929 (m-10) cc_final: 0.8576 (m-10) REVERT: LX 134 LYS cc_start: 0.7904 (tttt) cc_final: 0.7663 (tptt) REVERT: LX 139 ARG cc_start: 0.8984 (tpt-90) cc_final: 0.8476 (tpt-90) REVERT: LR 10 LEU cc_start: 0.9461 (mt) cc_final: 0.9238 (tp) REVERT: LR 34 ASN cc_start: 0.9143 (m110) cc_final: 0.8913 (m110) REVERT: LR 38 ARG cc_start: 0.9485 (mtt-85) cc_final: 0.8871 (mtt-85) REVERT: LR 51 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9093 (mp) REVERT: LR 76 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7178 (tmm) REVERT: LR 96 MET cc_start: 0.3597 (mmt) cc_final: 0.3337 (mmt) REVERT: LR 134 ASN cc_start: 0.9299 (m-40) cc_final: 0.9051 (m110) REVERT: Lr 33 LYS cc_start: 0.8429 (mtmt) cc_final: 0.7838 (mmmt) REVERT: Lr 41 ASN cc_start: 0.8982 (t0) cc_final: 0.8574 (t0) REVERT: Lr 44 ILE cc_start: 0.9503 (pp) cc_final: 0.9128 (pp) REVERT: Lr 56 ASP cc_start: 0.8991 (p0) cc_final: 0.8601 (p0) REVERT: Lr 58 LYS cc_start: 0.8950 (tppt) cc_final: 0.8645 (tppt) REVERT: Lr 65 LYS cc_start: 0.9395 (tppt) cc_final: 0.8943 (ttmm) REVERT: Lr 83 ASN cc_start: 0.8853 (t0) cc_final: 0.7989 (t0) REVERT: B 96 TYR cc_start: 0.7213 (m-80) cc_final: 0.6904 (m-80) REVERT: B 166 MET cc_start: -0.0467 (tmm) cc_final: -0.0845 (mmm) REVERT: B 625 LYS cc_start: 0.7980 (pttp) cc_final: 0.7682 (tptt) REVERT: C 18 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.6980 (p0) REVERT: C 60 MET cc_start: 0.5278 (mmm) cc_final: 0.4604 (mmm) REVERT: C 69 HIS cc_start: 0.3567 (t70) cc_final: 0.2024 (t-90) REVERT: C 98 MET cc_start: -0.4131 (tpt) cc_final: -0.5988 (mtt) REVERT: LU 21 PHE cc_start: 0.8964 (m-80) cc_final: 0.8680 (m-80) REVERT: LU 30 GLU cc_start: 0.9373 (mm-30) cc_final: 0.8801 (pp20) REVERT: LU 34 MET cc_start: 0.7945 (ppp) cc_final: 0.7491 (ppp) REVERT: Ld 44 ARG cc_start: 0.9407 (tpt90) cc_final: 0.9055 (tpt90) REVERT: Ld 48 GLU cc_start: 0.9263 (tm-30) cc_final: 0.8989 (tm-30) REVERT: Ld 50 ARG cc_start: 0.9400 (mtt180) cc_final: 0.9082 (mtt-85) REVERT: LP 7 ASP cc_start: 0.8629 (t0) cc_final: 0.8427 (t0) REVERT: LP 31 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8136 (mm-30) REVERT: LP 60 PHE cc_start: 0.9566 (m-80) cc_final: 0.9099 (m-80) outliers start: 103 outliers final: 77 residues processed: 482 average time/residue: 0.2751 time to fit residues: 215.1914 Evaluate side-chains 495 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 409 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 411 PHE Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain LC residue 44 LEU Chi-restraints excluded: chain LC residue 57 LEU Chi-restraints excluded: chain LC residue 62 THR Chi-restraints excluded: chain LC residue 71 ARG Chi-restraints excluded: chain LC residue 125 CYS Chi-restraints excluded: chain LC residue 144 ILE Chi-restraints excluded: chain LC residue 235 LEU Chi-restraints excluded: chain LC residue 285 ILE Chi-restraints excluded: chain LC residue 309 ILE Chi-restraints excluded: chain LC residue 317 ASN Chi-restraints excluded: chain LC residue 331 TYR Chi-restraints excluded: chain LC residue 361 LEU Chi-restraints excluded: chain LE residue 118 THR Chi-restraints excluded: chain LE residue 119 GLU Chi-restraints excluded: chain LE residue 200 LYS Chi-restraints excluded: chain LE residue 243 THR Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 12 SER Chi-restraints excluded: chain LY residue 52 ASP Chi-restraints excluded: chain LY residue 67 ILE Chi-restraints excluded: chain LY residue 106 ILE Chi-restraints excluded: chain Lh residue 4 ILE Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Lh residue 48 ARG Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain LX residue 96 LEU Chi-restraints excluded: chain LX residue 101 ASP Chi-restraints excluded: chain LX residue 118 ASP Chi-restraints excluded: chain LX residue 121 VAL Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 76 MET Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 24 THR Chi-restraints excluded: chain Lr residue 38 PHE Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 62 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 76 VAL Chi-restraints excluded: chain Ld residue 27 ILE Chi-restraints excluded: chain Ld residue 55 LYS Chi-restraints excluded: chain Ld residue 67 ARG Chi-restraints excluded: chain Ld residue 102 LEU Chi-restraints excluded: chain Ld residue 103 TYR Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain LP residue 22 LEU Chi-restraints excluded: chain LP residue 48 LEU Chi-restraints excluded: chain LP residue 113 VAL Chi-restraints excluded: chain LP residue 119 VAL Chi-restraints excluded: chain LP residue 142 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 62 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 281 optimal weight: 0.8980 chunk 256 optimal weight: 7.9990 chunk 413 optimal weight: 10.0000 chunk 41 optimal weight: 0.0470 chunk 244 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 356 optimal weight: 20.0000 chunk 249 optimal weight: 0.0670 chunk 218 optimal weight: 0.8980 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN D 257 ASN D 445 ASN ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 61 GLN ** LX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 36 ASN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.099832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.067273 restraints weight = 290400.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.067287 restraints weight = 237605.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.067363 restraints weight = 201827.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.067180 restraints weight = 187017.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.067193 restraints weight = 187200.539| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 45369 Z= 0.141 Angle : 0.711 19.705 64054 Z= 0.371 Chirality : 0.041 0.476 7532 Planarity : 0.005 0.057 5874 Dihedral : 23.017 177.917 13912 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 2.21 % Allowed : 20.29 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.52 (0.14), residues: 3650 helix: 0.11 (0.11), residues: 2052 sheet: -1.04 (0.33), residues: 265 loop : -0.73 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGLR 151 TYR 0.028 0.002 TYR A 122 PHE 0.052 0.002 PHE B 32 TRP 0.053 0.002 TRPLC 177 HIS 0.009 0.001 HISLE 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (45369) covalent geometry : angle 0.71080 / 0.37 (64054) hydrogen bonds : bond 0.05653 / 3.76 ( 2019) hydrogen bonds : angle 5.03079 / 3.56 ( 5326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 477 time to evaluate : 1.376 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.4756 (mmp) cc_final: 0.3593 (tpp) REVERT: D 316 MET cc_start: -0.5553 (OUTLIER) cc_final: -0.6062 (tpt) REVERT: D 838 MET cc_start: -0.1332 (mmm) cc_final: -0.1706 (mmm) REVERT: LC 33 ARG cc_start: 0.8603 (mmm-85) cc_final: 0.8227 (mmp-170) REVERT: LC 102 PHE cc_start: 0.8338 (t80) cc_final: 0.6760 (p90) REVERT: LC 124 ILE cc_start: 0.9642 (mp) cc_final: 0.9379 (mm) REVERT: LC 156 ASP cc_start: 0.7938 (m-30) cc_final: 0.7586 (m-30) REVERT: LC 203 GLN cc_start: 0.9363 (pm20) cc_final: 0.8766 (pm20) REVERT: LC 211 TYR cc_start: 0.9001 (p90) cc_final: 0.8683 (p90) REVERT: LC 325 MET cc_start: 0.8493 (mmp) cc_final: 0.8156 (mmt) REVERT: LC 331 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.7493 (m-10) REVERT: LE 115 TYR cc_start: 0.8653 (t80) cc_final: 0.8321 (t80) REVERT: LE 207 LYS cc_start: 0.8821 (mmpt) cc_final: 0.8566 (tppt) REVERT: Lk 30 ASP cc_start: 0.9119 (p0) cc_final: 0.8825 (p0) REVERT: LY 17 ARG cc_start: 0.9093 (ttp80) cc_final: 0.8876 (ttp80) REVERT: LY 37 GLU cc_start: 0.9062 (pm20) cc_final: 0.8728 (pm20) REVERT: LY 43 ASN cc_start: 0.9145 (t0) cc_final: 0.8861 (t0) REVERT: LY 67 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9195 (tp) REVERT: LY 80 ILE cc_start: 0.9494 (mp) cc_final: 0.9243 (tp) REVERT: Lh 32 ARG cc_start: 0.9463 (ttm110) cc_final: 0.9018 (ttm110) REVERT: Lh 35 LYS cc_start: 0.9490 (ptmm) cc_final: 0.8905 (tppt) REVERT: Lh 48 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7200 (mpt180) REVERT: LX 46 PHE cc_start: 0.6802 (t80) cc_final: 0.5125 (m-80) REVERT: LX 79 PHE cc_start: 0.8381 (m-80) cc_final: 0.7906 (m-80) REVERT: LX 114 LYS cc_start: 0.9517 (mmtp) cc_final: 0.9184 (mmmm) REVERT: LX 116 LEU cc_start: 0.9518 (tp) cc_final: 0.9080 (tp) REVERT: LX 117 TYR cc_start: 0.8900 (m-10) cc_final: 0.8521 (m-10) REVERT: LX 120 ASP cc_start: 0.9242 (m-30) cc_final: 0.8899 (m-30) REVERT: LX 139 ARG cc_start: 0.8963 (tpt-90) cc_final: 0.8401 (tpt-90) REVERT: LR 10 LEU cc_start: 0.9411 (mt) cc_final: 0.9207 (tp) REVERT: LR 28 GLU cc_start: 0.9376 (mm-30) cc_final: 0.8990 (mp0) REVERT: LR 34 ASN cc_start: 0.9177 (m110) cc_final: 0.8975 (m110) REVERT: LR 38 ARG cc_start: 0.9462 (mtt-85) cc_final: 0.8916 (mtt-85) REVERT: LR 51 ILE cc_start: 0.9365 (pt) cc_final: 0.9039 (mp) REVERT: LR 52 ARG cc_start: 0.9370 (ttm-80) cc_final: 0.8609 (ttm-80) REVERT: LR 76 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.6931 (tmm) REVERT: LR 96 MET cc_start: 0.3051 (mmt) cc_final: 0.2846 (mmt) REVERT: LR 111 GLU cc_start: 0.9382 (pm20) cc_final: 0.9163 (pm20) REVERT: LR 134 ASN cc_start: 0.9277 (m-40) cc_final: 0.9026 (m110) REVERT: Lr 16 PHE cc_start: 0.9676 (m-80) cc_final: 0.8834 (m-80) REVERT: Lr 33 LYS cc_start: 0.8376 (mtmt) cc_final: 0.7798 (mmmt) REVERT: Lr 41 ASN cc_start: 0.8945 (t0) cc_final: 0.8460 (t0) REVERT: Lr 44 ILE cc_start: 0.9406 (pp) cc_final: 0.9016 (pp) REVERT: Lr 56 ASP cc_start: 0.9071 (p0) cc_final: 0.8712 (p0) REVERT: Lr 58 LYS cc_start: 0.8941 (tppt) cc_final: 0.8723 (tppt) REVERT: Lr 65 LYS cc_start: 0.9398 (tppt) cc_final: 0.8926 (ttmm) REVERT: Lr 83 ASN cc_start: 0.8867 (t0) cc_final: 0.8157 (t0) REVERT: B 27 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7704 (tpt170) REVERT: B 96 TYR cc_start: 0.7448 (m-80) cc_final: 0.6774 (m-80) REVERT: B 166 MET cc_start: 0.0189 (tmm) cc_final: -0.0475 (mmm) REVERT: B 171 LEU cc_start: 0.6071 (mm) cc_final: 0.5862 (mt) REVERT: B 661 LEU cc_start: 0.2119 (mt) cc_final: 0.1766 (mt) REVERT: C 60 MET cc_start: 0.5046 (mmm) cc_final: 0.4259 (mmm) REVERT: C 69 HIS cc_start: 0.2874 (t70) cc_final: 0.1406 (t70) REVERT: C 98 MET cc_start: -0.4504 (tpt) cc_final: -0.6283 (mtt) REVERT: LU 21 PHE cc_start: 0.9018 (m-80) cc_final: 0.8687 (m-80) REVERT: LU 30 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8819 (pp20) REVERT: LU 34 MET cc_start: 0.7690 (ppp) cc_final: 0.7152 (ppp) REVERT: Ld 44 ARG cc_start: 0.9409 (tpt90) cc_final: 0.9079 (tpt90) REVERT: Ld 48 GLU cc_start: 0.9257 (tm-30) cc_final: 0.9009 (tm-30) REVERT: Ld 50 ARG cc_start: 0.9346 (mtt180) cc_final: 0.9017 (mtt-85) REVERT: Ld 73 TRP cc_start: 0.9009 (m100) cc_final: 0.8469 (m100) REVERT: LP 18 ARG cc_start: 0.8272 (ppt170) cc_final: 0.7947 (ptm-80) REVERT: LP 31 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8208 (mm-30) REVERT: LP 60 PHE cc_start: 0.9581 (m-80) cc_final: 0.9163 (m-80) outliers start: 72 outliers final: 54 residues processed: 515 average time/residue: 0.2175 time to fit residues: 179.4615 Evaluate side-chains 502 residues out of total 3262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 443 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain LC residue 52 TYR Chi-restraints excluded: chain LC residue 57 LEU Chi-restraints excluded: chain LC residue 62 THR Chi-restraints excluded: chain LC residue 71 ARG Chi-restraints excluded: chain LC residue 144 ILE Chi-restraints excluded: chain LC residue 227 ILE Chi-restraints excluded: chain LC residue 285 ILE Chi-restraints excluded: chain LC residue 331 TYR Chi-restraints excluded: chain LC residue 361 LEU Chi-restraints excluded: chain LE residue 118 THR Chi-restraints excluded: chain LE residue 119 GLU Chi-restraints excluded: chain LE residue 200 LYS Chi-restraints excluded: chain LY residue 47 MET Chi-restraints excluded: chain LY residue 67 ILE Chi-restraints excluded: chain LY residue 106 ILE Chi-restraints excluded: chain Lh residue 48 ARG Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain LX residue 101 ASP Chi-restraints excluded: chain LX residue 121 VAL Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 76 MET Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 36 ASN Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 81 THR Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain Ld residue 67 ARG Chi-restraints excluded: chain Ld residue 102 LEU Chi-restraints excluded: chain Ld residue 103 TYR Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain LP residue 22 LEU Chi-restraints excluded: chain LP residue 48 LEU Chi-restraints excluded: chain LP residue 150 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 301 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 397 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 36 ASN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 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 = 0.4103 r_free = 0.4103 target = 0.099575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.066858 restraints weight = 291984.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.067060 restraints weight = 240729.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.067061 restraints weight = 192024.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.066930 restraints weight = 167555.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.066986 restraints weight = 171028.803| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.337 45369 Z= 0.259 Angle : 0.784 58.977 64054 Z= 0.425 Chirality : 0.043 0.680 7532 Planarity : 0.005 0.070 5874 Dihedral : 23.012 177.892 13912 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.41 % Rotamer: Outliers : 2.05 % Allowed : 20.66 % Favored : 77.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.55 (0.14), residues: 3650 helix: 0.09 (0.11), residues: 2053 sheet: -1.03 (0.33), residues: 265 loop : -0.73 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C 4 TYR 0.098 0.002 TYR D 418 PHE 0.045 0.002 PHE B 32 TRP 0.061 0.003 TRPLC 177 HIS 0.018 0.001 HIS B 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.26 (45369) covalent geometry : angle 0.78407 / 0.42 (64054) hydrogen bonds : bond 0.05651 / 3.76 ( 2019) hydrogen bonds : angle 5.04573 / 3.57 ( 5326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13461.81 seconds wall clock time: 231 minutes 37.11 seconds (13897.11 seconds total)