Starting phenix.real_space_refine on Thu Mar 5 01:07:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7krn_23007/03_2026/7krn_23007.cif Found real_map, /net/cci-nas-00/data/ceres_data/7krn_23007/03_2026/7krn_23007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7krn_23007/03_2026/7krn_23007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7krn_23007/03_2026/7krn_23007.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7krn_23007/03_2026/7krn_23007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7krn_23007/03_2026/7krn_23007.map" } resolution = 3.4 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= 0.002 sd= 0.110 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: 9 Type Number sf(0) Gaussians Zn 5 6.06 5 Al 1 5.89 5 P 84 5.49 5 Mg 2 5.21 5 S 117 5.16 5 C 10706 2.51 5 N 2921 2.21 5 O 3512 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17351 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PTRANS': 30, 'TRANS': 896} Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1424 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1427 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 4602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4602 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 29, 'TRANS': 560} Chain: "P" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 776 Classifications: {'RNA': 37} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 36} Chain: "T" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 914 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 21, 'rna3p_pyr': 18} Link IDs: {'rna2p': 4, 'rna3p': 38} Chain breaks: 1 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 24.801 57.488 117.421 1.00 23.89 S ATOM 2495 SG CYS A 306 25.661 58.983 120.940 1.00 20.38 S ATOM 2527 SG CYS A 310 26.473 55.387 120.007 1.00 25.02 S ATOM 3935 SG CYS A 487 27.689 71.479 102.359 1.00 28.29 S ATOM 5188 SG CYS A 645 27.498 73.678 105.435 1.00 42.03 S ATOM 5194 SG CYS A 646 25.493 70.452 105.116 1.00 38.20 S ATOM 10924 SG CYS E 5 63.272 63.773 46.080 1.00 47.16 S ATOM 10945 SG CYS E 8 66.887 63.723 46.333 1.00 56.81 S ATOM 11083 SG CYS E 26 65.226 67.169 45.966 1.00 51.99 S ATOM 11104 SG CYS E 29 65.351 65.094 43.058 1.00 60.26 S ATOM 11269 SG CYS E 50 46.464 84.026 46.253 1.00 77.79 S ATOM 11299 SG CYS E 55 43.702 84.328 43.617 1.00 83.82 S ATOM 11432 SG CYS E 72 47.041 85.957 42.987 1.00 81.14 S ATOM 11006 SG CYS E 16 54.162 67.018 41.421 1.00 48.57 S ATOM 11021 SG CYS E 19 53.451 63.374 40.297 1.00 55.15 S Time building chain proxies: 4.31, per 1000 atoms: 0.25 Number of scatterers: 17351 At special positions: 0 Unit cell: (94.785, 160.815, 177.855, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 5 29.99 S 117 16.00 P 84 15.00 Al 1 13.00 Mg 2 11.99 F 3 9.00 O 3512 8.00 N 2921 7.00 C 10706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 761.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " Number of angles added : 16 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3758 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 22 sheets defined 44.9% alpha, 11.6% beta 33 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.536A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.617A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.783A pdb=" N GLN A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.814A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.749A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.870A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 4.105A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.672A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.432A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.733A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.978A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.963A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 579 removed outlier: 4.496A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 597 through 606 removed outlier: 4.020A pdb=" N TYR A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.531A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 648 through 662 removed outlier: 3.698A pdb=" N TYR A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 654 " --> pdb=" O HIS A 650 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 719 through 732 removed outlier: 3.944A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 789 removed outlier: 3.578A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 843 Processing helix chain 'A' and resid 848 through 852 removed outlier: 3.740A pdb=" N GLY A 852 " --> pdb=" O LYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 878 through 903 removed outlier: 4.160A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.277A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.667A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 97 removed outlier: 4.141A pdb=" N ARG B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.456A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.692A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 20 removed outlier: 3.675A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 42 removed outlier: 3.931A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.828A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 removed outlier: 3.573A pdb=" N GLU C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 32 through 63 Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.988A pdb=" N SER D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.655A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.693A pdb=" N ASN D 179 " --> pdb=" O ASN D 176 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 180 " --> pdb=" O SER D 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 176 through 180' Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.523A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR E 37 " --> pdb=" O HIS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.712A pdb=" N CYS E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 123 removed outlier: 4.150A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 145 Processing helix chain 'E' and resid 146 through 149 Processing helix chain 'E' and resid 260 through 264 removed outlier: 3.751A pdb=" N SER E 263 " --> pdb=" O ASP E 260 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER E 264 " --> pdb=" O GLU E 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 260 through 264' Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.717A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 325 Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 380 through 390 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 removed outlier: 3.572A pdb=" N ILE E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 456 removed outlier: 3.574A pdb=" N ALA E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL E 456 " --> pdb=" O VAL E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 499 removed outlier: 3.741A pdb=" N GLY E 494 " --> pdb=" O ARG E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.678A pdb=" N ARG E 507 " --> pdb=" O PRO E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 522 Processing helix chain 'E' and resid 522 through 527 Processing helix chain 'E' and resid 557 through 566 removed outlier: 3.592A pdb=" N PHE E 561 " --> pdb=" O ASN E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 585 removed outlier: 3.797A pdb=" N LEU E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.933A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.169A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 338 through 343 Processing sheet with id=AA7, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.698A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 556 through 560 Processing sheet with id=AB1, first strand: chain 'A' and resid 755 through 758 Processing sheet with id=AB2, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.306A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.306A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB6, first strand: chain 'E' and resid 14 through 15 removed outlier: 3.734A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AB8, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AB9, first strand: chain 'E' and resid 163 through 164 Processing sheet with id=AC1, first strand: chain 'E' and resid 355 through 359 removed outlier: 6.756A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N MET E 436 " --> pdb=" O TYR E 277 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR E 279 " --> pdb=" O MET E 436 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 366 through 367 removed outlier: 6.724A pdb=" N THR E 366 " --> pdb=" O ARG E 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 471 through 475 removed outlier: 6.432A pdb=" N PHE E 472 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N MET E 576 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N MET E 474 " --> pdb=" O MET E 576 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TYR E 541 " --> pdb=" O LYS E 569 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLY E 571 " --> pdb=" O TYR E 541 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR E 543 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU E 573 " --> pdb=" O TYR E 543 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE E 545 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE E 575 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR E 547 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 480 through 482 650 hydrogen bonds defined for protein. 1833 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 4.25 Time building geometry restraints manager: 1.87 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: 4674 1.33 - 1.45: 3903 1.45 - 1.58: 8919 1.58 - 1.70: 213 1.70 - 1.82: 175 Bond restraints: 17884 Sorted by residual: bond pdb=" F3 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" F1 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" F2 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" C17 1N7 A1005 " pdb=" C18 1N7 A1005 " ideal model delta sigma weight residual 1.528 1.635 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C17 1N7 A1006 " pdb=" C18 1N7 A1006 " ideal model delta sigma weight residual 1.528 1.628 -0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 17879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 24110 2.06 - 4.12: 452 4.12 - 6.19: 85 6.19 - 8.25: 16 8.25 - 10.31: 9 Bond angle restraints: 24672 Sorted by residual: angle pdb=" N TRP B 182 " pdb=" CA TRP B 182 " pdb=" C TRP B 182 " ideal model delta sigma weight residual 109.81 120.09 -10.28 2.21e+00 2.05e-01 2.17e+01 angle pdb=" N TRP D 182 " pdb=" CA TRP D 182 " pdb=" C TRP D 182 " ideal model delta sigma weight residual 109.81 119.65 -9.84 2.21e+00 2.05e-01 1.98e+01 angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 129.46 -7.92 1.91e+00 2.74e-01 1.72e+01 angle pdb=" O3' C P 25 " pdb=" C3' C P 25 " pdb=" C2' C P 25 " ideal model delta sigma weight residual 113.70 119.06 -5.36 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C23 1N7 A1005 " pdb=" C24 1N7 A1005 " pdb=" N1 1N7 A1005 " ideal model delta sigma weight residual 115.43 125.74 -10.31 3.00e+00 1.11e-01 1.18e+01 ... (remaining 24667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.04: 10371 29.04 - 58.08: 476 58.08 - 87.12: 110 87.12 - 116.15: 17 116.15 - 145.19: 8 Dihedral angle restraints: 10982 sinusoidal: 5162 harmonic: 5820 Sorted by residual: dihedral pdb=" CA ALA B 181 " pdb=" C ALA B 181 " pdb=" N TRP B 182 " pdb=" CA TRP B 182 " ideal model delta harmonic sigma weight residual 180.00 -145.50 -34.50 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA ALA D 181 " pdb=" C ALA D 181 " pdb=" N TRP D 182 " pdb=" CA TRP D 182 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA SER A 759 " pdb=" C SER A 759 " pdb=" N ASP A 760 " pdb=" CA ASP A 760 " ideal model delta harmonic sigma weight residual 180.00 155.56 24.44 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 10979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.041: 2874 1.041 - 2.082: 0 2.082 - 3.123: 0 3.123 - 4.164: 0 4.164 - 5.205: 2 Chirality restraints: 2876 Sorted by residual: chirality pdb=" C6 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C7 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.43 2.77 -5.21 2.00e-01 2.50e+01 6.77e+02 chirality pdb=" C18 1N7 A1005 " pdb=" C17 1N7 A1005 " pdb=" C19 1N7 A1005 " pdb=" C6 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.53 -2.52 5.05 2.00e-01 2.50e+01 6.39e+02 chirality pdb=" C17 1N7 E 707 " pdb=" C16 1N7 E 707 " pdb=" C18 1N7 E 707 " pdb=" O3 1N7 E 707 " both_signs ideal model delta sigma weight residual False 2.40 2.81 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 2873 not shown) Planarity restraints: 2832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 338 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO A 339 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 115 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO D 116 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 116 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 116 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 93 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 94 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.026 5.00e-02 4.00e+02 ... (remaining 2829 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 17 2.22 - 2.89: 6750 2.89 - 3.56: 24409 3.56 - 4.23: 40856 4.23 - 4.90: 68896 Nonbonded interactions: 140928 Sorted by model distance: nonbonded pdb=" O2B ADP E 704 " pdb="MG MG E 705 " model vdw 1.546 2.170 nonbonded pdb=" PB ADP E 704 " pdb="MG MG E 705 " model vdw 1.715 2.530 nonbonded pdb=" OD2 ASP A 218 " pdb=" O2A ADP A1004 " model vdw 1.784 3.040 nonbonded pdb="MG MG A1003 " pdb=" O2A ADP A1004 " model vdw 1.808 2.170 nonbonded pdb="MG MG A1003 " pdb=" O1A ADP A1004 " model vdw 1.859 2.170 ... (remaining 140923 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 'B' and resid 7 through 191) selection = (chain 'D' and (resid 7 through 19 or (resid 20 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 23 or (resid 24 through \ 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.170 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.008 0.163 17904 Z= 0.377 Angle : 0.775 10.311 24688 Z= 0.395 Chirality : 0.145 5.205 2876 Planarity : 0.004 0.052 2832 Dihedral : 17.651 145.193 7224 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 7.54 % Allowed : 10.99 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.51 (0.18), residues: 1953 helix: -0.86 (0.17), residues: 824 sheet: -1.70 (0.34), residues: 213 loop : -2.41 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 569 TYR 0.023 0.002 TYR A 788 PHE 0.026 0.002 PHE A 348 TRP 0.023 0.002 TRP B 182 HIS 0.010 0.001 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00848 (17884) covalent geometry : angle 0.76796 (24672) hydrogen bonds : bond 0.12702 ( 722) hydrogen bonds : angle 6.16976 ( 1995) metal coordination : bond 0.01249 ( 20) metal coordination : angle 4.24989 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 192 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8629 (t0) cc_final: 0.8352 (t0) REVERT: A 164 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: A 231 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8942 (p) REVERT: A 552 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8044 (m-40) REVERT: A 576 LEU cc_start: 0.8561 (mp) cc_final: 0.8283 (mt) REVERT: A 638 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.7963 (mp) REVERT: A 648 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8214 (tt) REVERT: A 666 MET cc_start: 0.7730 (mtt) cc_final: 0.7469 (mtt) REVERT: A 703 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8072 (m-40) REVERT: B 48 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6759 (mm-30) REVERT: B 51 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7161 (ttp80) REVERT: B 100 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8109 (t0) REVERT: B 122 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8162 (mp) REVERT: B 161 ASP cc_start: 0.7415 (p0) cc_final: 0.7171 (p0) REVERT: C 5 ASP cc_start: 0.8579 (t0) cc_final: 0.8059 (t0) REVERT: D 57 ARG cc_start: 0.7494 (ttp80) cc_final: 0.7027 (ttp-110) REVERT: E 121 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8214 (pt) REVERT: E 124 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7025 (t0) REVERT: E 263 SER cc_start: 0.8321 (p) cc_final: 0.7957 (t) REVERT: E 347 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7260 (ptpt) REVERT: E 349 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.6912 (m110) REVERT: E 376 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7520 (pp) REVERT: E 438 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7137 (pp) outliers start: 129 outliers final: 67 residues processed: 315 average time/residue: 0.1350 time to fit residues: 65.4592 Evaluate side-chains 236 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 154 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 291 PHE Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 362 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN C 63 GLN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN E 470 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.210045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.160661 restraints weight = 18789.087| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.53 r_work: 0.3740 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17904 Z= 0.159 Angle : 0.619 9.171 24688 Z= 0.310 Chirality : 0.042 0.383 2876 Planarity : 0.004 0.036 2832 Dihedral : 16.678 144.807 3757 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.56 % Allowed : 14.74 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.18), residues: 1953 helix: -0.28 (0.18), residues: 833 sheet: -1.44 (0.34), residues: 214 loop : -2.24 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 105 TYR 0.024 0.001 TYR E 476 PHE 0.016 0.001 PHE A 348 TRP 0.022 0.001 TRP B 182 HIS 0.006 0.001 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00366 (17884) covalent geometry : angle 0.61310 (24672) hydrogen bonds : bond 0.03925 ( 722) hydrogen bonds : angle 4.54204 ( 1995) metal coordination : bond 0.01161 ( 20) metal coordination : angle 3.43601 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 163 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7772 (mtm180) REVERT: A 41 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8315 (mtpp) REVERT: A 122 TYR cc_start: 0.8408 (m-80) cc_final: 0.8160 (m-80) REVERT: A 144 GLU cc_start: 0.7873 (tt0) cc_final: 0.7668 (tt0) REVERT: A 154 ASP cc_start: 0.8728 (t0) cc_final: 0.8410 (t0) REVERT: A 164 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: A 231 VAL cc_start: 0.9304 (OUTLIER) cc_final: 0.9100 (p) REVERT: A 348 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8457 (m-80) REVERT: A 349 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7569 (mtp85) REVERT: A 447 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8356 (p0) REVERT: A 576 LEU cc_start: 0.8613 (mp) cc_final: 0.8222 (mt) REVERT: A 638 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8157 (mp) REVERT: A 648 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8110 (tt) REVERT: A 666 MET cc_start: 0.8469 (mtt) cc_final: 0.8155 (mtt) REVERT: A 703 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.7968 (m-40) REVERT: A 733 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7010 (mmt90) REVERT: B 48 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: B 51 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7136 (ttp80) REVERT: B 161 ASP cc_start: 0.8066 (p0) cc_final: 0.7862 (p0) REVERT: C 5 ASP cc_start: 0.8631 (t0) cc_final: 0.8360 (t70) REVERT: C 71 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8135 (mt) REVERT: D 57 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7138 (ttp-110) REVERT: D 87 MET cc_start: 0.8357 (mmt) cc_final: 0.8129 (mmt) REVERT: E 121 ILE cc_start: 0.8656 (pt) cc_final: 0.8389 (pt) REVERT: E 236 SER cc_start: 0.8980 (p) cc_final: 0.8586 (t) REVERT: E 263 SER cc_start: 0.8512 (p) cc_final: 0.8176 (t) REVERT: E 347 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.6898 (ptpt) REVERT: E 349 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.6974 (m110) REVERT: E 376 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7683 (pp) REVERT: E 521 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7525 (m) outliers start: 95 outliers final: 55 residues processed: 249 average time/residue: 0.1354 time to fit residues: 51.7138 Evaluate side-chains 214 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 143 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 188 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 138 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.210372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.162286 restraints weight = 18866.639| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.62 r_work: 0.3741 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17904 Z= 0.167 Angle : 0.584 8.795 24688 Z= 0.293 Chirality : 0.041 0.260 2876 Planarity : 0.004 0.037 2832 Dihedral : 15.854 156.824 3708 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.67 % Allowed : 15.50 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.19), residues: 1953 helix: -0.08 (0.18), residues: 833 sheet: -1.31 (0.35), residues: 219 loop : -2.17 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 105 TYR 0.014 0.001 TYR A 788 PHE 0.016 0.001 PHE A 741 TRP 0.019 0.001 TRP B 182 HIS 0.005 0.001 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00391 (17884) covalent geometry : angle 0.57834 (24672) hydrogen bonds : bond 0.03735 ( 722) hydrogen bonds : angle 4.34510 ( 1995) metal coordination : bond 0.00929 ( 20) metal coordination : angle 3.24982 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 149 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7784 (mtm180) REVERT: A 41 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8310 (mtpp) REVERT: A 69 TYR cc_start: 0.8811 (m-80) cc_final: 0.8419 (m-80) REVERT: A 154 ASP cc_start: 0.8751 (t0) cc_final: 0.8524 (t0) REVERT: A 164 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.8033 (m-30) REVERT: A 348 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: A 349 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7464 (mtp85) REVERT: A 447 ASN cc_start: 0.8972 (OUTLIER) cc_final: 0.8397 (p0) REVERT: A 576 LEU cc_start: 0.8605 (mp) cc_final: 0.8182 (mt) REVERT: A 638 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8155 (mp) REVERT: A 648 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8270 (tt) REVERT: A 666 MET cc_start: 0.8398 (mtt) cc_final: 0.8034 (mtt) REVERT: A 703 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7917 (m-40) REVERT: A 733 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.6972 (mmt90) REVERT: A 911 ASN cc_start: 0.8193 (t0) cc_final: 0.7311 (t0) REVERT: B 48 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7140 (mm-30) REVERT: B 51 ARG cc_start: 0.8146 (ttp80) cc_final: 0.6898 (ttp80) REVERT: C 71 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8152 (mt) REVERT: D 57 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7160 (ttp-110) REVERT: D 78 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8190 (t0) REVERT: E 121 ILE cc_start: 0.8664 (pt) cc_final: 0.8393 (pt) REVERT: E 236 SER cc_start: 0.8987 (p) cc_final: 0.8584 (t) REVERT: E 263 SER cc_start: 0.8524 (p) cc_final: 0.8194 (t) REVERT: E 347 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.6913 (ptpt) REVERT: E 349 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7072 (m110) REVERT: E 376 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7686 (pp) REVERT: E 414 LYS cc_start: 0.8262 (mtmt) cc_final: 0.7413 (tptp) REVERT: E 521 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7557 (m) outliers start: 97 outliers final: 59 residues processed: 233 average time/residue: 0.1391 time to fit residues: 49.2196 Evaluate side-chains 218 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 143 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 291 PHE Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 378 MET Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 199 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 613 HIS D 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.211173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.164002 restraints weight = 18828.203| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 1.70 r_work: 0.3730 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17904 Z= 0.157 Angle : 0.566 8.984 24688 Z= 0.283 Chirality : 0.040 0.243 2876 Planarity : 0.003 0.042 2832 Dihedral : 15.641 176.346 3695 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 5.56 % Allowed : 16.55 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.19), residues: 1953 helix: 0.13 (0.18), residues: 832 sheet: -1.29 (0.36), residues: 208 loop : -2.07 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 105 TYR 0.013 0.001 TYR A 80 PHE 0.018 0.001 PHE A 340 TRP 0.016 0.001 TRP B 182 HIS 0.005 0.001 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00370 (17884) covalent geometry : angle 0.56009 (24672) hydrogen bonds : bond 0.03544 ( 722) hydrogen bonds : angle 4.18761 ( 1995) metal coordination : bond 0.00972 ( 20) metal coordination : angle 3.14041 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 152 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7782 (mtm180) REVERT: A 41 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8360 (mtpp) REVERT: A 69 TYR cc_start: 0.8829 (m-80) cc_final: 0.8378 (m-80) REVERT: A 154 ASP cc_start: 0.8793 (t0) cc_final: 0.8587 (t0) REVERT: A 164 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8035 (m-30) REVERT: A 348 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8460 (m-80) REVERT: A 349 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7413 (mtp85) REVERT: A 447 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8452 (p0) REVERT: A 576 LEU cc_start: 0.8594 (mp) cc_final: 0.8138 (mt) REVERT: A 638 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8178 (mp) REVERT: A 648 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8225 (tt) REVERT: A 666 MET cc_start: 0.8541 (mtt) cc_final: 0.8179 (mtt) REVERT: A 733 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.6956 (mmt90) REVERT: A 911 ASN cc_start: 0.8223 (t0) cc_final: 0.7321 (t0) REVERT: B 48 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7044 (mm-30) REVERT: B 51 ARG cc_start: 0.8192 (ttp80) cc_final: 0.6951 (ttp80) REVERT: B 62 MET cc_start: 0.8362 (mmm) cc_final: 0.7859 (tmm) REVERT: B 96 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.6771 (ttp80) REVERT: D 57 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7187 (ttp-110) REVERT: D 78 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8199 (t0) REVERT: E 121 ILE cc_start: 0.8729 (pt) cc_final: 0.8468 (pt) REVERT: E 236 SER cc_start: 0.8982 (p) cc_final: 0.8583 (t) REVERT: E 263 SER cc_start: 0.8567 (p) cc_final: 0.8222 (t) REVERT: E 347 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6908 (ptpp) REVERT: E 349 ASN cc_start: 0.7870 (OUTLIER) cc_final: 0.7042 (m110) REVERT: E 376 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7761 (pp) REVERT: E 414 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7407 (tptp) REVERT: E 474 MET cc_start: 0.3744 (ttm) cc_final: 0.3499 (ttm) REVERT: E 521 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7362 (m) outliers start: 95 outliers final: 60 residues processed: 235 average time/residue: 0.1384 time to fit residues: 48.9747 Evaluate side-chains 214 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 140 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 188 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 149 optimal weight: 6.9990 chunk 143 optimal weight: 0.1980 chunk 173 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 58 optimal weight: 0.0030 chunk 24 optimal weight: 0.6980 chunk 151 optimal weight: 7.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.210887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.163245 restraints weight = 18797.049| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.62 r_work: 0.3798 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17904 Z= 0.106 Angle : 0.523 9.867 24688 Z= 0.260 Chirality : 0.039 0.212 2876 Planarity : 0.003 0.037 2832 Dihedral : 15.272 170.202 3685 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.62 % Allowed : 17.54 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.19), residues: 1953 helix: 0.36 (0.19), residues: 838 sheet: -1.03 (0.37), residues: 199 loop : -1.90 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 105 TYR 0.017 0.001 TYR B 71 PHE 0.030 0.001 PHE A 340 TRP 0.017 0.001 TRP B 182 HIS 0.003 0.001 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00237 (17884) covalent geometry : angle 0.51803 (24672) hydrogen bonds : bond 0.03170 ( 722) hydrogen bonds : angle 3.98467 ( 1995) metal coordination : bond 0.00816 ( 20) metal coordination : angle 2.89611 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 170 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7803 (mtm180) REVERT: A 41 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8319 (mtpp) REVERT: A 69 TYR cc_start: 0.8724 (m-80) cc_final: 0.8322 (m-80) REVERT: A 154 ASP cc_start: 0.8748 (t0) cc_final: 0.8391 (t0) REVERT: A 164 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: A 312 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8172 (t0) REVERT: A 348 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: A 349 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7214 (mtp85) REVERT: A 447 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8397 (p0) REVERT: A 576 LEU cc_start: 0.8432 (mp) cc_final: 0.8038 (mt) REVERT: A 638 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8163 (mp) REVERT: A 648 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8119 (tt) REVERT: A 666 MET cc_start: 0.8443 (mtt) cc_final: 0.8002 (mtt) REVERT: A 703 ASN cc_start: 0.8261 (m-40) cc_final: 0.7934 (t0) REVERT: A 883 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8329 (tp) REVERT: A 911 ASN cc_start: 0.8149 (t0) cc_final: 0.7195 (t0) REVERT: B 48 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8021 (mm-30) REVERT: B 62 MET cc_start: 0.8323 (mmm) cc_final: 0.7811 (tmm) REVERT: B 96 ARG cc_start: 0.7317 (mtm-85) cc_final: 0.6717 (ttp80) REVERT: C 71 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8015 (mt) REVERT: D 57 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7170 (ttp-110) REVERT: D 78 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8248 (t0) REVERT: D 101 ASP cc_start: 0.7880 (t0) cc_final: 0.7642 (t0) REVERT: E 121 ILE cc_start: 0.8621 (pt) cc_final: 0.8337 (pt) REVERT: E 236 SER cc_start: 0.8949 (p) cc_final: 0.8553 (t) REVERT: E 263 SER cc_start: 0.8523 (p) cc_final: 0.8185 (t) REVERT: E 347 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6870 (ptpp) REVERT: E 349 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7078 (m-40) REVERT: E 414 LYS cc_start: 0.8233 (mtmt) cc_final: 0.7464 (tmtt) outliers start: 79 outliers final: 46 residues processed: 238 average time/residue: 0.1356 time to fit residues: 49.2249 Evaluate side-chains 210 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 150 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 99 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 96 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 177 optimal weight: 0.2980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 613 HIS A 790 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.164314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106821 restraints weight = 20175.344| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.24 r_work: 0.2911 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17904 Z= 0.174 Angle : 0.572 11.534 24688 Z= 0.284 Chirality : 0.041 0.272 2876 Planarity : 0.003 0.044 2832 Dihedral : 15.183 177.800 3676 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.38 % Allowed : 17.78 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.19), residues: 1953 helix: 0.30 (0.18), residues: 843 sheet: -1.14 (0.37), residues: 196 loop : -1.92 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 555 TYR 0.015 0.001 TYR A 788 PHE 0.036 0.002 PHE E 499 TRP 0.013 0.001 TRP B 182 HIS 0.005 0.001 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00412 (17884) covalent geometry : angle 0.56731 (24672) hydrogen bonds : bond 0.03459 ( 722) hydrogen bonds : angle 4.04293 ( 1995) metal coordination : bond 0.00998 ( 20) metal coordination : angle 3.07455 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 155 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6824 (mtm180) REVERT: A 41 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8343 (mtpp) REVERT: A 69 TYR cc_start: 0.8936 (m-80) cc_final: 0.8081 (m-80) REVERT: A 75 HIS cc_start: 0.8513 (t70) cc_final: 0.8141 (t70) REVERT: A 77 PHE cc_start: 0.7172 (t80) cc_final: 0.6700 (t80) REVERT: A 81 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7239 (mp10) REVERT: A 348 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: A 447 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8144 (p0) REVERT: A 576 LEU cc_start: 0.8106 (mp) cc_final: 0.7786 (mt) REVERT: A 638 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 648 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7646 (tt) REVERT: A 666 MET cc_start: 0.8293 (mtt) cc_final: 0.7788 (mtt) REVERT: A 911 ASN cc_start: 0.8049 (t0) cc_final: 0.7106 (t0) REVERT: B 48 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.8014 (mm-30) REVERT: B 62 MET cc_start: 0.8235 (mmm) cc_final: 0.7604 (tmm) REVERT: B 96 ARG cc_start: 0.6832 (mtm-85) cc_final: 0.6098 (ttp80) REVERT: C 5 ASP cc_start: 0.8596 (t70) cc_final: 0.8379 (t70) REVERT: C 71 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6875 (mt) REVERT: D 57 ARG cc_start: 0.7129 (ttp80) cc_final: 0.6470 (ttp-110) REVERT: D 78 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7749 (t0) REVERT: D 95 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8126 (mp) REVERT: D 134 ASP cc_start: 0.8277 (t0) cc_final: 0.7896 (t70) REVERT: E 121 ILE cc_start: 0.8315 (pt) cc_final: 0.8035 (pt) REVERT: E 236 SER cc_start: 0.8896 (p) cc_final: 0.8436 (t) REVERT: E 347 LYS cc_start: 0.6134 (OUTLIER) cc_final: 0.5701 (ptpp) REVERT: E 349 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.6887 (m110) REVERT: E 414 LYS cc_start: 0.7672 (mtmt) cc_final: 0.6745 (tmtt) outliers start: 92 outliers final: 60 residues processed: 234 average time/residue: 0.1344 time to fit residues: 48.0412 Evaluate side-chains 219 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 147 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 143 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 119 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.0170 chunk 127 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 171 optimal weight: 6.9990 chunk 94 optimal weight: 40.0000 chunk 45 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.210618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.164173 restraints weight = 18851.417| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.66 r_work: 0.3799 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17904 Z= 0.117 Angle : 0.535 11.384 24688 Z= 0.264 Chirality : 0.039 0.301 2876 Planarity : 0.003 0.037 2832 Dihedral : 14.967 173.000 3670 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.62 % Allowed : 18.30 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.19), residues: 1953 helix: 0.51 (0.19), residues: 836 sheet: -1.09 (0.37), residues: 194 loop : -1.83 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 555 TYR 0.014 0.001 TYR B 71 PHE 0.013 0.001 PHE A 741 TRP 0.014 0.001 TRP B 182 HIS 0.004 0.001 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00271 (17884) covalent geometry : angle 0.53034 (24672) hydrogen bonds : bond 0.03134 ( 722) hydrogen bonds : angle 3.93676 ( 1995) metal coordination : bond 0.00902 ( 20) metal coordination : angle 2.85387 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 150 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7766 (mtm180) REVERT: A 41 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8300 (mtpp) REVERT: A 69 TYR cc_start: 0.8767 (m-80) cc_final: 0.8331 (m-80) REVERT: A 77 PHE cc_start: 0.7597 (t80) cc_final: 0.7241 (t80) REVERT: A 81 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: A 447 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8358 (p0) REVERT: A 555 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7121 (mtt-85) REVERT: A 576 LEU cc_start: 0.8468 (mp) cc_final: 0.8069 (mt) REVERT: A 638 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8379 (mp) REVERT: A 648 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8121 (tt) REVERT: A 666 MET cc_start: 0.8535 (mtt) cc_final: 0.8117 (mtt) REVERT: A 733 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.6906 (mmt90) REVERT: A 883 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 911 ASN cc_start: 0.8142 (t0) cc_final: 0.7186 (t0) REVERT: B 48 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: B 62 MET cc_start: 0.8415 (mmm) cc_final: 0.7910 (tmm) REVERT: B 96 ARG cc_start: 0.7186 (mtm-85) cc_final: 0.6656 (ttp80) REVERT: B 112 ASP cc_start: 0.7872 (m-30) cc_final: 0.7308 (t0) REVERT: C 71 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7971 (mt) REVERT: D 57 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7175 (ttp-110) REVERT: D 78 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8241 (t0) REVERT: D 95 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8712 (mp) REVERT: D 101 ASP cc_start: 0.7849 (t0) cc_final: 0.7596 (t0) REVERT: E 121 ILE cc_start: 0.8596 (pt) cc_final: 0.8306 (pt) REVERT: E 236 SER cc_start: 0.8932 (p) cc_final: 0.8526 (t) REVERT: E 347 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6783 (ptpp) REVERT: E 349 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7150 (m110) REVERT: E 414 LYS cc_start: 0.8254 (mtmt) cc_final: 0.7413 (tmtt) outliers start: 79 outliers final: 58 residues processed: 218 average time/residue: 0.1430 time to fit residues: 47.2113 Evaluate side-chains 216 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 144 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 12 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 181 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 31 optimal weight: 0.0000 chunk 176 optimal weight: 0.0970 chunk 96 optimal weight: 10.0000 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.214123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.166349 restraints weight = 18781.298| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.65 r_work: 0.3810 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17904 Z= 0.096 Angle : 0.516 11.143 24688 Z= 0.255 Chirality : 0.038 0.252 2876 Planarity : 0.003 0.042 2832 Dihedral : 14.695 156.683 3666 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.27 % Allowed : 19.24 % Favored : 76.49 % 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: -0.86 (0.19), residues: 1953 helix: 0.73 (0.19), residues: 830 sheet: -1.03 (0.36), residues: 204 loop : -1.72 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 555 TYR 0.013 0.001 TYR B 71 PHE 0.027 0.001 PHE E 499 TRP 0.016 0.001 TRP B 182 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00213 (17884) covalent geometry : angle 0.51084 (24672) hydrogen bonds : bond 0.02921 ( 722) hydrogen bonds : angle 3.80573 ( 1995) metal coordination : bond 0.00914 ( 20) metal coordination : angle 2.78337 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 160 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7905 (mtm180) REVERT: A 41 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8288 (mtpp) REVERT: A 69 TYR cc_start: 0.8630 (m-80) cc_final: 0.8279 (m-80) REVERT: A 77 PHE cc_start: 0.7581 (t80) cc_final: 0.7210 (t80) REVERT: A 105 ARG cc_start: 0.8283 (tpp-160) cc_final: 0.8052 (tpp-160) REVERT: A 447 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8305 (p0) REVERT: A 576 LEU cc_start: 0.8350 (mp) cc_final: 0.7962 (mt) REVERT: A 648 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8187 (tt) REVERT: A 666 MET cc_start: 0.8390 (mtt) cc_final: 0.7945 (mtt) REVERT: A 703 ASN cc_start: 0.8150 (m-40) cc_final: 0.7812 (t0) REVERT: A 883 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8292 (tp) REVERT: A 902 MET cc_start: 0.8428 (ttm) cc_final: 0.8142 (ttp) REVERT: A 911 ASN cc_start: 0.8061 (t0) cc_final: 0.7124 (t0) REVERT: B 48 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8010 (mm-30) REVERT: B 62 MET cc_start: 0.8409 (mmm) cc_final: 0.7929 (tmm) REVERT: B 96 ARG cc_start: 0.7246 (mtm-85) cc_final: 0.6686 (ttp80) REVERT: B 112 ASP cc_start: 0.7839 (m-30) cc_final: 0.7354 (t0) REVERT: C 71 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8012 (mt) REVERT: D 57 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7303 (ttp-110) REVERT: D 78 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8203 (t0) REVERT: D 101 ASP cc_start: 0.7799 (t0) cc_final: 0.7541 (t0) REVERT: E 121 ILE cc_start: 0.8602 (pt) cc_final: 0.8335 (pt) REVERT: E 236 SER cc_start: 0.8863 (p) cc_final: 0.8501 (t) REVERT: E 311 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7117 (m-70) REVERT: E 347 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6748 (ptpp) REVERT: E 349 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7200 (m110) REVERT: E 414 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7499 (tmtt) REVERT: E 465 LYS cc_start: 0.4072 (OUTLIER) cc_final: 0.3118 (mptt) outliers start: 73 outliers final: 50 residues processed: 223 average time/residue: 0.1288 time to fit residues: 43.9989 Evaluate side-chains 211 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 150 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 28 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS E 243 GLN E 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.214367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.168463 restraints weight = 18721.781| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.61 r_work: 0.3757 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17904 Z= 0.167 Angle : 0.563 10.532 24688 Z= 0.279 Chirality : 0.041 0.245 2876 Planarity : 0.003 0.042 2832 Dihedral : 14.632 145.907 3659 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.56 % Allowed : 19.18 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.19), residues: 1953 helix: 0.57 (0.18), residues: 838 sheet: -0.98 (0.36), residues: 196 loop : -1.83 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 555 TYR 0.015 0.001 TYR A 748 PHE 0.016 0.001 PHE A 741 TRP 0.009 0.001 TRP B 182 HIS 0.007 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00394 (17884) covalent geometry : angle 0.55781 (24672) hydrogen bonds : bond 0.03356 ( 722) hydrogen bonds : angle 3.94746 ( 1995) metal coordination : bond 0.01053 ( 20) metal coordination : angle 2.94852 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 151 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7858 (mtm180) REVERT: A 41 LYS cc_start: 0.8547 (mtmm) cc_final: 0.8223 (mtpp) REVERT: A 69 TYR cc_start: 0.8714 (m-80) cc_final: 0.8317 (m-80) REVERT: A 77 PHE cc_start: 0.7633 (t80) cc_final: 0.7290 (t80) REVERT: A 105 ARG cc_start: 0.8329 (tpp-160) cc_final: 0.8110 (tpp80) REVERT: A 136 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: A 154 ASP cc_start: 0.8712 (t0) cc_final: 0.8420 (t0) REVERT: A 447 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8367 (p0) REVERT: A 555 ARG cc_start: 0.7218 (mtm-85) cc_final: 0.6935 (mtm-85) REVERT: A 576 LEU cc_start: 0.8458 (mp) cc_final: 0.8028 (mt) REVERT: A 638 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 648 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8343 (tt) REVERT: A 666 MET cc_start: 0.8341 (mtt) cc_final: 0.7927 (mtt) REVERT: A 733 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.6854 (mmt90) REVERT: A 883 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8496 (tp) REVERT: A 911 ASN cc_start: 0.8073 (t0) cc_final: 0.7122 (t0) REVERT: B 41 SER cc_start: 0.9041 (m) cc_final: 0.8751 (p) REVERT: B 48 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8090 (mm-30) REVERT: B 62 MET cc_start: 0.8422 (mmm) cc_final: 0.7920 (tmm) REVERT: B 96 ARG cc_start: 0.7108 (mtm-85) cc_final: 0.6733 (ttp80) REVERT: B 112 ASP cc_start: 0.7818 (m-30) cc_final: 0.7336 (t0) REVERT: C 71 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8126 (mt) REVERT: D 57 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7284 (ttp-110) REVERT: D 78 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8470 (t70) REVERT: D 101 ASP cc_start: 0.7941 (t0) cc_final: 0.7689 (t0) REVERT: E 121 ILE cc_start: 0.8641 (pt) cc_final: 0.8374 (pt) REVERT: E 311 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7285 (m-70) REVERT: E 347 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6725 (ptpp) REVERT: E 349 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7308 (m110) REVERT: E 414 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7466 (tmtt) REVERT: E 465 LYS cc_start: 0.4074 (OUTLIER) cc_final: 0.3136 (mptt) REVERT: E 474 MET cc_start: 0.4185 (ttm) cc_final: 0.3933 (ptp) outliers start: 78 outliers final: 55 residues processed: 220 average time/residue: 0.1378 time to fit residues: 46.0521 Evaluate side-chains 219 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 150 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 192 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 167 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS E 243 GLN E 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.210883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.163334 restraints weight = 18730.247| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.69 r_work: 0.3754 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17904 Z= 0.130 Angle : 0.547 12.210 24688 Z= 0.270 Chirality : 0.040 0.343 2876 Planarity : 0.003 0.041 2832 Dihedral : 14.597 138.485 3659 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.27 % Allowed : 19.47 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.19), residues: 1953 helix: 0.61 (0.18), residues: 841 sheet: -0.99 (0.37), residues: 194 loop : -1.83 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 555 TYR 0.012 0.001 TYR A 748 PHE 0.028 0.001 PHE E 499 TRP 0.010 0.001 TRP B 182 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00301 (17884) covalent geometry : angle 0.54226 (24672) hydrogen bonds : bond 0.03158 ( 722) hydrogen bonds : angle 3.89679 ( 1995) metal coordination : bond 0.00900 ( 20) metal coordination : angle 2.87862 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 146 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7874 (mtm180) REVERT: A 41 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8176 (mtpp) REVERT: A 69 TYR cc_start: 0.8510 (m-80) cc_final: 0.8167 (m-80) REVERT: A 77 PHE cc_start: 0.7511 (t80) cc_final: 0.7270 (t80) REVERT: A 136 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6784 (pm20) REVERT: A 154 ASP cc_start: 0.8539 (t0) cc_final: 0.8306 (t0) REVERT: A 380 MET cc_start: 0.7722 (mtp) cc_final: 0.7472 (mmt) REVERT: A 447 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8344 (p0) REVERT: A 555 ARG cc_start: 0.7076 (mtm-85) cc_final: 0.6839 (mtm-85) REVERT: A 576 LEU cc_start: 0.8339 (mp) cc_final: 0.7924 (mt) REVERT: A 638 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8163 (mp) REVERT: A 648 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8299 (tt) REVERT: A 666 MET cc_start: 0.8123 (mtt) cc_final: 0.7677 (mtt) REVERT: A 883 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8310 (tp) REVERT: A 911 ASN cc_start: 0.7994 (t0) cc_final: 0.7092 (t0) REVERT: B 41 SER cc_start: 0.8916 (m) cc_final: 0.8666 (p) REVERT: B 48 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7970 (mm-30) REVERT: B 62 MET cc_start: 0.8344 (mmm) cc_final: 0.7889 (tmm) REVERT: B 96 ARG cc_start: 0.7147 (mtm-85) cc_final: 0.6883 (ttp80) REVERT: B 112 ASP cc_start: 0.7559 (m-30) cc_final: 0.7238 (t0) REVERT: C 71 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8048 (mt) REVERT: D 57 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7254 (ttp-110) REVERT: D 78 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8174 (t0) REVERT: D 101 ASP cc_start: 0.7584 (t0) cc_final: 0.7351 (t0) REVERT: E 121 ILE cc_start: 0.8583 (pt) cc_final: 0.8321 (pt) REVERT: E 311 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.7188 (m-70) REVERT: E 347 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6693 (ptpp) REVERT: E 349 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7280 (m110) REVERT: E 414 LYS cc_start: 0.8239 (mtmt) cc_final: 0.7479 (tmtt) REVERT: E 465 LYS cc_start: 0.3877 (OUTLIER) cc_final: 0.3062 (mptt) outliers start: 73 outliers final: 55 residues processed: 209 average time/residue: 0.1359 time to fit residues: 43.3667 Evaluate side-chains 213 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 145 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 537 GLN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 144 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS E 243 GLN E 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.210773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.164788 restraints weight = 18807.626| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.63 r_work: 0.3792 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17904 Z= 0.127 Angle : 0.545 12.555 24688 Z= 0.270 Chirality : 0.040 0.335 2876 Planarity : 0.003 0.040 2832 Dihedral : 14.541 130.514 3659 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.50 % Allowed : 19.42 % Favored : 76.08 % 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: -0.95 (0.19), residues: 1953 helix: 0.65 (0.18), residues: 840 sheet: -0.93 (0.36), residues: 196 loop : -1.82 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 105 TYR 0.012 0.001 TYR A 748 PHE 0.014 0.001 PHE A 741 TRP 0.011 0.001 TRP B 182 HIS 0.009 0.001 HIS E 245 Details of bonding type rmsd covalent geometry : bond 0.00296 (17884) covalent geometry : angle 0.54009 (24672) hydrogen bonds : bond 0.03123 ( 722) hydrogen bonds : angle 3.85715 ( 1995) metal coordination : bond 0.00886 ( 20) metal coordination : angle 2.85413 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4600.78 seconds wall clock time: 79 minutes 33.57 seconds (4773.57 seconds total)