Starting phenix.real_space_refine on Sat Sep 28 02:29:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krn_23007/09_2024/7krn_23007.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krn_23007/09_2024/7krn_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krn_23007/09_2024/7krn_23007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krn_23007/09_2024/7krn_23007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krn_23007/09_2024/7krn_23007.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krn_23007/09_2024/7krn_23007.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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, 'ASN:plan1': 1, 'GLN: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: 10.59, per 1000 atoms: 0.61 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: 4.60 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 6.59 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: 7.47 Time building geometry restraints manager: 5.30 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: 1.560 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 49.670 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.710 ------------------------------------------------------------------------------- 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 17884 Z= 0.541 Angle : 0.768 10.311 24672 Z= 0.394 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.002 TRP B 182 HIS 0.010 0.001 HIS E 290 PHE 0.026 0.002 PHE A 348 TYR 0.023 0.002 TYR A 788 ARG 0.005 0.000 ARG A 569 *********************** 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 fitting. rotamer outliers: 129 poor density : 192 time to evaluate : 1.845 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: 0.7416 (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: 0.2764 time to fit residues: 133.0476 Evaluate side-chains 236 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 154 time to evaluate : 1.767 ------------------------------------------------------------------------------- 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 169 optimal weight: 7.9990 chunk 152 optimal weight: 0.0370 chunk 84 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 157 optimal weight: 40.0000 chunk 60 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17884 Z= 0.185 Angle : 0.596 8.925 24672 Z= 0.300 Chirality : 0.041 0.357 2876 Planarity : 0.004 0.037 2832 Dihedral : 16.608 144.933 3757 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.26 % Allowed : 14.85 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.19), residues: 1953 helix: -0.22 (0.18), residues: 832 sheet: -1.38 (0.34), residues: 214 loop : -2.19 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 182 HIS 0.005 0.001 HIS E 290 PHE 0.017 0.001 PHE A 812 TYR 0.027 0.001 TYR E 476 ARG 0.005 0.000 ARG A 105 *********************** 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 255 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 165 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8373 (mtmm) cc_final: 0.8126 (mtpp) REVERT: A 154 ASP cc_start: 0.8481 (t0) cc_final: 0.8258 (t0) REVERT: A 164 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: A 231 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8839 (p) REVERT: A 348 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8415 (m-80) REVERT: A 349 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7271 (mtp85) REVERT: A 576 LEU cc_start: 0.8456 (mp) cc_final: 0.8112 (mt) REVERT: A 638 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 666 MET cc_start: 0.7724 (mtt) cc_final: 0.7381 (mtt) REVERT: A 703 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7897 (m-40) REVERT: B 48 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6774 (mm-30) REVERT: B 51 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7279 (ttp80) REVERT: B 161 ASP cc_start: 0.7527 (p0) cc_final: 0.7287 (p0) REVERT: C 71 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7856 (mt) REVERT: D 57 ARG cc_start: 0.7451 (ttp80) cc_final: 0.7005 (ttp-110) REVERT: E 121 ILE cc_start: 0.8405 (pt) cc_final: 0.8170 (pt) REVERT: E 236 SER cc_start: 0.8750 (p) cc_final: 0.8465 (t) REVERT: E 263 SER cc_start: 0.8341 (p) cc_final: 0.7969 (t) REVERT: E 347 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7202 (ptpt) REVERT: E 349 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7177 (m110) REVERT: E 376 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7451 (pp) outliers start: 90 outliers final: 52 residues processed: 244 average time/residue: 0.2834 time to fit residues: 106.2612 Evaluate side-chains 206 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 143 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 468 GLN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 LEU 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 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 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 E residue 73 LYS 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 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 101 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 181 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- 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 D 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17884 Z= 0.264 Angle : 0.579 8.788 24672 Z= 0.293 Chirality : 0.041 0.265 2876 Planarity : 0.004 0.038 2832 Dihedral : 15.769 158.176 3705 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.15 % Allowed : 15.61 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.19), residues: 1953 helix: -0.08 (0.18), residues: 839 sheet: -1.30 (0.35), residues: 219 loop : -2.14 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 182 HIS 0.005 0.001 HIS E 290 PHE 0.016 0.002 PHE A 741 TYR 0.026 0.001 TYR E 476 ARG 0.005 0.000 ARG A 105 *********************** 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 240 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 152 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8435 (mtmm) cc_final: 0.8148 (mtpp) REVERT: A 69 TYR cc_start: 0.8316 (m-80) cc_final: 0.8013 (m-80) REVERT: A 154 ASP cc_start: 0.8537 (t0) cc_final: 0.8299 (t0) REVERT: A 164 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: A 231 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8886 (p) REVERT: A 348 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: A 349 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7031 (mtp85) REVERT: A 447 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8339 (p0) REVERT: A 576 LEU cc_start: 0.8473 (mp) cc_final: 0.8067 (mt) REVERT: A 638 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8025 (mp) REVERT: A 666 MET cc_start: 0.7544 (mtt) cc_final: 0.7148 (mtt) REVERT: A 733 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.6749 (mmt90) REVERT: A 911 ASN cc_start: 0.8082 (t0) cc_final: 0.7290 (t0) REVERT: B 48 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6878 (mm-30) REVERT: B 51 ARG cc_start: 0.8108 (ttp80) cc_final: 0.6989 (ttp80) REVERT: C 71 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7891 (mt) REVERT: D 57 ARG cc_start: 0.7458 (ttp80) cc_final: 0.7011 (ttp-110) REVERT: D 78 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8091 (t0) REVERT: E 121 ILE cc_start: 0.8483 (pt) cc_final: 0.8259 (pt) REVERT: E 236 SER cc_start: 0.8769 (p) cc_final: 0.8484 (t) REVERT: E 263 SER cc_start: 0.8334 (p) cc_final: 0.7987 (t) REVERT: E 295 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6479 (tt) REVERT: E 347 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7221 (ptpt) REVERT: E 349 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7192 (m110) REVERT: E 376 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7438 (pp) REVERT: E 414 LYS cc_start: 0.8182 (mtmt) cc_final: 0.7664 (tptp) outliers start: 88 outliers final: 54 residues processed: 229 average time/residue: 0.2965 time to fit residues: 102.8884 Evaluate side-chains 213 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 145 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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 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 231 VAL 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 447 ASN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 638 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 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 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 D residue 167 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 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 378 MET Chi-restraints excluded: chain E residue 452 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 180 optimal weight: 0.2980 chunk 137 optimal weight: 0.6980 chunk 94 optimal weight: 40.0000 chunk 20 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17884 Z= 0.245 Angle : 0.563 8.884 24672 Z= 0.283 Chirality : 0.040 0.242 2876 Planarity : 0.003 0.037 2832 Dihedral : 15.556 171.994 3691 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.03 % Allowed : 17.02 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1953 helix: 0.13 (0.18), residues: 833 sheet: -1.28 (0.35), residues: 208 loop : -2.04 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 182 HIS 0.005 0.001 HIS E 290 PHE 0.015 0.001 PHE A 812 TYR 0.013 0.001 TYR A 788 ARG 0.005 0.000 ARG A 105 *********************** 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 240 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 154 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8438 (mtmm) cc_final: 0.8166 (mtpp) REVERT: A 69 TYR cc_start: 0.8286 (m-80) cc_final: 0.7963 (m-80) REVERT: A 154 ASP cc_start: 0.8524 (t0) cc_final: 0.8289 (t0) REVERT: A 164 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: A 231 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8871 (p) REVERT: A 348 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: A 349 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6855 (mtp85) REVERT: A 447 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8327 (p0) REVERT: A 576 LEU cc_start: 0.8442 (mp) cc_final: 0.8015 (mt) REVERT: A 638 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 666 MET cc_start: 0.7719 (mtt) cc_final: 0.7349 (mtt) REVERT: A 703 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7870 (t0) REVERT: A 733 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.6699 (mmt90) REVERT: A 911 ASN cc_start: 0.8088 (t0) cc_final: 0.7285 (t0) REVERT: B 48 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6867 (mm-30) REVERT: B 51 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7068 (ttp80) REVERT: B 96 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6892 (ttp80) REVERT: C 5 ASP cc_start: 0.8392 (t70) cc_final: 0.8177 (t0) REVERT: D 57 ARG cc_start: 0.7464 (ttp80) cc_final: 0.7023 (ttp-110) REVERT: D 78 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8096 (t0) REVERT: E 121 ILE cc_start: 0.8411 (pt) cc_final: 0.8166 (pt) REVERT: E 236 SER cc_start: 0.8782 (p) cc_final: 0.8466 (t) REVERT: E 263 SER cc_start: 0.8320 (p) cc_final: 0.7986 (t) REVERT: E 295 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6342 (tt) REVERT: E 347 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7301 (ptpp) REVERT: E 349 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7184 (m110) REVERT: E 376 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7520 (pp) REVERT: E 414 LYS cc_start: 0.8153 (mtmt) cc_final: 0.7677 (tptp) outliers start: 86 outliers final: 50 residues processed: 228 average time/residue: 0.2987 time to fit residues: 103.0002 Evaluate side-chains 208 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 144 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 212 LEU Chi-restraints excluded: chain A residue 231 VAL 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 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 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 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 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 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 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 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 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 391 LEU Chi-restraints excluded: chain E residue 452 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 161 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 165 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17884 Z= 0.198 Angle : 0.538 9.922 24672 Z= 0.270 Chirality : 0.040 0.227 2876 Planarity : 0.003 0.037 2832 Dihedral : 15.310 170.080 3682 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.09 % Allowed : 17.31 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1953 helix: 0.30 (0.18), residues: 832 sheet: -1.10 (0.37), residues: 203 loop : -1.94 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 182 HIS 0.004 0.001 HIS E 290 PHE 0.014 0.001 PHE A 741 TYR 0.013 0.001 TYR A 80 ARG 0.005 0.000 ARG A 105 *********************** 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 241 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 154 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8441 (mtmm) cc_final: 0.8110 (mtpp) REVERT: A 69 TYR cc_start: 0.8212 (m-80) cc_final: 0.7880 (m-80) REVERT: A 154 ASP cc_start: 0.8519 (t0) cc_final: 0.8294 (t0) REVERT: A 164 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: A 231 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8862 (p) REVERT: A 348 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: A 349 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7058 (mtp85) REVERT: A 447 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8321 (p0) REVERT: A 576 LEU cc_start: 0.8343 (mp) cc_final: 0.7892 (mt) REVERT: A 638 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7975 (mp) REVERT: A 648 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8125 (tt) REVERT: A 666 MET cc_start: 0.7681 (mtt) cc_final: 0.7263 (mtt) REVERT: A 703 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7855 (t0) REVERT: A 733 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.6688 (mmt90) REVERT: A 911 ASN cc_start: 0.8042 (t0) cc_final: 0.7215 (t0) REVERT: C 71 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7787 (mt) REVERT: D 57 ARG cc_start: 0.7473 (ttp80) cc_final: 0.7038 (ttp-110) REVERT: D 78 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8089 (t0) REVERT: E 121 ILE cc_start: 0.8412 (pt) cc_final: 0.8171 (pt) REVERT: E 236 SER cc_start: 0.8763 (p) cc_final: 0.8435 (t) REVERT: E 263 SER cc_start: 0.8303 (p) cc_final: 0.7952 (t) REVERT: E 347 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7302 (ptpp) REVERT: E 349 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7253 (m110) REVERT: E 414 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7705 (tmtt) outliers start: 87 outliers final: 57 residues processed: 230 average time/residue: 0.2888 time to fit residues: 101.2171 Evaluate side-chains 217 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 147 time to evaluate : 1.941 ------------------------------------------------------------------------------- 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 76 THR 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 231 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL 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 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 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 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 820 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 39 LYS 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 194 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17884 Z= 0.300 Angle : 0.583 11.692 24672 Z= 0.293 Chirality : 0.041 0.246 2876 Planarity : 0.003 0.038 2832 Dihedral : 15.215 175.844 3673 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.73 % Allowed : 17.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1953 helix: 0.33 (0.18), residues: 832 sheet: -1.20 (0.36), residues: 201 loop : -1.95 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 182 HIS 0.005 0.001 HIS E 290 PHE 0.017 0.002 PHE A 741 TYR 0.016 0.001 TYR A 788 ARG 0.006 0.000 ARG A 555 *********************** 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 fitting. rotamer outliers: 98 poor density : 149 time to evaluate : 1.824 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8099 (mtpp) REVERT: A 69 TYR cc_start: 0.8251 (m-80) cc_final: 0.7941 (m-80) REVERT: A 81 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: A 154 ASP cc_start: 0.8515 (t0) cc_final: 0.8289 (t0) REVERT: A 164 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: A 231 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8875 (p) REVERT: A 348 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: A 447 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8361 (p0) REVERT: A 555 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6876 (mtt-85) REVERT: A 576 LEU cc_start: 0.8452 (mp) cc_final: 0.8062 (mt) REVERT: A 638 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.7977 (mp) REVERT: A 648 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 666 MET cc_start: 0.7585 (mtt) cc_final: 0.7170 (mtt) REVERT: A 703 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7938 (t0) REVERT: A 733 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.6689 (mmt90) REVERT: A 883 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8304 (tp) REVERT: A 911 ASN cc_start: 0.8040 (t0) cc_final: 0.7184 (t0) REVERT: C 71 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7873 (mt) REVERT: D 57 ARG cc_start: 0.7499 (ttp80) cc_final: 0.7047 (ttp-110) REVERT: D 78 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8114 (t0) REVERT: D 95 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8650 (mp) REVERT: E 121 ILE cc_start: 0.8432 (pt) cc_final: 0.8184 (pt) REVERT: E 263 SER cc_start: 0.8307 (p) cc_final: 0.7985 (t) REVERT: E 347 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7199 (ptpp) REVERT: E 349 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7332 (m110) REVERT: E 414 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7689 (tptp) outliers start: 98 outliers final: 67 residues processed: 233 average time/residue: 0.2919 time to fit residues: 102.9738 Evaluate side-chains 227 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 144 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 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 231 VAL 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 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 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 445 ASP 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 555 ARG Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 626 MET 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 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 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 78 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 LEU 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 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 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 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 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 397 VAL 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 187 optimal weight: 0.0060 chunk 21 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 142 optimal weight: 0.0870 chunk 163 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 overall best weight: 0.6776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17884 Z= 0.184 Angle : 0.536 10.917 24672 Z= 0.268 Chirality : 0.039 0.216 2876 Planarity : 0.003 0.037 2832 Dihedral : 15.033 175.354 3673 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.91 % Allowed : 18.13 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.19), residues: 1953 helix: 0.50 (0.19), residues: 829 sheet: -1.11 (0.37), residues: 194 loop : -1.88 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 182 HIS 0.004 0.001 HIS A 309 PHE 0.013 0.001 PHE A 812 TYR 0.011 0.001 TYR A 748 ARG 0.006 0.000 ARG B 96 *********************** 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 231 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 147 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8120 (mtpp) REVERT: A 69 TYR cc_start: 0.8231 (m-80) cc_final: 0.7954 (m-80) REVERT: A 105 ARG cc_start: 0.7988 (tpp80) cc_final: 0.7732 (tpp-160) REVERT: A 136 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: A 154 ASP cc_start: 0.8472 (t0) cc_final: 0.8272 (t0) REVERT: A 164 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: A 231 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8856 (p) REVERT: A 349 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6887 (mtp85) REVERT: A 447 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8320 (p0) REVERT: A 555 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6890 (mtm-85) REVERT: A 576 LEU cc_start: 0.8325 (mp) cc_final: 0.7971 (mt) REVERT: A 666 MET cc_start: 0.7741 (mtt) cc_final: 0.7277 (mtt) REVERT: A 883 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8189 (tp) REVERT: A 911 ASN cc_start: 0.8033 (t0) cc_final: 0.7183 (t0) REVERT: B 112 ASP cc_start: 0.7505 (m-30) cc_final: 0.7275 (t0) REVERT: C 71 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7756 (mt) REVERT: D 57 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7137 (ttp-110) REVERT: D 78 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8110 (t0) REVERT: D 95 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8580 (mp) REVERT: E 121 ILE cc_start: 0.8396 (pt) cc_final: 0.8143 (pt) REVERT: E 263 SER cc_start: 0.8281 (p) cc_final: 0.7943 (t) REVERT: E 290 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.7420 (t-90) REVERT: E 347 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7180 (ptpp) REVERT: E 349 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7304 (m110) REVERT: E 414 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7702 (tmtt) REVERT: E 465 LYS cc_start: 0.3876 (OUTLIER) cc_final: 0.3210 (mptt) outliers start: 84 outliers final: 57 residues processed: 218 average time/residue: 0.2941 time to fit residues: 97.5967 Evaluate side-chains 216 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 145 time to evaluate : 1.821 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 93 CYS 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 231 VAL 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 338 VAL 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 445 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 478 LYS 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 626 MET 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 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 924 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 95 LEU 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 128 LEU 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 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 391 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 465 LYS 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 77 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 152 optimal weight: 0.0270 chunk 176 optimal weight: 9.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17884 Z= 0.165 Angle : 0.529 10.746 24672 Z= 0.263 Chirality : 0.039 0.282 2876 Planarity : 0.003 0.041 2832 Dihedral : 14.781 163.892 3665 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.74 % Allowed : 18.48 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1953 helix: 0.61 (0.19), residues: 828 sheet: -1.07 (0.37), residues: 194 loop : -1.78 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 182 HIS 0.003 0.001 HIS E 290 PHE 0.027 0.001 PHE E 499 TYR 0.013 0.001 TYR A 748 ARG 0.007 0.000 ARG B 96 *********************** 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 227 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 146 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8124 (mtpp) REVERT: A 69 TYR cc_start: 0.8176 (m-80) cc_final: 0.7886 (m-80) REVERT: A 136 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6803 (pm20) REVERT: A 164 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: A 231 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8837 (p) REVERT: A 349 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6834 (mtp85) REVERT: A 447 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8315 (p0) REVERT: A 555 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6948 (mtm-85) REVERT: A 576 LEU cc_start: 0.8255 (mp) cc_final: 0.7896 (mt) REVERT: A 666 MET cc_start: 0.7698 (mtt) cc_final: 0.7220 (mtt) REVERT: A 883 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8164 (tp) REVERT: A 911 ASN cc_start: 0.8027 (t0) cc_final: 0.7177 (t0) REVERT: C 71 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7772 (mt) REVERT: D 57 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7096 (ttp-110) REVERT: D 78 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8163 (t0) REVERT: D 95 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8435 (mp) REVERT: E 121 ILE cc_start: 0.8374 (pt) cc_final: 0.8128 (pt) REVERT: E 263 SER cc_start: 0.8292 (p) cc_final: 0.7993 (t) REVERT: E 290 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7251 (t-90) REVERT: E 347 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7123 (ptpp) REVERT: E 349 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7371 (m110) REVERT: E 414 LYS cc_start: 0.8182 (mtmt) cc_final: 0.7677 (tmtt) REVERT: E 465 LYS cc_start: 0.3807 (OUTLIER) cc_final: 0.3159 (mptt) outliers start: 81 outliers final: 56 residues processed: 215 average time/residue: 0.3006 time to fit residues: 98.0790 Evaluate side-chains 213 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 143 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain A residue 93 CYS 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 231 VAL 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 338 VAL 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 447 ASN Chi-restraints excluded: chain A residue 478 LYS 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 626 MET 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 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 78 ASP Chi-restraints excluded: chain B residue 95 LEU 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 128 LEU 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 340 VAL 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 376 ILE Chi-restraints excluded: chain E residue 448 ILE 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 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 185 optimal weight: 0.0770 chunk 169 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 163 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17884 Z= 0.324 Angle : 0.586 10.890 24672 Z= 0.296 Chirality : 0.042 0.251 2876 Planarity : 0.004 0.040 2832 Dihedral : 14.777 156.341 3662 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.91 % Allowed : 18.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.19), residues: 1953 helix: 0.44 (0.18), residues: 828 sheet: -1.14 (0.36), residues: 201 loop : -1.86 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 154 HIS 0.006 0.001 HIS E 290 PHE 0.036 0.002 PHE A 77 TYR 0.019 0.001 TYR A 748 ARG 0.008 0.000 ARG B 96 *********************** 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 235 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 151 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8106 (mtpp) REVERT: A 69 TYR cc_start: 0.8243 (m-80) cc_final: 0.7978 (m-80) REVERT: A 136 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6814 (pm20) REVERT: A 164 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7720 (m-30) REVERT: A 231 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8870 (p) REVERT: A 349 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7708 (ptp90) REVERT: A 447 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8323 (p0) REVERT: A 576 LEU cc_start: 0.8423 (mp) cc_final: 0.8112 (mt) REVERT: A 666 MET cc_start: 0.7639 (mtt) cc_final: 0.7197 (mtt) REVERT: A 733 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.6709 (mmt90) REVERT: A 883 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8345 (tp) REVERT: A 911 ASN cc_start: 0.8007 (t0) cc_final: 0.7167 (t0) REVERT: C 71 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7891 (mt) REVERT: D 57 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7095 (ttp-110) REVERT: D 78 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8159 (t0) REVERT: D 95 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8664 (mp) REVERT: E 121 ILE cc_start: 0.8419 (pt) cc_final: 0.8162 (pt) REVERT: E 263 SER cc_start: 0.8330 (p) cc_final: 0.8037 (t) REVERT: E 347 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7140 (ptpp) REVERT: E 349 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7453 (m110) REVERT: E 414 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7644 (tptp) REVERT: E 465 LYS cc_start: 0.3849 (OUTLIER) cc_final: 0.3155 (mptt) outliers start: 84 outliers final: 64 residues processed: 225 average time/residue: 0.3059 time to fit residues: 103.8458 Evaluate side-chains 221 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 144 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain A residue 93 CYS 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 231 VAL 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 338 VAL 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 397 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 478 LYS 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 626 MET 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 883 LEU Chi-restraints excluded: chain A residue 904 SER 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 78 ASP Chi-restraints excluded: chain B residue 95 LEU 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 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 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 340 VAL 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 397 VAL Chi-restraints excluded: chain E residue 448 ILE 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 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 190 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 132 optimal weight: 0.0870 chunk 200 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 159 optimal weight: 0.0010 chunk 16 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.7566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS A 703 ASN E 243 GLN E 245 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17884 Z= 0.198 Angle : 0.544 11.140 24672 Z= 0.272 Chirality : 0.040 0.240 2876 Planarity : 0.003 0.040 2832 Dihedral : 14.679 146.691 3662 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.39 % Allowed : 19.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 1953 helix: 0.55 (0.19), residues: 835 sheet: -1.01 (0.37), residues: 194 loop : -1.85 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 114 HIS 0.004 0.001 HIS E 290 PHE 0.037 0.001 PHE A 77 TYR 0.014 0.001 TYR A 748 ARG 0.008 0.000 ARG B 96 ********************** 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 223 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 148 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8440 (mtmm) cc_final: 0.8132 (mtpp) REVERT: A 69 TYR cc_start: 0.8171 (m-80) cc_final: 0.7906 (m-80) REVERT: A 136 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6773 (pm20) REVERT: A 164 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7677 (m-30) REVERT: A 231 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8821 (p) REVERT: A 349 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7620 (ptp90) REVERT: A 447 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8299 (p0) REVERT: A 576 LEU cc_start: 0.8290 (mp) cc_final: 0.7924 (mt) REVERT: A 666 MET cc_start: 0.7624 (mtt) cc_final: 0.7142 (mtt) REVERT: A 883 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8213 (tp) REVERT: A 911 ASN cc_start: 0.8008 (t0) cc_final: 0.7151 (t0) REVERT: C 71 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7791 (mt) REVERT: D 57 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7101 (ttp-110) REVERT: D 78 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8146 (t0) REVERT: D 95 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8550 (mp) REVERT: E 121 ILE cc_start: 0.8423 (pt) cc_final: 0.8171 (pt) REVERT: E 263 SER cc_start: 0.8301 (p) cc_final: 0.7984 (t) REVERT: E 311 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.7095 (m-70) REVERT: E 347 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7026 (ptpp) REVERT: E 349 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7388 (m110) REVERT: E 414 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7654 (tmtt) REVERT: E 465 LYS cc_start: 0.3826 (OUTLIER) cc_final: 0.3165 (mptt) outliers start: 75 outliers final: 60 residues processed: 213 average time/residue: 0.2991 time to fit residues: 96.4114 Evaluate side-chains 216 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 143 time to evaluate : 1.862 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain A residue 93 CYS 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 231 VAL 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 338 VAL 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 397 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 478 LYS 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 626 MET 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 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 78 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 119 ILE 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 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 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 340 VAL 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 397 VAL Chi-restraints excluded: chain E residue 448 ILE 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 169 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 147 optimal weight: 0.0060 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 159 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS A 703 ASN E 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.213861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.164918 restraints weight = 18810.477| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.78 r_work: 0.3780 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17884 Z= 0.154 Angle : 0.533 11.226 24672 Z= 0.267 Chirality : 0.039 0.224 2876 Planarity : 0.004 0.074 2832 Dihedral : 14.579 137.694 3661 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.09 % Allowed : 19.53 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.19), residues: 1953 helix: 0.71 (0.19), residues: 827 sheet: -0.91 (0.37), residues: 196 loop : -1.78 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 182 HIS 0.011 0.001 HIS E 245 PHE 0.037 0.001 PHE A 77 TYR 0.017 0.001 TYR A 903 ARG 0.009 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3857.78 seconds wall clock time: 69 minutes 46.82 seconds (4186.82 seconds total)