Starting phenix.real_space_refine on Sun May 3 19:02:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6szv_10355/05_2026/6szv_10355.cif Found real_map, /net/cci-nas-00/data/ceres_data/6szv_10355/05_2026/6szv_10355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6szv_10355/05_2026/6szv_10355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6szv_10355/05_2026/6szv_10355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6szv_10355/05_2026/6szv_10355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6szv_10355/05_2026/6szv_10355.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 43 5.49 5 Mg 5 5.21 5 S 92 5.16 5 C 9073 2.51 5 N 2554 2.21 5 O 3080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14847 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5716 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 25, 'TRANS': 675} Chain breaks: 2 Chain: "B" Number of atoms: 5955 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 743, 5947 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 714} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 743, 5947 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 714} Chain breaks: 1 bond proxies already assigned to first conformer: 6052 Chain: "C" Number of atoms: 2025 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 250, 2015 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 250, 2015 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 2043 Chain: "V" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 307 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain: "R" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 3, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 10} Chain: "M" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 200 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' MG': 2, 'M4H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, '2KH': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "V" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS C 27 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHIS C 27 " occ=0.40 Time building chain proxies: 4.82, per 1000 atoms: 0.32 Number of scatterers: 14847 At special positions: 0 Unit cell: (103.213, 116.216, 112.965, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 92 16.00 P 43 15.00 Mg 5 11.99 O 3080 8.00 N 2554 7.00 C 9073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 896.8 milliseconds 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3204 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 14 sheets defined 52.7% alpha, 13.5% beta 11 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.705A pdb=" N ASP A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 188 through 194 removed outlier: 3.871A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 188 through 194' Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.672A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 400 through 410 Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 448 through 471 Processing helix chain 'A' and resid 524 through 533 removed outlier: 3.526A pdb=" N ASN A 527 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 529 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS A 530 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU A 533 " --> pdb=" O HIS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 removed outlier: 3.559A pdb=" N GLU A 575 " --> pdb=" O LYS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.586A pdb=" N LEU A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 608 Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 647 through 669 removed outlier: 4.445A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 692 through 713 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.567A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 115 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.618A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 154 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.505A pdb=" N GLU B 159 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.505A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.678A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 376 removed outlier: 4.670A pdb=" N SER B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 375 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.595A pdb=" N VAL B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.707A pdb=" N LYS B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 473 removed outlier: 3.593A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 537 removed outlier: 3.574A pdb=" N ASP B 522 " --> pdb=" O ASN B 518 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 582 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 removed outlier: 3.594A pdb=" N MET B 616 " --> pdb=" O TRP B 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 613 through 616' Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 683 through 698 removed outlier: 3.854A pdb=" N ARG B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B 698 " --> pdb=" O GLN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 731 Processing helix chain 'B' and resid 736 through 754 Processing helix chain 'C' and resid 0 through 12 removed outlier: 3.992A pdb=" N ILE C 4 " --> pdb=" O GLY C 0 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 33 removed outlier: 4.037A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.571A pdb=" N MET C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.917A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.887A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.554A pdb=" N GLN C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.315A pdb=" N PHE A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.278A pdb=" N TYR A 496 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 552 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU A 544 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS A 554 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP A 542 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 556 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 537 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A 541 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LYS A 319 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N MET A 543 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N TRP A 317 " --> pdb=" O MET A 543 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.345A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR A 475 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 373 removed outlier: 5.868A pdb=" N GLU A 372 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N GLN B 367 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 622 through 626 removed outlier: 6.281A pdb=" N GLY A 626 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 127 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 193 removed outlier: 3.517A pdb=" N LYS B 198 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ASN B 678 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG B 203 " --> pdb=" O ASN B 678 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.849A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 60 Processing sheet with id=AB4, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.585A pdb=" N GLN C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.339A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 1932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2335 1.31 - 1.43: 4139 1.43 - 1.56: 8292 1.56 - 1.69: 82 1.69 - 1.81: 162 Bond restraints: 15010 Sorted by residual: bond pdb=" N3A 2KH B 801 " pdb=" PA 2KH B 801 " ideal model delta sigma weight residual 1.933 1.673 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C2' 2KH B 801 " pdb=" C3' 2KH B 801 " ideal model delta sigma weight residual 1.548 1.309 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" O2A 2KH B 801 " pdb=" PA 2KH B 801 " ideal model delta sigma weight residual 1.666 1.466 0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" N3A 2KH B 801 " pdb=" PB 2KH B 801 " ideal model delta sigma weight residual 1.890 1.699 0.191 2.00e-02 2.50e+03 9.09e+01 bond pdb=" O3G 2KH B 801 " pdb=" PG 2KH B 801 " ideal model delta sigma weight residual 1.669 1.497 0.172 2.00e-02 2.50e+03 7.38e+01 ... (remaining 15005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.70: 20438 12.70 - 25.40: 6 25.40 - 38.10: 0 38.10 - 50.80: 0 50.80 - 63.50: 2 Bond angle restraints: 20446 Sorted by residual: angle pdb=" N3A 2KH B 801 " pdb=" PA 2KH B 801 " pdb=" O2A 2KH B 801 " ideal model delta sigma weight residual 48.17 111.67 -63.50 3.00e+00 1.11e-01 4.48e+02 angle pdb=" O2G 2KH B 801 " pdb=" PG 2KH B 801 " pdb=" O3G 2KH B 801 " ideal model delta sigma weight residual 53.94 109.34 -55.40 3.00e+00 1.11e-01 3.41e+02 angle pdb=" O1A 2KH B 801 " pdb=" PA 2KH B 801 " pdb=" O2A 2KH B 801 " ideal model delta sigma weight residual 130.82 108.40 22.42 3.00e+00 1.11e-01 5.59e+01 angle pdb=" O1B 2KH B 801 " pdb=" PB 2KH B 801 " pdb=" O2B 2KH B 801 " ideal model delta sigma weight residual 130.56 108.34 22.22 3.00e+00 1.11e-01 5.49e+01 angle pdb=" O1G 2KH B 801 " pdb=" PG 2KH B 801 " pdb=" O2G 2KH B 801 " ideal model delta sigma weight residual 130.21 109.09 21.12 3.00e+00 1.11e-01 4.95e+01 ... (remaining 20441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 8436 18.14 - 36.28: 526 36.28 - 54.42: 143 54.42 - 72.56: 95 72.56 - 90.70: 18 Dihedral angle restraints: 9218 sinusoidal: 4265 harmonic: 4953 Sorted by residual: dihedral pdb=" CA ILE B 302 " pdb=" C ILE B 302 " pdb=" N THR B 303 " pdb=" CA THR B 303 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA MET B 408 " pdb=" C MET B 408 " pdb=" N MET B 409 " pdb=" CA MET B 409 " ideal model delta harmonic sigma weight residual 180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LEU A 219 " pdb=" C LEU A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta harmonic sigma weight residual 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 9215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2086 0.077 - 0.154: 163 0.154 - 0.232: 7 0.232 - 0.309: 0 0.309 - 0.386: 1 Chirality restraints: 2257 Sorted by residual: chirality pdb=" C2' 2KH B 801 " pdb=" C1' 2KH B 801 " pdb=" C3' 2KH B 801 " pdb=" O2' 2KH B 801 " both_signs ideal model delta sigma weight residual False -2.85 -2.46 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C1' 2KH B 801 " pdb=" C2' 2KH B 801 " pdb=" N1 2KH B 801 " pdb=" O4' 2KH B 801 " both_signs ideal model delta sigma weight residual False 2.59 2.36 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3' 2KH B 801 " pdb=" C2' 2KH B 801 " pdb=" C4' 2KH B 801 " pdb=" O3' 2KH B 801 " both_signs ideal model delta sigma weight residual False -2.66 -2.45 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2254 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO A 620 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 509 " -0.039 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO B 510 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 510 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 510 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 604 " 0.035 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO A 605 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " 0.029 5.00e-02 4.00e+02 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 80 2.39 - 3.02: 7239 3.02 - 3.65: 23477 3.65 - 4.27: 38615 4.27 - 4.90: 60645 Nonbonded interactions: 130056 Sorted by model distance: nonbonded pdb=" O8 M4H A 801 " pdb="MG MG A 802 " model vdw 1.763 2.170 nonbonded pdb=" O ILE A 120 " pdb="MG MG A 803 " model vdw 1.892 2.170 nonbonded pdb=" O11 M4H A 801 " pdb="MG MG A 803 " model vdw 1.997 2.170 nonbonded pdb=" OD2 ASP A 108 " pdb="MG MG A 803 " model vdw 2.104 2.170 nonbonded pdb=" O10 M4H A 801 " pdb="MG MG A 802 " model vdw 2.111 2.170 ... (remaining 130051 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.760 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.006 0.260 15010 Z= 0.302 Angle : 0.934 63.500 20446 Z= 0.422 Chirality : 0.043 0.386 2257 Planarity : 0.005 0.059 2472 Dihedral : 14.854 90.704 6014 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.30 % Rotamer: Outliers : 3.65 % Allowed : 4.91 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.16), residues: 1688 helix: -1.94 (0.13), residues: 806 sheet: -0.88 (0.37), residues: 176 loop : -1.82 (0.19), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.013 0.001 TYR B 555 PHE 0.016 0.002 PHE B 447 TRP 0.018 0.002 TRP B 438 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00589 (15010) covalent geometry : angle 0.93363 (20446) hydrogen bonds : bond 0.16701 ( 722) hydrogen bonds : angle 6.52935 ( 1988) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 336 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.6466 (tpp) cc_final: 0.6137 (tpt) REVERT: A 43 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6857 (tm-30) REVERT: A 97 MET cc_start: 0.6883 (tmm) cc_final: 0.6404 (tmt) REVERT: A 116 LYS cc_start: 0.7528 (mmmm) cc_final: 0.7272 (mmtp) REVERT: A 174 ARG cc_start: 0.6943 (tpt90) cc_final: 0.6610 (tpt170) REVERT: A 315 TRP cc_start: 0.7243 (OUTLIER) cc_final: 0.6977 (m-90) REVERT: A 347 GLU cc_start: 0.7262 (pt0) cc_final: 0.6872 (pt0) REVERT: A 418 ILE cc_start: 0.8324 (mm) cc_final: 0.8005 (mm) REVERT: A 485 ARG cc_start: 0.7331 (mmt180) cc_final: 0.6827 (mtp-110) REVERT: A 492 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7714 (ttm170) REVERT: A 543 MET cc_start: 0.7917 (ttm) cc_final: 0.7662 (ttp) REVERT: A 568 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8321 (tp) REVERT: A 600 LYS cc_start: 0.8564 (ptpt) cc_final: 0.8337 (pttm) REVERT: A 616 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.7938 (pp) REVERT: B 48 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: B 187 LYS cc_start: 0.8014 (mttt) cc_final: 0.7392 (mtmm) REVERT: B 189 LYS cc_start: 0.7513 (pttt) cc_final: 0.6796 (ptpp) REVERT: B 428 GLN cc_start: 0.7837 (mt0) cc_final: 0.7524 (mt0) REVERT: B 567 ASN cc_start: 0.7836 (m-40) cc_final: 0.7629 (m110) REVERT: B 574 LYS cc_start: 0.8264 (mttt) cc_final: 0.7975 (mtpp) REVERT: B 687 ARG cc_start: 0.6544 (mtt180) cc_final: 0.6314 (mmm-85) REVERT: B 691 LYS cc_start: 0.7840 (mttt) cc_final: 0.7635 (mttt) REVERT: B 702 SER cc_start: 0.8268 (p) cc_final: 0.8050 (t) REVERT: C 6 GLU cc_start: 0.6977 (tt0) cc_final: 0.6771 (tt0) REVERT: C 134 LYS cc_start: 0.8372 (mttt) cc_final: 0.8155 (mmtm) REVERT: C 143 LYS cc_start: 0.7397 (mttt) cc_final: 0.7162 (mtpm) REVERT: C 187 LYS cc_start: 0.7980 (tttt) cc_final: 0.7602 (mmtm) REVERT: C 206 MET cc_start: 0.8105 (ttp) cc_final: 0.7819 (ttm) outliers start: 55 outliers final: 20 residues processed: 377 average time/residue: 0.8149 time to fit residues: 329.6015 Evaluate side-chains 301 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 199 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 416 ASN A 425 ASN A 585 GLN B 58 ASN B 115 GLN B 124 GLN B 202 GLN B 284 ASN B 313 GLN B 413 ASN B 454 HIS B 465 HIS B 479 GLN B 537 ASN C 138 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.150777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120053 restraints weight = 26333.847| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.80 r_work: 0.3109 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15010 Z= 0.146 Angle : 0.531 10.526 20446 Z= 0.281 Chirality : 0.041 0.209 2257 Planarity : 0.004 0.042 2472 Dihedral : 12.929 91.297 2598 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.92 % Allowed : 12.08 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.19), residues: 1688 helix: 0.24 (0.17), residues: 807 sheet: -0.40 (0.39), residues: 169 loop : -0.99 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 621 TYR 0.016 0.001 TYR B 217 PHE 0.017 0.001 PHE A 702 TRP 0.018 0.002 TRP B 309 HIS 0.004 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00318 (15010) covalent geometry : angle 0.53117 (20446) hydrogen bonds : bond 0.04739 ( 722) hydrogen bonds : angle 4.51255 ( 1988) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7286 (mmt-90) REVERT: A 19 LYS cc_start: 0.7003 (mttm) cc_final: 0.6555 (mtpt) REVERT: A 42 MET cc_start: 0.6435 (tpp) cc_final: 0.5735 (tpt) REVERT: A 43 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: A 97 MET cc_start: 0.7406 (tmm) cc_final: 0.6790 (tmt) REVERT: A 116 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7565 (mttp) REVERT: A 343 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7894 (tm-30) REVERT: A 347 GLU cc_start: 0.7928 (pt0) cc_final: 0.7718 (pt0) REVERT: A 378 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: A 418 ILE cc_start: 0.8488 (mm) cc_final: 0.8276 (mm) REVERT: A 485 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7165 (mtm110) REVERT: A 568 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8648 (tp) REVERT: A 600 LYS cc_start: 0.8743 (ptpt) cc_final: 0.8459 (pttm) REVERT: A 616 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8438 (pp) REVERT: B 48 ASP cc_start: 0.8324 (m-30) cc_final: 0.8080 (m-30) REVERT: B 187 LYS cc_start: 0.8454 (mttt) cc_final: 0.7679 (mtmm) REVERT: B 189 LYS cc_start: 0.7781 (pttt) cc_final: 0.7027 (ptpp) REVERT: B 290 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7282 (mtt) REVERT: B 454 HIS cc_start: 0.8071 (m-70) cc_final: 0.7843 (m90) REVERT: B 554 ASP cc_start: 0.8904 (t0) cc_final: 0.8671 (t0) REVERT: B 567 ASN cc_start: 0.8057 (m-40) cc_final: 0.7666 (m110) REVERT: B 569 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: B 574 LYS cc_start: 0.8662 (mttt) cc_final: 0.8372 (mtpp) REVERT: B 619 ASP cc_start: 0.7749 (m-30) cc_final: 0.7544 (m-30) REVERT: B 687 ARG cc_start: 0.7362 (mtt180) cc_final: 0.6950 (mmm-85) REVERT: C 5 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7676 (mtmt) REVERT: C 134 LYS cc_start: 0.8837 (mttt) cc_final: 0.8393 (mmtm) REVERT: C 187 LYS cc_start: 0.8125 (tttt) cc_final: 0.7591 (mmtm) REVERT: C 206 MET cc_start: 0.8715 (ttp) cc_final: 0.8513 (ttm) outliers start: 44 outliers final: 15 residues processed: 298 average time/residue: 0.8458 time to fit residues: 270.4063 Evaluate side-chains 278 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 569 GLU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 79 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 149 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 99 optimal weight: 9.9990 chunk 2 optimal weight: 0.0470 chunk 135 optimal weight: 6.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 505 HIS B 124 GLN B 202 GLN B 284 ASN B 413 ASN B 479 GLN B 633 HIS C 182 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.153176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122209 restraints weight = 30684.159| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.09 r_work: 0.3117 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15010 Z= 0.099 Angle : 0.463 9.467 20446 Z= 0.245 Chirality : 0.038 0.193 2257 Planarity : 0.003 0.039 2472 Dihedral : 12.385 88.328 2570 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.26 % Allowed : 13.60 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1688 helix: 1.15 (0.18), residues: 806 sheet: -0.12 (0.39), residues: 169 loop : -0.76 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 126 TYR 0.010 0.001 TYR B 217 PHE 0.010 0.001 PHE B 333 TRP 0.012 0.001 TRP B 309 HIS 0.002 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00204 (15010) covalent geometry : angle 0.46317 (20446) hydrogen bonds : bond 0.03849 ( 722) hydrogen bonds : angle 4.20513 ( 1988) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: A 19 LYS cc_start: 0.6982 (mttm) cc_final: 0.6555 (mtpt) REVERT: A 42 MET cc_start: 0.6363 (tpp) cc_final: 0.5661 (tpt) REVERT: A 43 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6359 (tm-30) REVERT: A 84 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7864 (mtp180) REVERT: A 97 MET cc_start: 0.7413 (tmm) cc_final: 0.6725 (tmt) REVERT: A 116 LYS cc_start: 0.7918 (mmmm) cc_final: 0.7547 (mmtp) REVERT: A 258 GLU cc_start: 0.8812 (pt0) cc_final: 0.8591 (pt0) REVERT: A 321 THR cc_start: 0.8536 (p) cc_final: 0.8303 (t) REVERT: A 343 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 347 GLU cc_start: 0.7994 (pt0) cc_final: 0.7680 (pt0) REVERT: A 485 ARG cc_start: 0.7981 (mmt180) cc_final: 0.7097 (mtm110) REVERT: A 487 THR cc_start: 0.6647 (OUTLIER) cc_final: 0.6320 (m) REVERT: A 568 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8677 (tp) REVERT: A 600 LYS cc_start: 0.8731 (ptpt) cc_final: 0.8437 (pttm) REVERT: B 48 ASP cc_start: 0.8382 (m-30) cc_final: 0.8118 (m-30) REVERT: B 187 LYS cc_start: 0.8470 (mttt) cc_final: 0.7701 (mtmm) REVERT: B 189 LYS cc_start: 0.7818 (pttt) cc_final: 0.7069 (ptpp) REVERT: B 290 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7379 (mtt) REVERT: B 454 HIS cc_start: 0.8020 (m-70) cc_final: 0.7780 (m-70) REVERT: B 461 GLN cc_start: 0.8665 (mt0) cc_final: 0.8373 (tt0) REVERT: B 619 ASP cc_start: 0.7791 (m-30) cc_final: 0.7572 (m-30) REVERT: B 687 ARG cc_start: 0.7384 (mtt180) cc_final: 0.6981 (mmm-85) REVERT: C 1 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7265 (mmm) REVERT: C 116 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8455 (tppt) REVERT: C 134 LYS cc_start: 0.8812 (mttt) cc_final: 0.8363 (mmtm) REVERT: C 187 LYS cc_start: 0.8085 (tttt) cc_final: 0.7582 (mmtm) REVERT: C 206 MET cc_start: 0.8626 (ttp) cc_final: 0.8384 (ttm) outliers start: 34 outliers final: 11 residues processed: 288 average time/residue: 0.8112 time to fit residues: 251.3480 Evaluate side-chains 266 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 425 ASN A 508 ASN B 124 GLN B 284 ASN B 413 ASN B 567 ASN B 634 HIS C 148 ASN C 170 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.149440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117400 restraints weight = 31594.432| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.23 r_work: 0.3031 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15010 Z= 0.169 Angle : 0.532 9.809 20446 Z= 0.280 Chirality : 0.042 0.207 2257 Planarity : 0.004 0.038 2472 Dihedral : 12.512 91.077 2555 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.92 % Allowed : 13.80 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1688 helix: 1.31 (0.18), residues: 808 sheet: -0.01 (0.39), residues: 174 loop : -0.63 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 621 TYR 0.016 0.002 TYR B 217 PHE 0.020 0.002 PHE A 702 TRP 0.014 0.002 TRP A 363 HIS 0.004 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00379 (15010) covalent geometry : angle 0.53181 (20446) hydrogen bonds : bond 0.04667 ( 722) hydrogen bonds : angle 4.27544 ( 1988) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6932 (mttm) cc_final: 0.6538 (mtpt) REVERT: A 42 MET cc_start: 0.6520 (tpp) cc_final: 0.5708 (tpt) REVERT: A 43 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6320 (tm-30) REVERT: A 84 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7846 (mtp180) REVERT: A 97 MET cc_start: 0.7404 (tmm) cc_final: 0.6738 (tmt) REVERT: A 116 LYS cc_start: 0.7851 (mmmm) cc_final: 0.7468 (mmtp) REVERT: A 258 GLU cc_start: 0.8931 (pt0) cc_final: 0.8684 (pt0) REVERT: A 343 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 347 GLU cc_start: 0.8105 (pt0) cc_final: 0.7747 (pt0) REVERT: A 418 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8293 (mm) REVERT: A 419 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: A 485 ARG cc_start: 0.8031 (mmt180) cc_final: 0.7092 (mtm110) REVERT: A 568 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8736 (tp) REVERT: A 600 LYS cc_start: 0.8770 (ptpt) cc_final: 0.8455 (pttm) REVERT: A 608 ARG cc_start: 0.7610 (mtt90) cc_final: 0.7293 (mmt90) REVERT: B 152 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8381 (mppt) REVERT: B 187 LYS cc_start: 0.8450 (mttt) cc_final: 0.7710 (mtmm) REVERT: B 189 LYS cc_start: 0.7841 (pttt) cc_final: 0.7068 (ptpp) REVERT: B 290 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7269 (mtt) REVERT: B 454 HIS cc_start: 0.8139 (m-70) cc_final: 0.7817 (m-70) REVERT: B 554 ASP cc_start: 0.8917 (t0) cc_final: 0.8683 (t0) REVERT: B 619 ASP cc_start: 0.7826 (m-30) cc_final: 0.7564 (m-30) REVERT: B 687 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7000 (mmm-85) REVERT: C 1 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7423 (mmm) REVERT: C 116 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8490 (tppt) REVERT: C 134 LYS cc_start: 0.8833 (mttt) cc_final: 0.8320 (mmtm) REVERT: C 157 ARG cc_start: 0.6957 (mtt90) cc_final: 0.6321 (ttm-80) outliers start: 44 outliers final: 19 residues processed: 281 average time/residue: 0.7942 time to fit residues: 240.1413 Evaluate side-chains 277 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 425 ASN B 124 GLN B 284 ASN B 413 ASN B 567 ASN B 634 HIS C 148 ASN C 170 ASN C 182 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.151909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120917 restraints weight = 27148.231| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.81 r_work: 0.3119 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15010 Z= 0.110 Angle : 0.469 9.205 20446 Z= 0.249 Chirality : 0.039 0.196 2257 Planarity : 0.003 0.036 2472 Dihedral : 12.310 88.531 2553 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.32 % Allowed : 14.86 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1688 helix: 1.56 (0.19), residues: 810 sheet: 0.08 (0.39), residues: 172 loop : -0.57 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 126 TYR 0.011 0.001 TYR B 217 PHE 0.011 0.001 PHE A 702 TRP 0.013 0.002 TRP C 98 HIS 0.002 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00234 (15010) covalent geometry : angle 0.46923 (20446) hydrogen bonds : bond 0.03924 ( 722) hydrogen bonds : angle 4.11162 ( 1988) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6945 (mttm) cc_final: 0.6546 (mtpt) REVERT: A 42 MET cc_start: 0.6461 (tpp) cc_final: 0.5649 (tpt) REVERT: A 43 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6250 (tm-30) REVERT: A 84 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7854 (mtp180) REVERT: A 97 MET cc_start: 0.7374 (tmm) cc_final: 0.6740 (tmt) REVERT: A 116 LYS cc_start: 0.7813 (mmmm) cc_final: 0.7418 (mmtp) REVERT: A 321 THR cc_start: 0.8571 (p) cc_final: 0.8330 (t) REVERT: A 343 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7781 (tm-30) REVERT: A 347 GLU cc_start: 0.8022 (pt0) cc_final: 0.7607 (pt0) REVERT: A 485 ARG cc_start: 0.7989 (mmt180) cc_final: 0.7095 (mtm110) REVERT: A 568 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8686 (tp) REVERT: A 600 LYS cc_start: 0.8757 (ptpt) cc_final: 0.8469 (pttm) REVERT: B 48 ASP cc_start: 0.8361 (m-30) cc_final: 0.8112 (m-30) REVERT: B 152 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8367 (mppt) REVERT: B 187 LYS cc_start: 0.8410 (mttt) cc_final: 0.7696 (mtmm) REVERT: B 189 LYS cc_start: 0.7784 (pttt) cc_final: 0.7052 (ptpp) REVERT: B 290 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7374 (mtt) REVERT: B 390 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7274 (pp20) REVERT: B 454 HIS cc_start: 0.8064 (m-70) cc_final: 0.7792 (m-70) REVERT: B 619 ASP cc_start: 0.7773 (m-30) cc_final: 0.7544 (m-30) REVERT: B 687 ARG cc_start: 0.7394 (mtt180) cc_final: 0.6958 (mmm-85) REVERT: B 691 LYS cc_start: 0.7966 (mttt) cc_final: 0.7683 (mttt) REVERT: C 116 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8479 (tppt) REVERT: C 134 LYS cc_start: 0.8803 (mttt) cc_final: 0.8339 (mmtm) outliers start: 35 outliers final: 12 residues processed: 274 average time/residue: 0.8018 time to fit residues: 236.2318 Evaluate side-chains 263 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 10 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 425 ASN B 124 GLN B 284 ASN B 413 ASN B 567 ASN B 634 HIS ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 170 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.147762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116919 restraints weight = 23997.606| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.74 r_work: 0.3067 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15010 Z= 0.209 Angle : 0.571 9.800 20446 Z= 0.300 Chirality : 0.044 0.215 2257 Planarity : 0.004 0.045 2472 Dihedral : 12.590 90.951 2551 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.99 % Allowed : 14.40 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1688 helix: 1.35 (0.18), residues: 814 sheet: 0.08 (0.39), residues: 174 loop : -0.58 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 621 TYR 0.017 0.002 TYR B 217 PHE 0.024 0.002 PHE A 702 TRP 0.016 0.002 TRP A 363 HIS 0.004 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00477 (15010) covalent geometry : angle 0.57146 (20446) hydrogen bonds : bond 0.04979 ( 722) hydrogen bonds : angle 4.31628 ( 1988) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3300 (OUTLIER) cc_final: 0.2903 (ttm) REVERT: A 19 LYS cc_start: 0.6891 (mttm) cc_final: 0.6503 (mtpt) REVERT: A 42 MET cc_start: 0.6497 (tpp) cc_final: 0.5687 (tpt) REVERT: A 43 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6243 (tm-30) REVERT: A 84 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7859 (mtp180) REVERT: A 97 MET cc_start: 0.7430 (tmm) cc_final: 0.7194 (tmm) REVERT: A 116 LYS cc_start: 0.7774 (mmmm) cc_final: 0.7377 (mmtp) REVERT: A 347 GLU cc_start: 0.8140 (pt0) cc_final: 0.7680 (pp20) REVERT: A 485 ARG cc_start: 0.8033 (mmt180) cc_final: 0.7163 (mtm110) REVERT: A 568 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8747 (tp) REVERT: A 598 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.7711 (mptp) REVERT: A 600 LYS cc_start: 0.8777 (ptpt) cc_final: 0.8475 (pttm) REVERT: B 41 ASP cc_start: 0.8412 (m-30) cc_final: 0.8151 (m-30) REVERT: B 135 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8292 (ppp80) REVERT: B 152 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8366 (mppt) REVERT: B 187 LYS cc_start: 0.8398 (mttt) cc_final: 0.7661 (mtmm) REVERT: B 189 LYS cc_start: 0.7827 (pttt) cc_final: 0.7066 (ptpp) REVERT: B 290 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7333 (mtt) REVERT: B 454 HIS cc_start: 0.8179 (m-70) cc_final: 0.7836 (m90) REVERT: B 554 ASP cc_start: 0.8848 (t0) cc_final: 0.8623 (t0) REVERT: B 619 ASP cc_start: 0.7767 (m-30) cc_final: 0.7534 (m-30) REVERT: B 687 ARG cc_start: 0.7459 (mtt180) cc_final: 0.6988 (mmm-85) REVERT: C 5 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7950 (mptp) REVERT: C 113 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8722 (tmm-80) REVERT: C 116 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8477 (tppt) REVERT: C 134 LYS cc_start: 0.8862 (mttt) cc_final: 0.8372 (mmtm) REVERT: C 157 ARG cc_start: 0.6986 (mtt90) cc_final: 0.6449 (mmm-85) outliers start: 45 outliers final: 18 residues processed: 268 average time/residue: 0.8275 time to fit residues: 238.0021 Evaluate side-chains 269 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 97 optimal weight: 0.0030 chunk 116 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 425 ASN B 116 GLN B 284 ASN B 413 ASN B 567 ASN B 634 HIS ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 170 ASN C 182 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.152884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122294 restraints weight = 26591.533| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.80 r_work: 0.3142 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15010 Z= 0.095 Angle : 0.459 8.534 20446 Z= 0.243 Chirality : 0.038 0.191 2257 Planarity : 0.003 0.035 2472 Dihedral : 12.339 86.827 2551 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.73 % Allowed : 15.59 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1688 helix: 1.77 (0.19), residues: 803 sheet: 0.18 (0.39), residues: 172 loop : -0.42 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 126 TYR 0.011 0.001 TYR B 555 PHE 0.011 0.001 PHE B 333 TRP 0.016 0.001 TRP C 49 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00193 (15010) covalent geometry : angle 0.45923 (20446) hydrogen bonds : bond 0.03642 ( 722) hydrogen bonds : angle 4.06677 ( 1988) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: A 19 LYS cc_start: 0.6942 (mttm) cc_final: 0.6553 (mtpt) REVERT: A 42 MET cc_start: 0.6425 (tpp) cc_final: 0.5551 (tpt) REVERT: A 43 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6265 (tm-30) REVERT: A 84 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7823 (mtp180) REVERT: A 97 MET cc_start: 0.7385 (tmm) cc_final: 0.6738 (tmt) REVERT: A 116 LYS cc_start: 0.7773 (mmmm) cc_final: 0.7328 (mttp) REVERT: A 321 THR cc_start: 0.8565 (p) cc_final: 0.8359 (t) REVERT: A 343 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7713 (tm-30) REVERT: A 347 GLU cc_start: 0.8133 (pt0) cc_final: 0.7682 (pp20) REVERT: A 485 ARG cc_start: 0.7994 (mmt180) cc_final: 0.7098 (mtm110) REVERT: A 600 LYS cc_start: 0.8772 (ptpt) cc_final: 0.8469 (pttm) REVERT: B 48 ASP cc_start: 0.8344 (m-30) cc_final: 0.8091 (m-30) REVERT: B 152 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8382 (mppt) REVERT: B 187 LYS cc_start: 0.8368 (mttt) cc_final: 0.7669 (mtmm) REVERT: B 189 LYS cc_start: 0.7745 (pttt) cc_final: 0.6999 (ptpp) REVERT: B 290 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7357 (mtt) REVERT: B 454 HIS cc_start: 0.8005 (m-70) cc_final: 0.7773 (m-70) REVERT: B 619 ASP cc_start: 0.7762 (m-30) cc_final: 0.7533 (m-30) REVERT: B 687 ARG cc_start: 0.7391 (mtt180) cc_final: 0.6954 (mmm-85) REVERT: C 116 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8435 (tppt) REVERT: C 134 LYS cc_start: 0.8804 (mttt) cc_final: 0.8358 (mmtm) outliers start: 26 outliers final: 11 residues processed: 267 average time/residue: 0.8076 time to fit residues: 232.2970 Evaluate side-chains 263 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 131 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 425 ASN B 124 GLN B 284 ASN B 413 ASN B 567 ASN B 634 HIS ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 170 ASN C 182 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.149443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117781 restraints weight = 29818.669| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.94 r_work: 0.3057 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15010 Z= 0.167 Angle : 0.532 10.939 20446 Z= 0.279 Chirality : 0.042 0.204 2257 Planarity : 0.004 0.036 2472 Dihedral : 12.453 90.090 2549 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.06 % Allowed : 15.86 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1688 helix: 1.58 (0.18), residues: 816 sheet: 0.15 (0.38), residues: 174 loop : -0.46 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 353 TYR 0.015 0.002 TYR B 217 PHE 0.019 0.002 PHE A 702 TRP 0.016 0.002 TRP A 614 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00376 (15010) covalent geometry : angle 0.53236 (20446) hydrogen bonds : bond 0.04517 ( 722) hydrogen bonds : angle 4.20268 ( 1988) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6995 (mttm) cc_final: 0.6601 (mtpt) REVERT: A 42 MET cc_start: 0.6535 (tpp) cc_final: 0.5762 (tpt) REVERT: A 43 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6317 (tm-30) REVERT: A 84 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7976 (mtp180) REVERT: A 97 MET cc_start: 0.7490 (tmm) cc_final: 0.6825 (tmt) REVERT: A 116 LYS cc_start: 0.7847 (mmmm) cc_final: 0.7435 (mttp) REVERT: A 224 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8227 (mmtt) REVERT: A 225 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7974 (t0) REVERT: A 343 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 347 GLU cc_start: 0.8235 (pt0) cc_final: 0.7712 (pp20) REVERT: A 367 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8463 (tp30) REVERT: A 485 ARG cc_start: 0.8057 (mmt180) cc_final: 0.7203 (mtm110) REVERT: A 598 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.7682 (mptp) REVERT: A 600 LYS cc_start: 0.8804 (ptpt) cc_final: 0.8515 (pttm) REVERT: B 152 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8467 (mppt) REVERT: B 187 LYS cc_start: 0.8443 (mttt) cc_final: 0.7721 (mtmm) REVERT: B 189 LYS cc_start: 0.7868 (pttt) cc_final: 0.7111 (ptpp) REVERT: B 290 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7396 (mtt) REVERT: B 454 HIS cc_start: 0.8210 (m-70) cc_final: 0.7935 (m-70) REVERT: B 554 ASP cc_start: 0.8891 (t0) cc_final: 0.8684 (t0) REVERT: B 619 ASP cc_start: 0.7897 (m-30) cc_final: 0.7643 (m-30) REVERT: B 687 ARG cc_start: 0.7549 (mtt180) cc_final: 0.7099 (mmm-85) REVERT: C 113 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8778 (tmm-80) REVERT: C 116 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8532 (tppt) REVERT: C 134 LYS cc_start: 0.8886 (mttt) cc_final: 0.8415 (mmtm) REVERT: C 157 ARG cc_start: 0.7008 (mtt90) cc_final: 0.6472 (mmm-85) outliers start: 31 outliers final: 14 residues processed: 264 average time/residue: 0.8230 time to fit residues: 233.1854 Evaluate side-chains 266 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 30 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 425 ASN B 124 GLN B 284 ASN B 413 ASN B 567 ASN B 634 HIS ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 170 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.150099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119271 restraints weight = 23490.110| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.71 r_work: 0.3113 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15010 Z= 0.133 Angle : 0.508 13.406 20446 Z= 0.266 Chirality : 0.040 0.201 2257 Planarity : 0.004 0.036 2472 Dihedral : 12.401 89.047 2549 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.73 % Allowed : 16.06 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.20), residues: 1688 helix: 1.67 (0.19), residues: 808 sheet: 0.18 (0.38), residues: 174 loop : -0.39 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 353 TYR 0.013 0.001 TYR B 217 PHE 0.015 0.001 PHE A 702 TRP 0.019 0.002 TRP A 614 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00292 (15010) covalent geometry : angle 0.50811 (20446) hydrogen bonds : bond 0.04215 ( 722) hydrogen bonds : angle 4.15623 ( 1988) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3269 (ttp) cc_final: 0.2904 (ttm) REVERT: A 19 LYS cc_start: 0.6958 (mttm) cc_final: 0.6575 (mtpt) REVERT: A 42 MET cc_start: 0.6463 (tpp) cc_final: 0.5635 (tpt) REVERT: A 43 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6224 (tm-30) REVERT: A 84 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7834 (mtp180) REVERT: A 97 MET cc_start: 0.7377 (tmm) cc_final: 0.6718 (tmt) REVERT: A 116 LYS cc_start: 0.7779 (mmmm) cc_final: 0.7357 (mttp) REVERT: A 225 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7835 (t0) REVERT: A 258 GLU cc_start: 0.8862 (pt0) cc_final: 0.8655 (pt0) REVERT: A 343 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 347 GLU cc_start: 0.8150 (pt0) cc_final: 0.7639 (pp20) REVERT: A 367 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8378 (tp30) REVERT: A 485 ARG cc_start: 0.7974 (mmt180) cc_final: 0.7107 (mtm110) REVERT: A 600 LYS cc_start: 0.8787 (ptpt) cc_final: 0.8485 (pttm) REVERT: B 152 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8369 (mppt) REVERT: B 187 LYS cc_start: 0.8360 (mttt) cc_final: 0.7668 (mtmm) REVERT: B 189 LYS cc_start: 0.7801 (pttt) cc_final: 0.7063 (ptpp) REVERT: B 290 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7426 (mtt) REVERT: B 454 HIS cc_start: 0.8065 (m-70) cc_final: 0.7812 (m-70) REVERT: B 619 ASP cc_start: 0.7765 (m-30) cc_final: 0.7527 (m-30) REVERT: B 687 ARG cc_start: 0.7428 (mtt180) cc_final: 0.6983 (mmm-85) REVERT: C 113 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8698 (tmm-80) REVERT: C 116 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8508 (tppt) REVERT: C 134 LYS cc_start: 0.8805 (mttt) cc_final: 0.8361 (mmtm) REVERT: C 157 ARG cc_start: 0.6847 (mtt90) cc_final: 0.6331 (mmm-85) outliers start: 26 outliers final: 11 residues processed: 255 average time/residue: 0.8261 time to fit residues: 226.6041 Evaluate side-chains 259 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 123 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 104 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 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 27 ASN A 425 ASN B 124 GLN B 284 ASN B 413 ASN B 567 ASN B 634 HIS ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 170 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120708 restraints weight = 31424.767| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.15 r_work: 0.3102 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15010 Z= 0.102 Angle : 0.473 13.380 20446 Z= 0.248 Chirality : 0.039 0.190 2257 Planarity : 0.003 0.035 2472 Dihedral : 12.251 86.940 2549 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.46 % Allowed : 16.32 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.21), residues: 1688 helix: 1.84 (0.19), residues: 802 sheet: 0.28 (0.39), residues: 172 loop : -0.35 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 379 TYR 0.010 0.001 TYR B 217 PHE 0.011 0.001 PHE A 211 TRP 0.020 0.002 TRP A 614 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00213 (15010) covalent geometry : angle 0.47344 (20446) hydrogen bonds : bond 0.03752 ( 722) hydrogen bonds : angle 4.05613 ( 1988) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3341 (ttp) cc_final: 0.2949 (ttm) REVERT: A 19 LYS cc_start: 0.6953 (mttm) cc_final: 0.6568 (mtpt) REVERT: A 42 MET cc_start: 0.6449 (tpp) cc_final: 0.5626 (tpt) REVERT: A 43 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6257 (tm-30) REVERT: A 84 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7893 (mtp180) REVERT: A 97 MET cc_start: 0.7410 (tmm) cc_final: 0.6719 (tmt) REVERT: A 116 LYS cc_start: 0.7828 (mmmm) cc_final: 0.7389 (mttp) REVERT: A 225 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7941 (t0) REVERT: A 258 GLU cc_start: 0.8881 (pt0) cc_final: 0.8643 (pt0) REVERT: A 321 THR cc_start: 0.8576 (p) cc_final: 0.8356 (t) REVERT: A 343 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 347 GLU cc_start: 0.8133 (pt0) cc_final: 0.7619 (pp20) REVERT: A 367 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8424 (tp30) REVERT: A 485 ARG cc_start: 0.8038 (mmt180) cc_final: 0.7125 (mtm110) REVERT: A 598 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.7656 (mptp) REVERT: A 600 LYS cc_start: 0.8787 (ptpt) cc_final: 0.8477 (pttm) REVERT: B 48 ASP cc_start: 0.8437 (m-30) cc_final: 0.8175 (m-30) REVERT: B 152 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8424 (mppt) REVERT: B 187 LYS cc_start: 0.8421 (mttt) cc_final: 0.7681 (mtmm) REVERT: B 189 LYS cc_start: 0.7777 (pttt) cc_final: 0.7032 (ptpp) REVERT: B 290 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7438 (mtt) REVERT: B 454 HIS cc_start: 0.8150 (m-70) cc_final: 0.7905 (m-70) REVERT: B 619 ASP cc_start: 0.7859 (m-30) cc_final: 0.7587 (m-30) REVERT: B 687 ARG cc_start: 0.7446 (mtt180) cc_final: 0.7009 (mmm-85) REVERT: C 5 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7999 (mptp) REVERT: C 116 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8492 (tppt) REVERT: C 134 LYS cc_start: 0.8831 (mttt) cc_final: 0.8357 (mmtm) REVERT: C 157 ARG cc_start: 0.6877 (mtt90) cc_final: 0.6339 (mmm-85) outliers start: 22 outliers final: 8 residues processed: 267 average time/residue: 0.8118 time to fit residues: 233.3442 Evaluate side-chains 263 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 171 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 161 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 82 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 156 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 158 optimal weight: 0.0980 chunk 154 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 284 ASN B 413 ASN B 567 ASN B 634 HIS ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 170 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.124481 restraints weight = 26841.895| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.68 r_work: 0.3142 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15010 Z= 0.091 Angle : 0.464 13.278 20446 Z= 0.242 Chirality : 0.038 0.183 2257 Planarity : 0.003 0.034 2472 Dihedral : 12.135 85.647 2549 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.19 % Allowed : 16.85 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1688 helix: 1.93 (0.19), residues: 803 sheet: 0.32 (0.39), residues: 172 loop : -0.32 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 175 TYR 0.010 0.001 TYR B 555 PHE 0.010 0.001 PHE A 211 TRP 0.017 0.001 TRP A 614 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00188 (15010) covalent geometry : angle 0.46419 (20446) hydrogen bonds : bond 0.03480 ( 722) hydrogen bonds : angle 3.99131 ( 1988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7225.47 seconds wall clock time: 123 minutes 46.54 seconds (7426.54 seconds total)