Starting phenix.real_space_refine on Wed Mar 4 21:20:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jn7_22402/03_2026/7jn7_22402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jn7_22402/03_2026/7jn7_22402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jn7_22402/03_2026/7jn7_22402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jn7_22402/03_2026/7jn7_22402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jn7_22402/03_2026/7jn7_22402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jn7_22402/03_2026/7jn7_22402.map" } resolution = 3.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 B 2 2.79 5 C 10586 2.51 5 N 2784 2.21 5 O 3019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16455 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6816 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 791} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2153 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 252} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1023 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 12, 'TRANS': 114} Chain: "D" Number of atoms: 6433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6433 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 52, 'TRANS': 746} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'GK2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'GK2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.90, per 1000 atoms: 0.24 Number of scatterers: 16455 At special positions: 0 Unit cell: (121.986, 128.536, 131.811, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 O 3019 8.00 N 2784 7.00 C 10586 6.00 B 2 5.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 726.2 milliseconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3826 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 32 sheets defined 19.0% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.879A pdb=" N ARG A 23 " --> pdb=" O PRO A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 42 Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.502A pdb=" N ARG A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 661 through 671 removed outlier: 3.830A pdb=" N ASN A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 700 through 716 Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 763 through 771 removed outlier: 4.243A pdb=" N ARG A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 770 " --> pdb=" O TYR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 784 Processing helix chain 'A' and resid 785 through 793 removed outlier: 4.141A pdb=" N VAL A 790 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU A 791 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 827 removed outlier: 4.221A pdb=" N THR A 816 " --> pdb=" O HIS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 863 Processing helix chain 'B' and resid 317 through 321 removed outlier: 4.205A pdb=" N LEU B 320 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B 321 " --> pdb=" O ASN B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 317 through 321' Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'C' and resid 348 through 359 removed outlier: 3.979A pdb=" N VAL C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 42 Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 294 through 298 removed outlier: 3.533A pdb=" N GLU D 297 " --> pdb=" O ALA D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 583 through 587 removed outlier: 3.677A pdb=" N LYS D 587 " --> pdb=" O PRO D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 671 removed outlier: 3.791A pdb=" N ASN D 665 " --> pdb=" O TYR D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 691 Processing helix chain 'D' and resid 692 through 694 No H-bonds generated for 'chain 'D' and resid 692 through 694' Processing helix chain 'D' and resid 700 through 716 Processing helix chain 'D' and resid 730 through 743 removed outlier: 3.500A pdb=" N SER D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 762 Processing helix chain 'D' and resid 763 through 772 removed outlier: 3.877A pdb=" N ARG D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR D 770 " --> pdb=" O TYR D 766 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP D 772 " --> pdb=" O GLU D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 785 Processing helix chain 'D' and resid 786 through 793 removed outlier: 4.201A pdb=" N VAL D 790 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU D 791 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 827 removed outlier: 4.037A pdb=" N THR D 816 " --> pdb=" O HIS D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 863 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 60 removed outlier: 3.532A pdb=" N HIS A 54 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE A 56 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR A 73 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE A 58 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG A 71 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLN A 60 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N SER A 69 " --> pdb=" O GLN A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 103 removed outlier: 3.563A pdb=" N LEU B 278 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 4.638A pdb=" N LEU A 159 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 193 removed outlier: 6.544A pdb=" N SER A 202 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE A 193 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE A 200 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 239 Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 258 removed outlier: 8.951A pdb=" N LEU A 317 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 338 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 332 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 287 through 291 Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 357 removed outlier: 5.679A pdb=" N ILE A 352 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 369 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 354 " --> pdb=" O MET A 367 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 413 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU A 380 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL A 411 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 445 removed outlier: 3.659A pdb=" N HIS A 453 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU A 454 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA A 488 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS A 456 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU A 486 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A 458 " --> pdb=" O LYS A 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 507 Processing sheet with id=AB2, first strand: chain 'A' and resid 547 through 552 removed outlier: 6.181A pdb=" N VAL A 572 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS A 576 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N PHE A 591 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER A 578 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 609 through 614 removed outlier: 4.103A pdb=" N TYR A 622 " --> pdb=" O ASP A 678 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE A 677 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N HIS A 637 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG A 723 " --> pdb=" O HIS A 637 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 749 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 724 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE A 751 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 726 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLY A 753 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY A 728 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA A 750 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU A 803 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA A 752 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY A 805 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 171 through 174 removed outlier: 6.761A pdb=" N ARG B 179 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AB6, first strand: chain 'B' and resid 211 through 212 removed outlier: 3.936A pdb=" N LEU B 234 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 266 through 267 Processing sheet with id=AB8, first strand: chain 'B' and resid 326 through 334 removed outlier: 3.891A pdb=" N LYS B 345 " --> pdb=" O HIS B 326 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 396 through 398 removed outlier: 6.838A pdb=" N ARG B 422 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B 439 " --> pdb=" O ARG B 422 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY B 424 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 437 " --> pdb=" O GLY B 424 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 426 " --> pdb=" O VAL B 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 322 through 323 removed outlier: 3.593A pdb=" N VAL C 376 " --> pdb=" O TYR C 323 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC3, first strand: chain 'C' and resid 396 through 397 removed outlier: 3.982A pdb=" N ASP C 436 " --> pdb=" O LEU C 426 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP C 428 " --> pdb=" O PRO C 434 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 54 through 60 removed outlier: 5.991A pdb=" N ASP D 55 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU D 75 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS D 70 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR D 88 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS D 106 " --> pdb=" O TYR D 88 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 removed outlier: 4.571A pdb=" N LEU D 159 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 189 through 193 removed outlier: 6.557A pdb=" N SER D 202 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE D 193 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N PHE D 200 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 237 through 239 removed outlier: 3.558A pdb=" N PHE D 322 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 256 through 258 removed outlier: 9.244A pdb=" N LEU D 317 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU D 338 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 323 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER D 332 " --> pdb=" O GLN D 323 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 287 through 291 Processing sheet with id=AD1, first strand: chain 'D' and resid 351 through 355 removed outlier: 5.632A pdb=" N ILE D 352 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU D 369 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG D 354 " --> pdb=" O MET D 367 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 413 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU D 380 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL D 411 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 440 through 445 removed outlier: 3.543A pdb=" N HIS D 453 " --> pdb=" O ASN D 445 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU D 454 " --> pdb=" O ALA D 488 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA D 488 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LYS D 456 " --> pdb=" O GLU D 486 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU D 486 " --> pdb=" O LYS D 456 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR D 458 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 505 through 507 Processing sheet with id=AD4, first strand: chain 'D' and resid 547 through 552 removed outlier: 6.265A pdb=" N VAL D 574 " --> pdb=" O SER D 594 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N SER D 594 " --> pdb=" O VAL D 574 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LYS D 576 " --> pdb=" O TRP D 592 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP D 592 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER D 578 " --> pdb=" O ARG D 590 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG D 590 " --> pdb=" O SER D 578 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 609 through 614 removed outlier: 4.083A pdb=" N TYR D 622 " --> pdb=" O ASP D 678 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE D 677 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N HIS D 637 " --> pdb=" O LEU D 721 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG D 723 " --> pdb=" O HIS D 637 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL D 749 " --> pdb=" O SER D 722 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL D 724 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE D 751 " --> pdb=" O VAL D 724 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 726 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLY D 753 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLY D 728 " --> pdb=" O GLY D 753 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA D 750 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU D 803 " --> pdb=" O ALA D 750 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA D 752 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N GLY D 805 " --> pdb=" O ALA D 752 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2765 1.32 - 1.44: 4784 1.44 - 1.57: 9296 1.57 - 1.69: 4 1.69 - 1.82: 100 Bond restraints: 16949 Sorted by residual: bond pdb=" B15 GK2 D 901 " pdb=" O17 GK2 D 901 " ideal model delta sigma weight residual 1.360 1.536 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" B15 GK2 A 901 " pdb=" O17 GK2 A 901 " ideal model delta sigma weight residual 1.360 1.533 -0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" B15 GK2 A 901 " pdb=" O16 GK2 A 901 " ideal model delta sigma weight residual 1.369 1.535 -0.166 2.00e-02 2.50e+03 6.93e+01 bond pdb=" B15 GK2 D 901 " pdb=" O16 GK2 D 901 " ideal model delta sigma weight residual 1.369 1.533 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" CA SER A 730 " pdb=" C SER A 730 " ideal model delta sigma weight residual 1.528 1.478 0.050 8.80e-03 1.29e+04 3.23e+01 ... (remaining 16944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 22724 4.45 - 8.90: 278 8.90 - 13.35: 29 13.35 - 17.81: 2 17.81 - 22.26: 1 Bond angle restraints: 23034 Sorted by residual: angle pdb=" CA PRO D 429 " pdb=" N PRO D 429 " pdb=" CD PRO D 429 " ideal model delta sigma weight residual 112.00 99.80 12.20 1.40e+00 5.10e-01 7.60e+01 angle pdb=" CA GLU D 486 " pdb=" CB GLU D 486 " pdb=" CG GLU D 486 " ideal model delta sigma weight residual 114.10 126.04 -11.94 2.00e+00 2.50e-01 3.57e+01 angle pdb=" C GLU A 321 " pdb=" CA GLU A 321 " pdb=" CB GLU A 321 " ideal model delta sigma weight residual 110.45 100.79 9.66 1.73e+00 3.34e-01 3.12e+01 angle pdb=" C TYR D 428 " pdb=" N PRO D 429 " pdb=" CD PRO D 429 " ideal model delta sigma weight residual 125.00 102.74 22.26 4.10e+00 5.95e-02 2.95e+01 angle pdb=" C SER A 730 " pdb=" CA SER A 730 " pdb=" CB SER A 730 " ideal model delta sigma weight residual 116.63 110.63 6.00 1.16e+00 7.43e-01 2.68e+01 ... (remaining 23029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 8977 18.01 - 36.02: 884 36.02 - 54.03: 138 54.03 - 72.04: 35 72.04 - 90.05: 12 Dihedral angle restraints: 10046 sinusoidal: 4094 harmonic: 5952 Sorted by residual: dihedral pdb=" CA ALA A 155 " pdb=" C ALA A 155 " pdb=" N SER A 156 " pdb=" CA SER A 156 " ideal model delta harmonic sigma weight residual -180.00 -129.78 -50.22 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA MET D 771 " pdb=" C MET D 771 " pdb=" N ASP D 772 " pdb=" CA ASP D 772 " ideal model delta harmonic sigma weight residual -180.00 -131.82 -48.18 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CA SER C 362 " pdb=" C SER C 362 " pdb=" N PRO C 363 " pdb=" CA PRO C 363 " ideal model delta harmonic sigma weight residual -180.00 -141.28 -38.72 0 5.00e+00 4.00e-02 6.00e+01 ... (remaining 10043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1951 0.084 - 0.169: 405 0.169 - 0.253: 64 0.253 - 0.337: 9 0.337 - 0.422: 3 Chirality restraints: 2432 Sorted by residual: chirality pdb=" CG LEU A 664 " pdb=" CB LEU A 664 " pdb=" CD1 LEU A 664 " pdb=" CD2 LEU A 664 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB VAL D 457 " pdb=" CA VAL D 457 " pdb=" CG1 VAL D 457 " pdb=" CG2 VAL D 457 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CB ILE B 347 " pdb=" CA ILE B 347 " pdb=" CG1 ILE B 347 " pdb=" CG2 ILE B 347 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 2429 not shown) Planarity restraints: 2983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 428 " 0.153 5.00e-02 4.00e+02 2.20e-01 7.74e+01 pdb=" N PRO D 429 " -0.379 5.00e-02 4.00e+02 pdb=" CA PRO D 429 " 0.132 5.00e-02 4.00e+02 pdb=" CD PRO D 429 " 0.095 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 808 " -0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" CG ASP D 808 " 0.077 2.00e-02 2.50e+03 pdb=" OD1 ASP D 808 " -0.027 2.00e-02 2.50e+03 pdb=" OD2 ASP D 808 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 768 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C GLU D 768 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU D 768 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG D 769 " -0.023 2.00e-02 2.50e+03 ... (remaining 2980 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 3 2.05 - 2.76: 2408 2.76 - 3.47: 22536 3.47 - 4.19: 42074 4.19 - 4.90: 71685 Nonbonded interactions: 138706 Sorted by model distance: nonbonded pdb=" OG SER A 730 " pdb=" O16 GK2 A 901 " model vdw 1.335 3.040 nonbonded pdb=" OG SER A 730 " pdb=" B15 GK2 A 901 " model vdw 1.434 2.370 nonbonded pdb=" NE ARG A 131 " pdb=" OE1 GLU A 248 " model vdw 1.960 3.120 nonbonded pdb=" O GLY B 259 " pdb=" OH TYR B 322 " model vdw 2.228 3.040 nonbonded pdb=" O ASN D 406 " pdb=" OG SER D 463 " model vdw 2.268 3.040 ... (remaining 138701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 43 or resid 53 through 76 or resid 86 through 1 \ 09 or resid 139 through 901)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 4.250 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: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.700 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.176 16950 Z= 0.372 Angle : 1.285 22.257 23034 Z= 0.697 Chirality : 0.072 0.422 2432 Planarity : 0.010 0.220 2983 Dihedral : 14.787 90.049 6220 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.51 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.11 % 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: -3.14 (0.16), residues: 2028 helix: -1.55 (0.24), residues: 294 sheet: -2.16 (0.18), residues: 630 loop : -2.18 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A 616 TYR 0.058 0.004 TYR A 351 PHE 0.045 0.004 PHE D 556 TRP 0.039 0.003 TRP D 258 HIS 0.017 0.003 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00821 (16949) covalent geometry : angle 1.28542 (23034) hydrogen bonds : bond 0.15699 ( 523) hydrogen bonds : angle 8.03501 ( 1407) Misc. bond : bond 0.01332 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.614 Fit side-chains REVERT: A 125 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7502 (mp0) REVERT: A 179 GLU cc_start: 0.7309 (tp30) cc_final: 0.6926 (tp30) REVERT: A 575 TYR cc_start: 0.8384 (m-80) cc_final: 0.7782 (m-80) REVERT: A 745 GLN cc_start: 0.7986 (pm20) cc_final: 0.7414 (tp40) REVERT: B 264 SER cc_start: 0.8429 (p) cc_final: 0.8152 (p) REVERT: B 317 SER cc_start: 0.7873 (m) cc_final: 0.7580 (p) REVERT: B 344 THR cc_start: 0.6293 (t) cc_final: 0.5991 (t) REVERT: C 343 LEU cc_start: 0.3916 (mm) cc_final: 0.3714 (mm) REVERT: C 365 MET cc_start: 0.4285 (mmm) cc_final: 0.3925 (mmm) REVERT: D 24 PHE cc_start: 0.6340 (t80) cc_final: 0.5917 (t80) REVERT: D 31 TRP cc_start: 0.5525 (t-100) cc_final: 0.5064 (t-100) REVERT: D 319 LEU cc_start: 0.8140 (mm) cc_final: 0.7804 (mm) REVERT: D 595 MET cc_start: 0.5250 (tpt) cc_final: 0.4624 (tpt) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1356 time to fit residues: 73.3677 Evaluate side-chains 297 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 60 GLN A 68 HIS ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 HIS ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.196806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149937 restraints weight = 21370.833| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.11 r_work: 0.3587 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16950 Z= 0.173 Angle : 0.687 8.674 23034 Z= 0.357 Chirality : 0.047 0.185 2432 Planarity : 0.006 0.068 2983 Dihedral : 6.446 52.779 2259 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.18 % Allowed : 9.41 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.17), residues: 2028 helix: 0.06 (0.29), residues: 305 sheet: -1.47 (0.19), residues: 620 loop : -1.83 (0.16), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 688 TYR 0.027 0.002 TYR D 731 PHE 0.016 0.002 PHE D 386 TRP 0.013 0.001 TRP D 375 HIS 0.010 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00402 (16949) covalent geometry : angle 0.68692 (23034) hydrogen bonds : bond 0.04014 ( 523) hydrogen bonds : angle 6.46556 ( 1407) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 342 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.7409 (t70) cc_final: 0.7140 (t70) REVERT: A 179 GLU cc_start: 0.7605 (tp30) cc_final: 0.7339 (tp30) REVERT: A 298 ARG cc_start: 0.7601 (mtm180) cc_final: 0.7232 (ttp-110) REVERT: A 325 ASP cc_start: 0.8164 (p0) cc_final: 0.7637 (p0) REVERT: A 575 TYR cc_start: 0.8622 (m-80) cc_final: 0.8165 (m-80) REVERT: A 745 GLN cc_start: 0.8298 (pm20) cc_final: 0.7495 (tp40) REVERT: A 834 ILE cc_start: 0.8868 (mm) cc_final: 0.8667 (mm) REVERT: B 264 SER cc_start: 0.8459 (p) cc_final: 0.8198 (p) REVERT: B 310 ARG cc_start: 0.7487 (mmm160) cc_final: 0.7231 (mmm160) REVERT: D 24 PHE cc_start: 0.6516 (t80) cc_final: 0.6301 (t80) REVERT: D 31 TRP cc_start: 0.5593 (t-100) cc_final: 0.4746 (t-100) REVERT: D 210 TRP cc_start: 0.7959 (m100) cc_final: 0.7757 (m-10) REVERT: D 319 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8050 (mm) REVERT: D 595 MET cc_start: 0.5116 (tpt) cc_final: 0.4720 (tpt) REVERT: D 650 GLN cc_start: 0.7891 (tt0) cc_final: 0.7602 (tt0) REVERT: D 839 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.7160 (mmt-90) outliers start: 21 outliers final: 11 residues processed: 354 average time/residue: 0.1390 time to fit residues: 74.2246 Evaluate side-chains 307 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 295 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 20 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN D 377 GLN D 629 HIS D 777 ASN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.193264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144957 restraints weight = 21675.219| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.87 r_work: 0.3532 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 16950 Z= 0.226 Angle : 0.682 7.656 23034 Z= 0.351 Chirality : 0.047 0.205 2432 Planarity : 0.005 0.059 2983 Dihedral : 6.137 44.698 2259 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.30 % Allowed : 13.11 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.17), residues: 2028 helix: 0.20 (0.29), residues: 294 sheet: -1.26 (0.20), residues: 623 loop : -1.66 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 825 TYR 0.023 0.002 TYR B 335 PHE 0.017 0.002 PHE D 556 TRP 0.016 0.001 TRP D 258 HIS 0.014 0.002 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00527 (16949) covalent geometry : angle 0.68183 (23034) hydrogen bonds : bond 0.03844 ( 523) hydrogen bonds : angle 6.18099 ( 1407) Misc. bond : bond 0.00148 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 316 time to evaluate : 0.618 Fit side-chains REVERT: A 297 GLU cc_start: 0.8239 (tp30) cc_final: 0.7859 (mt-10) REVERT: A 298 ARG cc_start: 0.7974 (mtm180) cc_final: 0.7399 (ttp-110) REVERT: A 325 ASP cc_start: 0.8282 (p0) cc_final: 0.7860 (p0) REVERT: A 336 LYS cc_start: 0.8258 (mttm) cc_final: 0.7608 (mttm) REVERT: A 479 PHE cc_start: 0.7907 (m-80) cc_final: 0.7457 (m-80) REVERT: A 575 TYR cc_start: 0.8818 (m-80) cc_final: 0.8434 (m-80) REVERT: A 667 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 696 GLN cc_start: 0.8069 (pm20) cc_final: 0.7794 (pm20) REVERT: D 31 TRP cc_start: 0.5804 (t-100) cc_final: 0.4667 (t-100) REVERT: D 319 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8092 (mm) REVERT: D 595 MET cc_start: 0.5064 (tpt) cc_final: 0.4737 (tpt) REVERT: D 650 GLN cc_start: 0.7937 (tt0) cc_final: 0.7650 (tt0) REVERT: D 839 ARG cc_start: 0.7958 (mtt-85) cc_final: 0.7679 (mtt-85) outliers start: 41 outliers final: 30 residues processed: 335 average time/residue: 0.1400 time to fit residues: 70.7923 Evaluate side-chains 320 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 288 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 82 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 247 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN B 378 ASN ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 373 GLN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.195470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.148446 restraints weight = 21393.794| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.95 r_work: 0.3586 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.004 0.060 16950 Z= 0.157 Angle : 0.629 8.001 23034 Z= 0.321 Chirality : 0.045 0.180 2432 Planarity : 0.005 0.050 2983 Dihedral : 5.825 44.769 2259 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.69 % Allowed : 14.90 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.18), residues: 2028 helix: 0.51 (0.29), residues: 295 sheet: -1.01 (0.20), residues: 634 loop : -1.54 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 688 TYR 0.021 0.002 TYR B 335 PHE 0.013 0.001 PHE D 556 TRP 0.021 0.002 TRP D 258 HIS 0.012 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00369 (16949) covalent geometry : angle 0.62905 (23034) hydrogen bonds : bond 0.03415 ( 523) hydrogen bonds : angle 5.89838 ( 1407) Misc. bond : bond 0.00128 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7648 (tp30) cc_final: 0.7285 (tp30) REVERT: A 297 GLU cc_start: 0.8046 (tp30) cc_final: 0.7691 (mt-10) REVERT: A 325 ASP cc_start: 0.8150 (p0) cc_final: 0.7702 (p0) REVERT: A 575 TYR cc_start: 0.8684 (m-80) cc_final: 0.8300 (m-80) REVERT: A 664 LEU cc_start: 0.8251 (mt) cc_final: 0.8036 (mt) REVERT: A 667 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8156 (mp) REVERT: A 678 ASP cc_start: 0.7898 (m-30) cc_final: 0.7466 (m-30) REVERT: B 248 ILE cc_start: 0.8218 (mp) cc_final: 0.7997 (mm) REVERT: B 310 ARG cc_start: 0.7603 (mmm160) cc_final: 0.7308 (mmm160) REVERT: D 31 TRP cc_start: 0.5841 (t-100) cc_final: 0.4741 (t-100) REVERT: D 314 LYS cc_start: 0.6989 (mptt) cc_final: 0.6625 (pttp) REVERT: D 319 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7989 (mm) REVERT: D 497 LEU cc_start: 0.8003 (mp) cc_final: 0.7708 (mp) REVERT: D 587 LYS cc_start: 0.6560 (mtpt) cc_final: 0.6220 (mmtp) REVERT: D 595 MET cc_start: 0.5277 (tpt) cc_final: 0.4969 (tpt) REVERT: D 650 GLN cc_start: 0.7854 (tt0) cc_final: 0.7564 (tt0) REVERT: D 737 LEU cc_start: 0.8209 (mp) cc_final: 0.7855 (mp) REVERT: D 839 ARG cc_start: 0.7861 (mtt-85) cc_final: 0.7446 (mtt-85) outliers start: 48 outliers final: 27 residues processed: 346 average time/residue: 0.1410 time to fit residues: 73.4240 Evaluate side-chains 317 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 288 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 373 GLN Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 1 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 60 GLN A 247 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 HIS B 369 ASN ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN D 377 GLN D 555 ASN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.193907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146193 restraints weight = 21465.407| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.97 r_work: 0.3533 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16950 Z= 0.184 Angle : 0.636 8.010 23034 Z= 0.325 Chirality : 0.046 0.183 2432 Planarity : 0.005 0.048 2983 Dihedral : 5.782 45.817 2259 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.03 % Allowed : 15.85 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.18), residues: 2028 helix: 0.53 (0.29), residues: 301 sheet: -0.94 (0.21), residues: 625 loop : -1.52 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 825 TYR 0.029 0.002 TYR B 323 PHE 0.017 0.002 PHE A 747 TRP 0.026 0.002 TRP D 258 HIS 0.013 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00433 (16949) covalent geometry : angle 0.63624 (23034) hydrogen bonds : bond 0.03404 ( 523) hydrogen bonds : angle 5.86929 ( 1407) Misc. bond : bond 0.00129 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 312 time to evaluate : 0.550 Fit side-chains REVERT: A 325 ASP cc_start: 0.8233 (p0) cc_final: 0.7887 (p0) REVERT: A 336 LYS cc_start: 0.8016 (mttm) cc_final: 0.7702 (mttm) REVERT: A 462 LYS cc_start: 0.8084 (pptt) cc_final: 0.7525 (pttp) REVERT: A 479 PHE cc_start: 0.7807 (m-80) cc_final: 0.7469 (m-80) REVERT: A 575 TYR cc_start: 0.8653 (m-80) cc_final: 0.8330 (m-80) REVERT: A 667 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 678 ASP cc_start: 0.7872 (m-30) cc_final: 0.7536 (m-30) REVERT: B 248 ILE cc_start: 0.8233 (mp) cc_final: 0.8000 (mm) REVERT: C 411 LYS cc_start: 0.2201 (mmmt) cc_final: 0.1103 (mmtt) REVERT: D 31 TRP cc_start: 0.5936 (t-100) cc_final: 0.4728 (t-100) REVERT: D 171 MET cc_start: 0.0734 (ppp) cc_final: 0.0237 (ppp) REVERT: D 314 LYS cc_start: 0.7038 (mptt) cc_final: 0.6675 (pttp) REVERT: D 319 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7965 (mm) REVERT: D 336 LYS cc_start: 0.7848 (mttm) cc_final: 0.7583 (mmtm) REVERT: D 587 LYS cc_start: 0.6594 (mtpt) cc_final: 0.6220 (mmtp) REVERT: D 595 MET cc_start: 0.5430 (tpt) cc_final: 0.5113 (tpt) REVERT: D 650 GLN cc_start: 0.7951 (tt0) cc_final: 0.7682 (tt0) REVERT: D 702 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7602 (mm) REVERT: D 839 ARG cc_start: 0.7914 (mtt-85) cc_final: 0.7459 (mtt-85) outliers start: 54 outliers final: 42 residues processed: 343 average time/residue: 0.1334 time to fit residues: 69.1380 Evaluate side-chains 332 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 625 ILE Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 854 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 9 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 133 optimal weight: 0.2980 chunk 45 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 200 optimal weight: 0.5980 chunk 109 optimal weight: 0.0870 chunk 164 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 418 ASN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.194176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146836 restraints weight = 21409.215| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.24 r_work: 0.3565 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16950 Z= 0.164 Angle : 0.621 8.152 23034 Z= 0.317 Chirality : 0.045 0.172 2432 Planarity : 0.005 0.047 2983 Dihedral : 5.728 45.592 2259 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.25 % Allowed : 16.75 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.18), residues: 2028 helix: 0.67 (0.30), residues: 301 sheet: -0.88 (0.21), residues: 627 loop : -1.46 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 825 TYR 0.029 0.002 TYR B 323 PHE 0.020 0.001 PHE D 711 TRP 0.027 0.001 TRP D 258 HIS 0.011 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00387 (16949) covalent geometry : angle 0.62129 (23034) hydrogen bonds : bond 0.03269 ( 523) hydrogen bonds : angle 5.78247 ( 1407) Misc. bond : bond 0.00122 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 310 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7690 (tp30) cc_final: 0.7131 (tp30) REVERT: A 325 ASP cc_start: 0.8227 (p0) cc_final: 0.7893 (p0) REVERT: A 336 LYS cc_start: 0.7969 (mttm) cc_final: 0.7615 (mttm) REVERT: A 462 LYS cc_start: 0.8001 (pptt) cc_final: 0.7431 (pttp) REVERT: A 575 TYR cc_start: 0.8672 (m-80) cc_final: 0.8316 (m-80) REVERT: A 667 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8131 (mp) REVERT: A 678 ASP cc_start: 0.7916 (m-30) cc_final: 0.7542 (m-30) REVERT: B 248 ILE cc_start: 0.8279 (mp) cc_final: 0.8075 (mm) REVERT: C 411 LYS cc_start: 0.2112 (mmmt) cc_final: 0.1023 (mmtt) REVERT: D 31 TRP cc_start: 0.5903 (t-100) cc_final: 0.4609 (t-100) REVERT: D 171 MET cc_start: 0.0644 (ppp) cc_final: 0.0127 (ppp) REVERT: D 314 LYS cc_start: 0.6937 (mptt) cc_final: 0.6552 (pttp) REVERT: D 336 LYS cc_start: 0.7745 (mttm) cc_final: 0.7484 (mmtm) REVERT: D 587 LYS cc_start: 0.6660 (mtpt) cc_final: 0.6254 (mmtp) REVERT: D 595 MET cc_start: 0.5392 (tpt) cc_final: 0.5035 (tpt) REVERT: D 650 GLN cc_start: 0.7912 (tt0) cc_final: 0.7646 (tt0) REVERT: D 702 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7589 (mm) REVERT: D 839 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7366 (mtt-85) outliers start: 58 outliers final: 44 residues processed: 343 average time/residue: 0.1311 time to fit residues: 68.4060 Evaluate side-chains 342 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 296 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 625 ILE Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 179 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 85 optimal weight: 0.0670 chunk 7 optimal weight: 0.8980 chunk 163 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.194208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.147603 restraints weight = 21375.776| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.86 r_work: 0.3547 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16950 Z= 0.152 Angle : 0.616 8.434 23034 Z= 0.313 Chirality : 0.045 0.251 2432 Planarity : 0.005 0.046 2983 Dihedral : 5.643 45.594 2259 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.31 % Allowed : 17.54 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.18), residues: 2028 helix: 0.79 (0.30), residues: 301 sheet: -0.86 (0.22), residues: 605 loop : -1.46 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 96 TYR 0.037 0.002 TYR B 323 PHE 0.015 0.001 PHE D 711 TRP 0.021 0.001 TRP D 258 HIS 0.012 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00358 (16949) covalent geometry : angle 0.61601 (23034) hydrogen bonds : bond 0.03218 ( 523) hydrogen bonds : angle 5.71237 ( 1407) Misc. bond : bond 0.00125 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 306 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7886 (tp30) cc_final: 0.7343 (tp30) REVERT: A 325 ASP cc_start: 0.8410 (p0) cc_final: 0.7893 (p0) REVERT: A 336 LYS cc_start: 0.8166 (mttm) cc_final: 0.7749 (mttt) REVERT: A 462 LYS cc_start: 0.8000 (pptt) cc_final: 0.7424 (pttp) REVERT: A 479 PHE cc_start: 0.7806 (m-80) cc_final: 0.7415 (m-80) REVERT: A 575 TYR cc_start: 0.8774 (m-80) cc_final: 0.8458 (m-80) REVERT: A 667 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8161 (mp) REVERT: A 678 ASP cc_start: 0.8030 (m-30) cc_final: 0.7679 (m-30) REVERT: B 248 ILE cc_start: 0.8257 (mp) cc_final: 0.8048 (mm) REVERT: C 411 LYS cc_start: 0.2151 (mmmt) cc_final: 0.1106 (mmtt) REVERT: D 31 TRP cc_start: 0.6020 (t-100) cc_final: 0.4645 (t-100) REVERT: D 171 MET cc_start: 0.0672 (ppp) cc_final: 0.0153 (ppp) REVERT: D 314 LYS cc_start: 0.6996 (mptt) cc_final: 0.6597 (pttp) REVERT: D 335 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6957 (mm-30) REVERT: D 336 LYS cc_start: 0.7810 (mttm) cc_final: 0.7447 (mmtp) REVERT: D 497 LEU cc_start: 0.8136 (mp) cc_final: 0.7923 (mp) REVERT: D 587 LYS cc_start: 0.6718 (mtpt) cc_final: 0.6232 (mmtp) REVERT: D 595 MET cc_start: 0.5319 (tpt) cc_final: 0.4943 (tpt) REVERT: D 650 GLN cc_start: 0.7958 (tt0) cc_final: 0.7693 (tt0) REVERT: D 702 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7616 (mm) REVERT: D 839 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7391 (mtt-85) outliers start: 59 outliers final: 49 residues processed: 340 average time/residue: 0.1374 time to fit residues: 71.1097 Evaluate side-chains 339 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 625 ILE Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 15 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 191 optimal weight: 0.0050 chunk 144 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 2 optimal weight: 0.0170 chunk 168 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.4232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 516 GLN A 654 ASN B 224 HIS ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 ASN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 860 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.192973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147722 restraints weight = 21340.150| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.48 r_work: 0.3599 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16950 Z= 0.130 Angle : 0.613 8.361 23034 Z= 0.311 Chirality : 0.045 0.204 2432 Planarity : 0.005 0.045 2983 Dihedral : 5.526 45.077 2259 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.69 % Allowed : 18.43 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z 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: -1.31 (0.19), residues: 2028 helix: 0.96 (0.30), residues: 305 sheet: -0.79 (0.22), residues: 608 loop : -1.45 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 96 TYR 0.034 0.002 TYR B 323 PHE 0.014 0.001 PHE D 711 TRP 0.020 0.001 TRP D 258 HIS 0.011 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00312 (16949) covalent geometry : angle 0.61312 (23034) hydrogen bonds : bond 0.03157 ( 523) hydrogen bonds : angle 5.57636 ( 1407) Misc. bond : bond 0.00123 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 312 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7829 (tp30) cc_final: 0.7105 (tp30) REVERT: A 325 ASP cc_start: 0.8391 (p0) cc_final: 0.7875 (p0) REVERT: A 336 LYS cc_start: 0.8102 (mttm) cc_final: 0.7689 (mttt) REVERT: A 462 LYS cc_start: 0.7981 (pptt) cc_final: 0.7405 (pttp) REVERT: A 575 TYR cc_start: 0.8760 (m-80) cc_final: 0.8436 (m-80) REVERT: A 678 ASP cc_start: 0.7978 (m-30) cc_final: 0.7564 (m-30) REVERT: B 248 ILE cc_start: 0.8225 (mp) cc_final: 0.8018 (mm) REVERT: C 411 LYS cc_start: 0.2048 (mmmt) cc_final: 0.0853 (mmtt) REVERT: D 24 PHE cc_start: 0.6639 (t80) cc_final: 0.6293 (t80) REVERT: D 31 TRP cc_start: 0.6001 (t-100) cc_final: 0.4672 (t-100) REVERT: D 171 MET cc_start: 0.0545 (ppp) cc_final: -0.0024 (ppp) REVERT: D 314 LYS cc_start: 0.6960 (mptt) cc_final: 0.6568 (pttp) REVERT: D 335 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6897 (mm-30) REVERT: D 336 LYS cc_start: 0.7755 (mttm) cc_final: 0.7386 (mmtp) REVERT: D 587 LYS cc_start: 0.6717 (mtpt) cc_final: 0.6236 (mmtp) REVERT: D 595 MET cc_start: 0.5557 (tpt) cc_final: 0.5340 (tpt) REVERT: D 702 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7680 (mm) outliers start: 48 outliers final: 32 residues processed: 343 average time/residue: 0.1352 time to fit residues: 70.0391 Evaluate side-chains 326 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 43 optimal weight: 0.0060 chunk 193 optimal weight: 0.1980 chunk 161 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 84 optimal weight: 0.0570 chunk 106 optimal weight: 4.9990 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 395 GLN A 516 GLN B 227 GLN B 401 HIS C 369 ASN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.193459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.148563 restraints weight = 21321.577| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.66 r_work: 0.3550 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16950 Z= 0.130 Angle : 0.626 10.126 23034 Z= 0.313 Chirality : 0.045 0.212 2432 Planarity : 0.005 0.046 2983 Dihedral : 5.461 45.424 2259 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.24 % Allowed : 18.82 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.19), residues: 2028 helix: 1.15 (0.30), residues: 299 sheet: -0.75 (0.22), residues: 610 loop : -1.39 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 839 TYR 0.041 0.002 TYR B 323 PHE 0.016 0.001 PHE D 711 TRP 0.022 0.001 TRP D 258 HIS 0.011 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00312 (16949) covalent geometry : angle 0.62576 (23034) hydrogen bonds : bond 0.03112 ( 523) hydrogen bonds : angle 5.51336 ( 1407) Misc. bond : bond 0.00119 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 305 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7824 (tp30) cc_final: 0.7099 (tp30) REVERT: A 325 ASP cc_start: 0.8405 (p0) cc_final: 0.7904 (p0) REVERT: A 336 LYS cc_start: 0.8151 (mttm) cc_final: 0.7750 (mttt) REVERT: A 462 LYS cc_start: 0.7954 (pptt) cc_final: 0.7310 (pttp) REVERT: A 575 TYR cc_start: 0.8809 (m-80) cc_final: 0.8490 (m-80) REVERT: A 678 ASP cc_start: 0.8007 (m-30) cc_final: 0.7588 (m-30) REVERT: B 227 GLN cc_start: 0.7101 (mm110) cc_final: 0.6748 (mm-40) REVERT: B 248 ILE cc_start: 0.8230 (mp) cc_final: 0.8024 (mm) REVERT: B 309 THR cc_start: 0.7643 (p) cc_final: 0.7211 (p) REVERT: C 411 LYS cc_start: 0.1700 (mmmt) cc_final: 0.0843 (mmtt) REVERT: D 24 PHE cc_start: 0.6654 (t80) cc_final: 0.6346 (t80) REVERT: D 171 MET cc_start: 0.0367 (ppp) cc_final: -0.0174 (ppp) REVERT: D 297 GLU cc_start: 0.8041 (mp0) cc_final: 0.7822 (mp0) REVERT: D 314 LYS cc_start: 0.7039 (mptt) cc_final: 0.6659 (pttp) REVERT: D 319 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8045 (mt) REVERT: D 335 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6885 (mm-30) REVERT: D 336 LYS cc_start: 0.7748 (mttm) cc_final: 0.7428 (mmtp) REVERT: D 587 LYS cc_start: 0.6711 (mtpt) cc_final: 0.6202 (mmtp) REVERT: D 595 MET cc_start: 0.5683 (tpt) cc_final: 0.5462 (tpt) REVERT: D 650 GLN cc_start: 0.7860 (tt0) cc_final: 0.7524 (tt0) REVERT: D 702 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7697 (mm) outliers start: 40 outliers final: 34 residues processed: 332 average time/residue: 0.1374 time to fit residues: 68.9614 Evaluate side-chains 331 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 295 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 155 optimal weight: 0.0370 chunk 2 optimal weight: 0.0570 chunk 185 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 192 optimal weight: 0.0970 chunk 167 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 516 GLN B 401 HIS ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.198026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.151921 restraints weight = 21464.226| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.89 r_work: 0.3555 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16950 Z= 0.122 Angle : 0.632 9.923 23034 Z= 0.317 Chirality : 0.045 0.204 2432 Planarity : 0.005 0.045 2983 Dihedral : 5.395 45.380 2259 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.35 % Allowed : 19.10 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.19), residues: 2028 helix: 1.17 (0.30), residues: 299 sheet: -0.73 (0.22), residues: 606 loop : -1.38 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 825 TYR 0.047 0.002 TYR B 323 PHE 0.014 0.001 PHE D 711 TRP 0.021 0.001 TRP D 258 HIS 0.012 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00292 (16949) covalent geometry : angle 0.63212 (23034) hydrogen bonds : bond 0.03082 ( 523) hydrogen bonds : angle 5.43769 ( 1407) Misc. bond : bond 0.00118 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7710 (tp30) cc_final: 0.7005 (tp30) REVERT: A 325 ASP cc_start: 0.8250 (p0) cc_final: 0.7775 (p0) REVERT: A 336 LYS cc_start: 0.7955 (mttm) cc_final: 0.7638 (mttm) REVERT: A 462 LYS cc_start: 0.7897 (pptt) cc_final: 0.7566 (pttt) REVERT: A 552 MET cc_start: 0.8065 (mmm) cc_final: 0.7826 (mmm) REVERT: A 575 TYR cc_start: 0.8673 (m-80) cc_final: 0.8352 (m-80) REVERT: A 678 ASP cc_start: 0.7924 (m-30) cc_final: 0.7496 (m-30) REVERT: A 843 ARG cc_start: 0.7564 (mtt-85) cc_final: 0.6715 (ttm-80) REVERT: B 248 ILE cc_start: 0.8192 (mp) cc_final: 0.7969 (mm) REVERT: B 309 THR cc_start: 0.7522 (p) cc_final: 0.7181 (p) REVERT: C 411 LYS cc_start: 0.1637 (mmmt) cc_final: 0.0916 (mmtt) REVERT: D 24 PHE cc_start: 0.6654 (t80) cc_final: 0.6372 (t80) REVERT: D 171 MET cc_start: 0.0395 (ppp) cc_final: -0.0185 (ppp) REVERT: D 297 GLU cc_start: 0.7898 (mp0) cc_final: 0.7657 (mp0) REVERT: D 314 LYS cc_start: 0.6976 (mptt) cc_final: 0.6676 (pttp) REVERT: D 319 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7782 (mt) REVERT: D 335 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6688 (mm-30) REVERT: D 336 LYS cc_start: 0.7669 (mttm) cc_final: 0.7359 (mmtp) REVERT: D 587 LYS cc_start: 0.6676 (mtpt) cc_final: 0.6192 (mmtp) REVERT: D 595 MET cc_start: 0.5827 (tpt) cc_final: 0.5608 (tpt) REVERT: D 650 GLN cc_start: 0.7784 (tt0) cc_final: 0.7424 (tt0) outliers start: 42 outliers final: 33 residues processed: 335 average time/residue: 0.1382 time to fit residues: 69.8021 Evaluate side-chains 330 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 296 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 189 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 197 optimal weight: 0.0470 chunk 9 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 GLN B 227 GLN B 401 HIS ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.193040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147916 restraints weight = 21252.978| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.64 r_work: 0.3602 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16950 Z= 0.144 Angle : 0.642 9.694 23034 Z= 0.322 Chirality : 0.045 0.200 2432 Planarity : 0.005 0.045 2983 Dihedral : 5.419 45.885 2259 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.46 % Allowed : 19.33 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.19), residues: 2028 helix: 1.00 (0.30), residues: 307 sheet: -0.75 (0.22), residues: 604 loop : -1.39 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 825 TYR 0.042 0.002 TYR B 323 PHE 0.017 0.001 PHE D 813 TRP 0.018 0.001 TRP D 258 HIS 0.011 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00347 (16949) covalent geometry : angle 0.64228 (23034) hydrogen bonds : bond 0.03124 ( 523) hydrogen bonds : angle 5.44395 ( 1407) Misc. bond : bond 0.00112 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4914.16 seconds wall clock time: 85 minutes 1.12 seconds (5101.12 seconds total)