Starting phenix.real_space_refine on Wed Mar 4 19:34:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x6c_22075/03_2026/6x6c_22075.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x6c_22075/03_2026/6x6c_22075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x6c_22075/03_2026/6x6c_22075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x6c_22075/03_2026/6x6c_22075.map" model { file = "/net/cci-nas-00/data/ceres_data/6x6c_22075/03_2026/6x6c_22075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x6c_22075/03_2026/6x6c_22075.cif" } resolution = 2.9 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= 0.002 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 71 5.16 5 B 2 2.79 5 C 10190 2.51 5 N 2694 2.21 5 O 2878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15835 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: "D" 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: "E" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1068 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 10, 'TRANS': 123} Chain: "F" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1105 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 127} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 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: 3.95, per 1000 atoms: 0.25 Number of scatterers: 15835 At special positions: 0 Unit cell: (127.05, 143.55, 97.35, 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 71 16.00 O 2878 8.00 N 2694 7.00 C 10190 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 795.1 milliseconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 31 sheets defined 20.8% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.964A pdb=" N ARG A 23 " --> pdb=" O PRO A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 42 removed outlier: 3.572A pdb=" N ARG A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 removed outlier: 3.671A pdb=" N ILE A 48 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 294 through 298 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 661 through 671 removed outlier: 3.701A 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 removed outlier: 3.579A pdb=" N PHE A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 762 Processing helix chain 'A' and resid 763 through 772 removed outlier: 4.069A pdb=" N ARG A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 784 Processing helix chain 'A' and resid 785 through 793 removed outlier: 3.679A pdb=" N VAL A 790 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU A 791 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 827 removed outlier: 4.289A 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 'D' and resid 30 through 42 removed outlier: 3.664A pdb=" N ARG D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.520A pdb=" N GLY D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 removed outlier: 3.674A pdb=" N GLU D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 294 through 298 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: 3.532A pdb=" N HIS D 586 " --> pdb=" O ASP D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 671 removed outlier: 3.716A 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 Processing helix chain 'D' and resid 758 through 762 Processing helix chain 'D' and resid 763 through 771 removed outlier: 4.100A pdb=" N ARG D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR D 770 " --> pdb=" O TYR D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 784 Processing helix chain 'D' and resid 785 through 793 removed outlier: 4.103A pdb=" N VAL D 790 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLU D 791 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 827 Processing helix chain 'D' and resid 844 through 863 Processing helix chain 'E' and resid 1131 through 1139 removed outlier: 4.512A pdb=" N PHE E1135 " --> pdb=" O VAL E1131 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E1138 " --> pdb=" O GLN E1134 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE E1139 " --> pdb=" O PHE E1135 " (cutoff:3.500A) Processing helix chain 'F' and resid 1256 through 1270 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 60 removed outlier: 3.723A pdb=" N HIS A 54 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A 56 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR A 73 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE A 58 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG A 71 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLN A 60 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N SER A 69 " --> pdb=" O GLN A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 4.529A 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: 6.528A pdb=" N SER A 202 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE A 193 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.629A 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: 3.503A pdb=" N PHE A 322 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N LEU A 317 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A 338 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 323 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 4.079A 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: 5.755A pdb=" N ILE A 352 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU A 369 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 354 " --> pdb=" O MET A 367 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 413 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU A 380 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL A 411 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 440 through 445 removed outlier: 3.504A pdb=" N HIS A 453 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 7.328A 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: 5.878A pdb=" N LYS A 456 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU A 486 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 6.581A 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: 6.360A pdb=" N VAL A 572 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS A 576 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE A 591 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 6.813A 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: 4.425A pdb=" N ILE A 677 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N HIS A 637 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG A 723 " --> pdb=" O HIS A 637 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 749 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL A 724 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE A 751 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 726 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLY A 753 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLY A 728 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA A 750 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU A 803 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA A 752 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLY A 805 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 60 removed outlier: 4.335A pdb=" N PHE D 56 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR D 73 " --> pdb=" O PHE D 56 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE D 58 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG D 71 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLN D 60 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N SER D 69 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS D 106 " --> pdb=" O TYR D 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 142 through 145 removed outlier: 4.531A pdb=" N LEU D 159 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 189 through 193 removed outlier: 6.604A pdb=" N SER D 202 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE D 193 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE D 200 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 237 through 239 removed outlier: 3.527A pdb=" N VAL D 280 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE D 322 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER D 263 " --> pdb=" O THR D 272 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 256 through 258 removed outlier: 8.958A pdb=" N LEU D 317 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU D 338 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN D 323 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER D 332 " --> pdb=" O GLN D 323 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 287 through 291 Processing sheet with id=AC1, first strand: chain 'D' and resid 351 through 355 removed outlier: 5.809A pdb=" N ILE D 352 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU D 369 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG D 354 " --> pdb=" O MET D 367 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR D 413 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU D 380 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL D 411 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 427 through 429 removed outlier: 7.368A pdb=" N LEU D 454 " --> pdb=" O ALA D 488 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ALA D 488 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS D 456 " --> pdb=" O GLU D 486 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU D 486 " --> pdb=" O LYS D 456 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR D 458 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 505 through 507 Processing sheet with id=AC4, first strand: chain 'D' and resid 547 through 552 removed outlier: 6.700A pdb=" N VAL D 572 " --> pdb=" O MET D 595 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS D 576 " --> pdb=" O PHE D 591 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE D 591 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER D 578 " --> pdb=" O PRO D 589 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 609 through 614 removed outlier: 4.358A pdb=" N ILE D 677 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N HIS D 637 " --> pdb=" O LEU D 721 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG D 723 " --> pdb=" O HIS D 637 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP D 729 " --> pdb=" O VAL D 643 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL D 749 " --> pdb=" O SER D 722 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL D 724 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE D 751 " --> pdb=" O VAL D 724 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE D 726 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLY D 753 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY D 728 " --> pdb=" O GLY D 753 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA D 750 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU D 803 " --> pdb=" O ALA D 750 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA D 752 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLY D 805 " --> pdb=" O ALA D 752 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 1080 through 1081 removed outlier: 3.562A pdb=" N GLY E1081 " --> pdb=" O GLY E1084 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 1089 through 1092 removed outlier: 3.636A pdb=" N GLU E1089 " --> pdb=" O ARG E1099 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG E1099 " --> pdb=" O GLU E1089 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL E1091 " --> pdb=" O LEU E1097 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU E1097 " --> pdb=" O VAL E1091 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE E1102 " --> pdb=" O VAL E1123 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL E1123 " --> pdb=" O PHE E1102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 1116 through 1118 removed outlier: 3.544A pdb=" N ARG E1199 " --> pdb=" O VAL E1206 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 1145 through 1147 Processing sheet with id=AD1, first strand: chain 'F' and resid 1230 through 1231 removed outlier: 3.710A pdb=" N LEU F1284 " --> pdb=" O VAL F1231 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 1234 through 1236 removed outlier: 3.975A pdb=" N ILE F1253 " --> pdb=" O VAL F1234 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL F1246 " --> pdb=" O VAL F1325 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 1238 through 1239 removed outlier: 3.558A pdb=" N VAL F1273 " --> pdb=" O HIS F1239 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 1306 through 1308 removed outlier: 3.654A pdb=" N LEU F1334 " --> pdb=" O ALA F1348 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA F1348 " --> pdb=" O LEU F1334 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL F1336 " --> pdb=" O TRP F1346 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP F1346 " --> pdb=" O VAL F1336 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP F1338 " --> pdb=" O LEU F1344 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU F1344 " --> pdb=" O ASP F1338 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1386 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: 3.46 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2574 1.31 - 1.43: 4653 1.43 - 1.56: 8967 1.56 - 1.69: 9 1.69 - 1.81: 109 Bond restraints: 16312 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 7.76e+01 bond pdb=" B15 GK2 A 901 " pdb=" O17 GK2 A 901 " ideal model delta sigma weight residual 1.360 1.534 -0.174 2.00e-02 2.50e+03 7.53e+01 bond pdb=" B15 GK2 A 901 " pdb=" O16 GK2 A 901 " ideal model delta sigma weight residual 1.369 1.534 -0.165 2.00e-02 2.50e+03 6.85e+01 bond pdb=" B15 GK2 D 901 " pdb=" O16 GK2 D 901 " ideal model delta sigma weight residual 1.369 1.534 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" CA ARG D 839 " pdb=" C ARG D 839 " ideal model delta sigma weight residual 1.533 1.500 0.033 5.60e-03 3.19e+04 3.43e+01 ... (remaining 16307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 21138 3.04 - 6.08: 883 6.08 - 9.13: 119 9.13 - 12.17: 7 12.17 - 15.21: 5 Bond angle restraints: 22152 Sorted by residual: angle pdb=" N SER D 146 " pdb=" CA SER D 146 " pdb=" C SER D 146 " ideal model delta sigma weight residual 111.28 122.28 -11.00 1.09e+00 8.42e-01 1.02e+02 angle pdb=" N LEU D 229 " pdb=" CA LEU D 229 " pdb=" C LEU D 229 " ideal model delta sigma weight residual 111.28 120.27 -8.99 1.09e+00 8.42e-01 6.80e+01 angle pdb=" N ASP D 772 " pdb=" CA ASP D 772 " pdb=" C ASP D 772 " ideal model delta sigma weight residual 110.97 118.45 -7.48 1.09e+00 8.42e-01 4.71e+01 angle pdb=" N VAL D 811 " pdb=" CA VAL D 811 " pdb=" C VAL D 811 " ideal model delta sigma weight residual 107.51 98.12 9.39 1.49e+00 4.50e-01 3.97e+01 angle pdb=" C ALA A 52 " pdb=" N PRO A 53 " pdb=" CA PRO A 53 " ideal model delta sigma weight residual 119.90 126.20 -6.30 1.02e+00 9.61e-01 3.82e+01 ... (remaining 22147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 8780 18.11 - 36.23: 728 36.23 - 54.34: 95 54.34 - 72.45: 45 72.45 - 90.56: 10 Dihedral angle restraints: 9658 sinusoidal: 3956 harmonic: 5702 Sorted by residual: dihedral pdb=" CA GLY A 435 " pdb=" C GLY A 435 " pdb=" N GLU A 436 " pdb=" CA GLU A 436 " ideal model delta harmonic sigma weight residual -180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ASP D 235 " pdb=" C ASP D 235 " pdb=" N PRO D 236 " pdb=" CA PRO D 236 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA GLU A 436 " pdb=" C GLU A 436 " pdb=" N ASP A 437 " pdb=" CA ASP A 437 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 9655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1812 0.090 - 0.180: 432 0.180 - 0.269: 68 0.269 - 0.359: 9 0.359 - 0.449: 4 Chirality restraints: 2325 Sorted by residual: chirality pdb=" CA SER D 146 " pdb=" N SER D 146 " pdb=" C SER D 146 " pdb=" CB SER D 146 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CB ILE A 726 " pdb=" CA ILE A 726 " pdb=" CG1 ILE A 726 " pdb=" CG2 ILE A 726 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CG LEU D 103 " pdb=" CB LEU D 103 " pdb=" CD1 LEU D 103 " pdb=" CD2 LEU D 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 2322 not shown) Planarity restraints: 2872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 173 " -0.092 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO D 174 " 0.245 5.00e-02 4.00e+02 pdb=" CA PRO D 174 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO D 174 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 726 " 0.024 2.00e-02 2.50e+03 4.80e-02 2.30e+01 pdb=" C ILE D 726 " -0.083 2.00e-02 2.50e+03 pdb=" O ILE D 726 " 0.031 2.00e-02 2.50e+03 pdb=" N HIS D 727 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 247 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C GLN A 247 " 0.070 2.00e-02 2.50e+03 pdb=" O GLN A 247 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU A 248 " -0.024 2.00e-02 2.50e+03 ... (remaining 2869 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 317 2.66 - 3.22: 13937 3.22 - 3.78: 26228 3.78 - 4.34: 36073 4.34 - 4.90: 58876 Nonbonded interactions: 135431 Sorted by model distance: nonbonded pdb=" N GLU A 809 " pdb=" OE1 GLU A 809 " model vdw 2.098 3.120 nonbonded pdb=" OH TYR A 466 " pdb=" OE2 GLU A 478 " model vdw 2.211 3.040 nonbonded pdb=" O ALA D 713 " pdb=" O TYR D 716 " model vdw 2.226 3.040 nonbonded pdb=" NE ARG A 131 " pdb=" OE1 GLU A 248 " model vdw 2.250 3.120 nonbonded pdb=" O TYR F1285 " pdb=" OH TYR F1290 " model vdw 2.258 3.040 ... (remaining 135426 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' 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: 6.750 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.450 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.009 0.176 16314 Z= 0.461 Angle : 1.369 15.212 22152 Z= 0.786 Chirality : 0.080 0.449 2325 Planarity : 0.010 0.141 2872 Dihedral : 13.939 90.562 6002 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.49 % Favored : 93.40 % Rotamer: Outliers : 0.58 % Allowed : 1.05 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.84 (0.17), residues: 1956 helix: -1.04 (0.27), residues: 287 sheet: -2.42 (0.18), residues: 548 loop : -1.81 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.002 ARG D 359 TYR 0.043 0.004 TYR D 781 PHE 0.038 0.004 PHE D 201 TRP 0.044 0.004 TRP E1132 HIS 0.020 0.003 HIS F1223 Details of bonding type rmsd covalent geometry : bond 0.00931 (16312) covalent geometry : angle 1.36906 (22152) hydrogen bonds : bond 0.15750 ( 525) hydrogen bonds : angle 8.23254 ( 1386) Misc. bond : bond 0.03626 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.599 Fit side-chains REVERT: A 256 TYR cc_start: 0.8719 (p90) cc_final: 0.8407 (p90) REVERT: A 624 MET cc_start: 0.8248 (mtm) cc_final: 0.7945 (mtp) REVERT: A 771 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8201 (mmm) REVERT: D 107 GLN cc_start: 0.7942 (mm110) cc_final: 0.7529 (mp10) REVERT: D 175 MET cc_start: 0.6550 (ppp) cc_final: 0.6201 (tpp) REVERT: D 229 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6376 (pp) REVERT: D 251 ASP cc_start: 0.7451 (t70) cc_final: 0.7215 (t0) REVERT: E 1184 MET cc_start: 0.5417 (tmm) cc_final: 0.5179 (tmm) outliers start: 10 outliers final: 4 residues processed: 204 average time/residue: 0.7350 time to fit residues: 163.2015 Evaluate side-chains 128 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 773 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0970 chunk 149 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 107 GLN A 161 HIS A 432 GLN ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 HIS D 334 GLN D 340 GLN D 742 HIS D 776 ASN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 837 ASN ** E1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1335 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.150392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106190 restraints weight = 21506.769| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.74 r_work: 0.3194 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16314 Z= 0.156 Angle : 0.648 8.629 22152 Z= 0.343 Chirality : 0.045 0.155 2325 Planarity : 0.006 0.073 2872 Dihedral : 6.538 94.689 2195 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.75 % Allowed : 8.58 % Favored : 89.67 % 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: -1.83 (0.18), residues: 1956 helix: 0.26 (0.29), residues: 309 sheet: -1.76 (0.19), residues: 558 loop : -1.30 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 274 TYR 0.022 0.002 TYR A 532 PHE 0.014 0.001 PHE D 153 TRP 0.015 0.001 TRP A 420 HIS 0.008 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00353 (16312) covalent geometry : angle 0.64820 (22152) hydrogen bonds : bond 0.04149 ( 525) hydrogen bonds : angle 6.41281 ( 1386) Misc. bond : bond 0.00327 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.545 Fit side-chains REVERT: A 178 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8434 (mt) REVERT: A 256 TYR cc_start: 0.9179 (p90) cc_final: 0.8870 (p90) REVERT: A 778 GLN cc_start: 0.8090 (mp10) cc_final: 0.7649 (mp10) REVERT: D 107 GLN cc_start: 0.8108 (mm110) cc_final: 0.7631 (mp10) REVERT: D 229 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6445 (pp) REVERT: D 251 ASP cc_start: 0.8461 (t70) cc_final: 0.7964 (t0) REVERT: F 1218 LEU cc_start: 0.7079 (pp) cc_final: 0.6870 (pt) REVERT: F 1286 MET cc_start: 0.4906 (mmt) cc_final: 0.3357 (pmm) outliers start: 30 outliers final: 10 residues processed: 165 average time/residue: 0.6966 time to fit residues: 125.8128 Evaluate side-chains 132 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 773 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 113 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 186 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 159 optimal weight: 0.0870 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 GLN ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 HIS D 742 HIS ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1223 HIS ** 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 = 0.3920 r_free = 0.3920 target = 0.148328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103102 restraints weight = 21803.218| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.65 r_work: 0.3147 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16314 Z= 0.157 Angle : 0.586 6.032 22152 Z= 0.306 Chirality : 0.044 0.144 2325 Planarity : 0.005 0.057 2872 Dihedral : 5.867 75.412 2192 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.87 % Allowed : 10.79 % Favored : 87.34 % 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: -1.27 (0.18), residues: 1956 helix: 0.67 (0.29), residues: 313 sheet: -1.22 (0.20), residues: 568 loop : -1.04 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 42 TYR 0.016 0.002 TYR D 835 PHE 0.013 0.001 PHE D 153 TRP 0.010 0.001 TRP A 264 HIS 0.005 0.001 HIS D 857 Details of bonding type rmsd covalent geometry : bond 0.00362 (16312) covalent geometry : angle 0.58615 (22152) hydrogen bonds : bond 0.03544 ( 525) hydrogen bonds : angle 5.86724 ( 1386) Misc. bond : bond 0.00089 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.510 Fit side-chains REVERT: A 462 LYS cc_start: 0.8073 (pptt) cc_final: 0.7680 (ptmm) REVERT: A 778 GLN cc_start: 0.8151 (mp10) cc_final: 0.7741 (mp10) REVERT: D 107 GLN cc_start: 0.8242 (mm110) cc_final: 0.7792 (mp10) REVERT: D 251 ASP cc_start: 0.8551 (t70) cc_final: 0.8141 (t70) REVERT: D 314 LYS cc_start: 0.8634 (mmpt) cc_final: 0.8231 (mppt) REVERT: D 394 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8153 (mm-30) REVERT: E 1192 MET cc_start: 0.7654 (mtp) cc_final: 0.7215 (ttp) REVERT: F 1218 LEU cc_start: 0.7194 (pp) cc_final: 0.6934 (pt) REVERT: F 1231 VAL cc_start: 0.4417 (OUTLIER) cc_final: 0.3943 (m) REVERT: F 1286 MET cc_start: 0.5236 (mmt) cc_final: 0.4126 (pmm) outliers start: 32 outliers final: 13 residues processed: 151 average time/residue: 0.6989 time to fit residues: 115.3983 Evaluate side-chains 130 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 779 HIS Chi-restraints excluded: chain F residue 1231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 32 optimal weight: 0.0870 chunk 180 optimal weight: 8.9990 chunk 1 optimal weight: 0.4980 chunk 134 optimal weight: 3.9990 chunk 91 optimal weight: 0.0670 chunk 100 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 113 optimal weight: 0.0970 chunk 160 optimal weight: 2.9990 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 GLN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1223 HIS ** 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 = 0.3932 r_free = 0.3932 target = 0.149363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106088 restraints weight = 21559.313| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.82 r_work: 0.3175 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16314 Z= 0.114 Angle : 0.538 6.415 22152 Z= 0.280 Chirality : 0.043 0.146 2325 Planarity : 0.005 0.058 2872 Dihedral : 5.649 84.994 2190 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.93 % Allowed : 12.08 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.19), residues: 1956 helix: 1.07 (0.30), residues: 313 sheet: -0.87 (0.21), residues: 527 loop : -0.86 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 590 TYR 0.014 0.001 TYR D 835 PHE 0.019 0.001 PHE D 591 TRP 0.009 0.001 TRP E1132 HIS 0.004 0.001 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00263 (16312) covalent geometry : angle 0.53802 (22152) hydrogen bonds : bond 0.03068 ( 525) hydrogen bonds : angle 5.47932 ( 1386) Misc. bond : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7527 (ttp80) REVERT: A 103 LEU cc_start: 0.9063 (mt) cc_final: 0.8852 (mm) REVERT: A 256 TYR cc_start: 0.9165 (p90) cc_final: 0.8851 (p90) REVERT: A 462 LYS cc_start: 0.8089 (pptt) cc_final: 0.7841 (ptmm) REVERT: A 778 GLN cc_start: 0.8122 (mp10) cc_final: 0.7722 (mp10) REVERT: D 107 GLN cc_start: 0.8247 (mm110) cc_final: 0.7801 (mp10) REVERT: D 314 LYS cc_start: 0.8548 (mmpt) cc_final: 0.8083 (mppt) REVERT: D 394 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: D 684 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: E 1147 VAL cc_start: 0.5340 (t) cc_final: 0.4957 (t) REVERT: E 1192 MET cc_start: 0.7730 (mtp) cc_final: 0.7416 (ttp) REVERT: F 1218 LEU cc_start: 0.7173 (pp) cc_final: 0.6955 (pt) REVERT: F 1286 MET cc_start: 0.5095 (mmt) cc_final: 0.4521 (pmm) outliers start: 33 outliers final: 12 residues processed: 153 average time/residue: 0.7069 time to fit residues: 118.5879 Evaluate side-chains 125 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 697 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 176 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.0470 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 GLN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1223 HIS ** 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 = 0.3884 r_free = 0.3884 target = 0.145689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100460 restraints weight = 21652.247| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.72 r_work: 0.3100 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16314 Z= 0.206 Angle : 0.578 6.242 22152 Z= 0.300 Chirality : 0.044 0.139 2325 Planarity : 0.005 0.060 2872 Dihedral : 5.614 83.309 2187 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.68 % Allowed : 12.78 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 1956 helix: 1.16 (0.30), residues: 309 sheet: -0.73 (0.21), residues: 545 loop : -0.74 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 405 TYR 0.018 0.002 TYR D 835 PHE 0.012 0.002 PHE A 250 TRP 0.012 0.002 TRP D 375 HIS 0.007 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00487 (16312) covalent geometry : angle 0.57791 (22152) hydrogen bonds : bond 0.03326 ( 525) hydrogen bonds : angle 5.44979 ( 1386) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8184 (pptt) cc_final: 0.7929 (ptmm) REVERT: A 778 GLN cc_start: 0.8163 (mp10) cc_final: 0.7799 (mp10) REVERT: D 71 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.5909 (ttp-170) REVERT: D 107 GLN cc_start: 0.8306 (mm110) cc_final: 0.7861 (mp10) REVERT: D 314 LYS cc_start: 0.8528 (mmpt) cc_final: 0.8118 (mppt) REVERT: D 394 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8126 (mm-30) REVERT: D 684 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: E 1147 VAL cc_start: 0.5475 (t) cc_final: 0.5047 (m) REVERT: E 1190 GLU cc_start: 0.4449 (mm-30) cc_final: 0.4218 (mm-30) REVERT: E 1192 MET cc_start: 0.7811 (mtp) cc_final: 0.7570 (ttp) REVERT: F 1231 VAL cc_start: 0.4140 (OUTLIER) cc_final: 0.3859 (m) REVERT: F 1286 MET cc_start: 0.5166 (mmt) cc_final: 0.4701 (pmm) outliers start: 46 outliers final: 20 residues processed: 153 average time/residue: 0.7206 time to fit residues: 120.6445 Evaluate side-chains 134 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain E residue 1100 VAL Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 80 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 189 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 193 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN A 525 HIS A 573 HIS ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 815 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.145166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099611 restraints weight = 21582.930| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.71 r_work: 0.3083 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16314 Z= 0.181 Angle : 0.564 10.557 22152 Z= 0.292 Chirality : 0.044 0.135 2325 Planarity : 0.005 0.059 2872 Dihedral : 5.242 42.951 2185 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.28 % Allowed : 14.24 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 1956 helix: 1.15 (0.30), residues: 313 sheet: -0.56 (0.22), residues: 533 loop : -0.68 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 405 TYR 0.019 0.001 TYR D 835 PHE 0.019 0.001 PHE D 591 TRP 0.010 0.001 TRP D 210 HIS 0.005 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00421 (16312) covalent geometry : angle 0.56374 (22152) hydrogen bonds : bond 0.03190 ( 525) hydrogen bonds : angle 5.35420 ( 1386) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8208 (pptt) cc_final: 0.7955 (ptmm) REVERT: A 778 GLN cc_start: 0.8132 (mp10) cc_final: 0.7738 (mp10) REVERT: D 107 GLN cc_start: 0.8313 (mm110) cc_final: 0.7903 (mp10) REVERT: D 590 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7539 (mtt-85) REVERT: D 684 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: E 1147 VAL cc_start: 0.5622 (t) cc_final: 0.5364 (m) REVERT: E 1189 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6467 (tm-30) REVERT: E 1195 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6929 (mp0) REVERT: F 1215 LEU cc_start: 0.6866 (mm) cc_final: 0.6573 (mm) REVERT: F 1231 VAL cc_start: 0.4177 (OUTLIER) cc_final: 0.3972 (m) REVERT: F 1286 MET cc_start: 0.5068 (mmt) cc_final: 0.4781 (pmm) outliers start: 39 outliers final: 25 residues processed: 147 average time/residue: 0.6865 time to fit residues: 111.0926 Evaluate side-chains 134 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain E residue 1100 VAL Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1231 VAL Chi-restraints excluded: chain F residue 1264 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 49 optimal weight: 0.0170 chunk 81 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 125 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.146716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.101208 restraints weight = 21427.306| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.85 r_work: 0.3112 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16314 Z= 0.129 Angle : 0.540 6.117 22152 Z= 0.280 Chirality : 0.043 0.134 2325 Planarity : 0.005 0.067 2872 Dihedral : 5.126 43.010 2185 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.28 % Allowed : 14.94 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1956 helix: 1.41 (0.31), residues: 307 sheet: -0.43 (0.22), residues: 533 loop : -0.64 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 405 TYR 0.017 0.001 TYR D 835 PHE 0.009 0.001 PHE A 250 TRP 0.021 0.001 TRP A 375 HIS 0.006 0.001 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00303 (16312) covalent geometry : angle 0.54048 (22152) hydrogen bonds : bond 0.02936 ( 525) hydrogen bonds : angle 5.22068 ( 1386) Misc. bond : bond 0.00052 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8199 (pptt) cc_final: 0.7931 (ptmm) REVERT: A 778 GLN cc_start: 0.8113 (mp10) cc_final: 0.7716 (mp10) REVERT: D 107 GLN cc_start: 0.8310 (mm110) cc_final: 0.7843 (mp10) REVERT: D 394 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8044 (mm-30) REVERT: D 438 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7650 (pt0) REVERT: D 684 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: E 1147 VAL cc_start: 0.5641 (t) cc_final: 0.5424 (m) REVERT: E 1190 GLU cc_start: 0.4679 (mm-30) cc_final: 0.4323 (mm-30) REVERT: F 1215 LEU cc_start: 0.6764 (mm) cc_final: 0.6467 (mm) REVERT: F 1218 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7050 (pt) REVERT: F 1286 MET cc_start: 0.5072 (mmt) cc_final: 0.4796 (pmm) outliers start: 39 outliers final: 19 residues processed: 149 average time/residue: 0.6507 time to fit residues: 106.8649 Evaluate side-chains 138 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 36 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 187 optimal weight: 0.0010 chunk 143 optimal weight: 2.9990 chunk 121 optimal weight: 0.0970 chunk 77 optimal weight: 0.2980 chunk 164 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 0.0000 chunk 38 optimal weight: 5.9990 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 68 HIS ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS D 742 HIS ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.148081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103756 restraints weight = 21743.739| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.71 r_work: 0.3151 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16314 Z= 0.105 Angle : 0.520 6.623 22152 Z= 0.269 Chirality : 0.042 0.133 2325 Planarity : 0.004 0.065 2872 Dihedral : 4.941 43.175 2185 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.04 % Allowed : 15.64 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 1956 helix: 1.59 (0.31), residues: 307 sheet: -0.34 (0.23), residues: 519 loop : -0.62 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 405 TYR 0.016 0.001 TYR D 835 PHE 0.020 0.001 PHE D 591 TRP 0.018 0.001 TRP A 375 HIS 0.005 0.001 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00246 (16312) covalent geometry : angle 0.51994 (22152) hydrogen bonds : bond 0.02761 ( 525) hydrogen bonds : angle 5.04733 ( 1386) Misc. bond : bond 0.00046 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.7587 (ttp80) REVERT: A 462 LYS cc_start: 0.8166 (pptt) cc_final: 0.7884 (ptmm) REVERT: A 778 GLN cc_start: 0.8113 (mp10) cc_final: 0.7713 (mp10) REVERT: D 107 GLN cc_start: 0.8308 (mm110) cc_final: 0.7870 (mp10) REVERT: D 394 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8024 (mm-30) REVERT: D 438 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: D 684 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7942 (mt0) REVERT: E 1147 VAL cc_start: 0.5680 (t) cc_final: 0.5470 (m) REVERT: E 1190 GLU cc_start: 0.4486 (mm-30) cc_final: 0.4242 (mm-30) REVERT: F 1215 LEU cc_start: 0.6679 (mm) cc_final: 0.6409 (mm) REVERT: F 1218 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7116 (pt) outliers start: 35 outliers final: 17 residues processed: 151 average time/residue: 0.6530 time to fit residues: 108.5550 Evaluate side-chains 139 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1264 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 91 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 134 optimal weight: 0.0040 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 HIS ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.147378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102526 restraints weight = 21499.695| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.50 r_work: 0.3121 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16314 Z= 0.131 Angle : 0.532 7.048 22152 Z= 0.276 Chirality : 0.043 0.135 2325 Planarity : 0.004 0.062 2872 Dihedral : 4.961 44.581 2185 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.75 % Allowed : 16.39 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 1956 helix: 1.57 (0.31), residues: 307 sheet: -0.31 (0.23), residues: 519 loop : -0.57 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 405 TYR 0.019 0.001 TYR D 74 PHE 0.010 0.001 PHE D 153 TRP 0.016 0.001 TRP A 375 HIS 0.003 0.001 HIS D 742 Details of bonding type rmsd covalent geometry : bond 0.00311 (16312) covalent geometry : angle 0.53219 (22152) hydrogen bonds : bond 0.02824 ( 525) hydrogen bonds : angle 5.03085 ( 1386) Misc. bond : bond 0.00044 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7599 (ttp80) REVERT: A 462 LYS cc_start: 0.8202 (pptt) cc_final: 0.7909 (ptmm) REVERT: A 552 MET cc_start: 0.9071 (mmm) cc_final: 0.8774 (mmt) REVERT: A 745 GLN cc_start: 0.8458 (pm20) cc_final: 0.8210 (pm20) REVERT: A 778 GLN cc_start: 0.8121 (mp10) cc_final: 0.7715 (mp10) REVERT: D 107 GLN cc_start: 0.8359 (mm110) cc_final: 0.7908 (mp10) REVERT: D 393 GLU cc_start: 0.7766 (tp30) cc_final: 0.7340 (tp30) REVERT: D 394 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: D 438 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7532 (pm20) REVERT: D 684 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: E 1189 GLU cc_start: 0.6531 (tm-30) cc_final: 0.6330 (tm-30) REVERT: F 1218 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7079 (pt) outliers start: 30 outliers final: 19 residues processed: 143 average time/residue: 0.6826 time to fit residues: 107.5554 Evaluate side-chains 140 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1264 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 181 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 chunk 47 optimal weight: 0.0050 chunk 45 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 189 optimal weight: 0.0170 chunk 11 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.4432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102891 restraints weight = 21452.542| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.75 r_work: 0.3129 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16314 Z= 0.125 Angle : 0.536 6.751 22152 Z= 0.278 Chirality : 0.043 0.136 2325 Planarity : 0.004 0.060 2872 Dihedral : 4.927 40.414 2185 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.63 % Allowed : 16.45 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 1956 helix: 1.60 (0.31), residues: 307 sheet: -0.32 (0.23), residues: 522 loop : -0.53 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 405 TYR 0.018 0.001 TYR D 74 PHE 0.017 0.001 PHE D 591 TRP 0.016 0.001 TRP A 375 HIS 0.011 0.001 HIS D 742 Details of bonding type rmsd covalent geometry : bond 0.00295 (16312) covalent geometry : angle 0.53601 (22152) hydrogen bonds : bond 0.02793 ( 525) hydrogen bonds : angle 4.99935 ( 1386) Misc. bond : bond 0.00049 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7882 (ttp-110) cc_final: 0.7543 (ttp80) REVERT: A 462 LYS cc_start: 0.8191 (pptt) cc_final: 0.7897 (ptmm) REVERT: A 552 MET cc_start: 0.9051 (mmm) cc_final: 0.8761 (mmt) REVERT: A 745 GLN cc_start: 0.8429 (pm20) cc_final: 0.8177 (pm20) REVERT: A 778 GLN cc_start: 0.8117 (mp10) cc_final: 0.7726 (mp10) REVERT: D 107 GLN cc_start: 0.8317 (mm110) cc_final: 0.7882 (mp10) REVERT: D 163 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7861 (tpp-160) REVERT: D 393 GLU cc_start: 0.7766 (tp30) cc_final: 0.7339 (tp30) REVERT: D 394 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: D 438 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7532 (pm20) REVERT: D 684 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8026 (mt0) REVERT: E 1189 GLU cc_start: 0.6336 (tm-30) cc_final: 0.6124 (tm-30) REVERT: F 1218 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7060 (pt) outliers start: 28 outliers final: 18 residues processed: 140 average time/residue: 0.6996 time to fit residues: 107.1946 Evaluate side-chains 138 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1264 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 87 optimal weight: 0.6980 chunk 177 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 94 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 166 optimal weight: 0.0670 chunk 50 optimal weight: 0.0050 chunk 76 optimal weight: 1.9990 overall best weight: 0.3132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 742 HIS ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1143 HIS ** 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 = 0.3917 r_free = 0.3917 target = 0.148227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104213 restraints weight = 21372.892| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.61 r_work: 0.3155 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16314 Z= 0.111 Angle : 0.531 6.653 22152 Z= 0.276 Chirality : 0.042 0.138 2325 Planarity : 0.004 0.060 2872 Dihedral : 4.864 41.531 2185 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.40 % Allowed : 16.86 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1956 helix: 1.52 (0.31), residues: 317 sheet: -0.25 (0.23), residues: 517 loop : -0.48 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 405 TYR 0.017 0.001 TYR D 74 PHE 0.009 0.001 PHE D 153 TRP 0.016 0.001 TRP A 375 HIS 0.006 0.001 HIS D 742 Details of bonding type rmsd covalent geometry : bond 0.00262 (16312) covalent geometry : angle 0.53136 (22152) hydrogen bonds : bond 0.02727 ( 525) hydrogen bonds : angle 4.94043 ( 1386) Misc. bond : bond 0.00074 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6233.46 seconds wall clock time: 106 minutes 47.18 seconds (6407.18 seconds total)