Starting phenix.real_space_refine on Wed Mar 4 11:58:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5v_10704/03_2026/6y5v_10704.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5v_10704/03_2026/6y5v_10704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y5v_10704/03_2026/6y5v_10704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5v_10704/03_2026/6y5v_10704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y5v_10704/03_2026/6y5v_10704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5v_10704/03_2026/6y5v_10704.map" } resolution = 4.08 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= 0.003 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 8728 2.51 5 N 2215 2.21 5 O 2365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 13400 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 6641 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 3, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 106 Chain: "B" Number of atoms: 6653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 6653 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 14, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.31, per 1000 atoms: 0.25 Number of scatterers: 13400 At special positions: 0 Unit cell: (149.4, 107.07, 94.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2365 8.00 N 2215 7.00 C 8728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 640 " distance=2.04 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 640 " distance=2.02 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A1204 " - " ASN A 377 " " NAG B1204 " - " ASN B 377 " " NAG C 1 " - " ASN A 328 " " NAG D 1 " - " ASN B 328 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 362.6 milliseconds 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3232 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 6 sheets defined 62.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.536A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 156 through 193 removed outlier: 6.493A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 243 removed outlier: 3.651A pdb=" N MET A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.716A pdb=" N VAL A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 removed outlier: 3.621A pdb=" N GLY A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.685A pdb=" N VAL A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 376' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.854A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.650A pdb=" N SER A 452 " --> pdb=" O MET A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 491 Proline residue: A 466 - end of helix removed outlier: 3.836A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.965A pdb=" N LEU A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 550 removed outlier: 4.277A pdb=" N ILE A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Proline residue: A 541 - end of helix removed outlier: 3.520A pdb=" N ASP A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.872A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 584 removed outlier: 3.577A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 616 Proline residue: A 593 - end of helix removed outlier: 3.745A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 675 removed outlier: 3.607A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N TYR A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 removed outlier: 3.612A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.186A pdb=" N LEU A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 751 Processing helix chain 'A' and resid 752 through 770 Processing helix chain 'A' and resid 783 through 795 removed outlier: 3.937A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 881 Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 906 through 917 removed outlier: 3.745A pdb=" N PHE A 912 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 931 No H-bonds generated for 'chain 'A' and resid 929 through 931' Processing helix chain 'A' and resid 932 through 946 removed outlier: 4.052A pdb=" N GLU A 938 " --> pdb=" O ALA A 934 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 946 " --> pdb=" O MET A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1048 Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1066 through 1078 Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.567A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.540A pdb=" N CYS B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 156 through 193 removed outlier: 6.320A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 243 removed outlier: 3.615A pdb=" N MET B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 261 through 284 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.712A pdb=" N VAL B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 removed outlier: 3.530A pdb=" N GLY B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.637A pdb=" N VAL B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.849A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 460 through 489 Proline residue: B 466 - end of helix removed outlier: 3.667A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 517 through 550 removed outlier: 4.210A pdb=" N ILE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Proline residue: B 541 - end of helix removed outlier: 3.502A pdb=" N ASP B 550 " --> pdb=" O ALA B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 removed outlier: 3.998A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 584 Processing helix chain 'B' and resid 587 through 616 Proline residue: B 593 - end of helix removed outlier: 3.728A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 675 removed outlier: 3.795A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TYR B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 696 removed outlier: 3.669A pdb=" N GLU B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 3.996A pdb=" N LEU B 726 " --> pdb=" O HIS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 751 Processing helix chain 'B' and resid 752 through 770 Processing helix chain 'B' and resid 783 through 795 removed outlier: 3.879A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 835 removed outlier: 3.722A pdb=" N LYS B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 881 removed outlier: 4.065A pdb=" N LEU B 872 " --> pdb=" O ASP B 868 " (cutoff:3.500A) Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 884 through 886 No H-bonds generated for 'chain 'B' and resid 884 through 886' Processing helix chain 'B' and resid 906 through 917 removed outlier: 3.518A pdb=" N ALA B 910 " --> pdb=" O LYS B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 931 No H-bonds generated for 'chain 'B' and resid 929 through 931' Processing helix chain 'B' and resid 932 through 946 removed outlier: 3.954A pdb=" N GLU B 938 " --> pdb=" O ALA B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1048 Processing helix chain 'B' and resid 1066 through 1078 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA3, first strand: chain 'A' and resid 775 through 781 removed outlier: 6.463A pdb=" N LEU A 708 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLY A 742 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 805 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA A 842 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET A 807 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU A1054 " --> pdb=" O ASN A 859 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP A 861 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ASN A1056 " --> pdb=" O ASP A 861 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TRP A 863 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 921 " --> pdb=" O ILE A 890 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA5, first strand: chain 'B' and resid 342 through 345 Processing sheet with id=AA6, first strand: chain 'B' and resid 775 through 781 removed outlier: 6.534A pdb=" N LEU B 708 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY B 742 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 805 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ALA B 842 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N MET B 807 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B1054 " --> pdb=" O ASN B 859 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP B 861 " --> pdb=" O LEU B1054 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN B1056 " --> pdb=" O ASP B 861 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N TRP B 863 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N GLU B 921 " --> pdb=" O CYS B 888 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE B 890 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU B 923 " --> pdb=" O ILE B 890 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE B 892 " --> pdb=" O GLU B 923 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2307 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: 2.12 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4188 1.35 - 1.47: 3417 1.47 - 1.59: 5955 1.59 - 1.71: 0 1.71 - 1.83: 146 Bond restraints: 13706 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 NAG A1204 " pdb=" O5 NAG A1204 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" C1 NAG B1204 " pdb=" O5 NAG B1204 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" CG1 ILE B 473 " pdb=" CD1 ILE B 473 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.12e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 ... (remaining 13701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 18054 1.65 - 3.30: 497 3.30 - 4.95: 78 4.95 - 6.60: 19 6.60 - 8.24: 4 Bond angle restraints: 18652 Sorted by residual: angle pdb=" N TRP A 864 " pdb=" CA TRP A 864 " pdb=" C TRP A 864 " ideal model delta sigma weight residual 108.23 116.47 -8.24 1.72e+00 3.38e-01 2.30e+01 angle pdb=" C ILE B 639 " pdb=" N CYS B 640 " pdb=" CA CYS B 640 " ideal model delta sigma weight residual 122.38 115.97 6.41 1.81e+00 3.05e-01 1.26e+01 angle pdb=" C VAL A 866 " pdb=" N HIS A 867 " pdb=" CA HIS A 867 " ideal model delta sigma weight residual 122.59 117.57 5.02 1.57e+00 4.06e-01 1.02e+01 angle pdb=" N PHE B 442 " pdb=" CA PHE B 442 " pdb=" C PHE B 442 " ideal model delta sigma weight residual 109.81 116.76 -6.95 2.21e+00 2.05e-01 9.88e+00 angle pdb=" N VAL B 866 " pdb=" CA VAL B 866 " pdb=" C VAL B 866 " ideal model delta sigma weight residual 109.34 115.77 -6.43 2.08e+00 2.31e-01 9.55e+00 ... (remaining 18647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 7721 21.80 - 43.59: 324 43.59 - 65.39: 32 65.39 - 87.19: 14 87.19 - 108.99: 8 Dihedral angle restraints: 8099 sinusoidal: 3068 harmonic: 5031 Sorted by residual: dihedral pdb=" CA CYS B 640 " pdb=" C CYS B 640 " pdb=" N LEU B 641 " pdb=" CA LEU B 641 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ILE B 865 " pdb=" C ILE B 865 " pdb=" N VAL B 866 " pdb=" CA VAL B 866 " ideal model delta harmonic sigma weight residual 180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLN B 707 " pdb=" C GLN B 707 " pdb=" N LEU B 708 " pdb=" CA LEU B 708 " ideal model delta harmonic sigma weight residual -180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 8096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1778 0.055 - 0.110: 389 0.110 - 0.165: 54 0.165 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 2224 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE B 865 " pdb=" CA ILE B 865 " pdb=" CG1 ILE B 865 " pdb=" CG2 ILE B 865 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 2221 not shown) Planarity restraints: 2309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B1034 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C HIS B1034 " -0.073 2.00e-02 2.50e+03 pdb=" O HIS B1034 " 0.027 2.00e-02 2.50e+03 pdb=" N THR B1035 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 536 " -0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C SER A 536 " 0.071 2.00e-02 2.50e+03 pdb=" O SER A 536 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU A 537 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 536 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.17e+01 pdb=" C SER B 536 " 0.059 2.00e-02 2.50e+03 pdb=" O SER B 536 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 537 " -0.020 2.00e-02 2.50e+03 ... (remaining 2306 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2441 2.77 - 3.30: 13570 3.30 - 3.83: 22102 3.83 - 4.37: 25069 4.37 - 4.90: 43729 Nonbonded interactions: 106911 Sorted by model distance: nonbonded pdb=" O PRO A1058 " pdb=" OH TYR A1070 " model vdw 2.232 3.040 nonbonded pdb=" NH1 ARG A 680 " pdb=" O PRO B 698 " model vdw 2.241 3.120 nonbonded pdb=" OD1 ASN B 859 " pdb=" OG SER B 889 " model vdw 2.277 3.040 nonbonded pdb=" O SER A 789 " pdb=" NE2 GLN A 793 " model vdw 2.313 3.120 nonbonded pdb=" O PHE B 825 " pdb=" OG1 THR B 828 " model vdw 2.313 3.040 ... (remaining 106906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 102 through 312 or (resid 313 and (name N or name CA or na \ me C or name O or name CB )) or resid 314 through 341 or (resid 342 and (name N \ or name CA or name C or name O or name CB )) or resid 343 through 393 or (resid \ 394 and (name N or name CA or name C or name O or name CB )) or resid 395 throug \ h 491 or (resid 492 and (name N or name CA or name C or name O or name CB )) or \ resid 493 through 504 or (resid 505 and (name N or name CA or name C or name O o \ r name CB )) or resid 506 through 715 or (resid 716 and (name N or name CA or na \ me C or name O or name CB )) or resid 717 through 772 or (resid 773 and (name N \ or name CA or name C or name O or name CB )) or resid 774 through 856 or (resid \ 857 and (name N or name CA or name C or name O or name CB )) or resid 858 throug \ h 872 or (resid 873 and (name N or name CA or name C or name O or name CB )) or \ resid 874 through 882 or (resid 883 and (name N or name CA or name C or name O o \ r name CB )) or resid 884 through 913 or (resid 914 and (name N or name CA or na \ me C or name O or name CB )) or resid 915 through 918 or (resid 919 through 920 \ and (name N or name CA or name C or name O or name CB )) or resid 921 through 92 \ 6 or (resid 927 and (name N or name CA or name C or name O or name CB )) or resi \ d 928 through 937 or (resid 938 through 946 and (name N or name CA or name C or \ name O or name CB )) or resid 1028 or (resid 1029 and (name N or name CA or name \ C or name O or name CB )) or resid 1030 through 1045 or (resid 1046 and (name N \ or name CA or name C or name O or name CB )) or resid 1047 through 1078 or (res \ id 1079 and (name N or name CA or name C or name O or name CB )) or resid 1080 t \ hrough 1081 or (resid 1082 and (name N or name CA or name C or name O or name CB \ )) or resid 1083 through 1204)) selection = (chain 'B' and (resid 102 through 112 or (resid 113 through 114 and (name N or n \ ame CA or name C or name O or name CB )) or resid 115 through 116 or (resid 117 \ through 121 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 3 through 211 or (resid 212 and (name N or name CA or name C or name O or name C \ B )) or resid 213 through 286 or (resid 287 and (name N or name CA or name C or \ name O or name CB )) or resid 288 through 290 or (resid 291 and (name N or name \ CA or name C or name O or name CB )) or resid 292 through 346 or (resid 347 thro \ ugh 348 and (name N or name CA or name C or name O or name CB )) or resid 349 th \ rough 364 or (resid 365 through 367 and (name N or name CA or name C or name O o \ r name CB )) or resid 368 through 417 or (resid 418 and (name N or name CA or na \ me C or name O or name CB )) or resid 419 through 420 or (resid 421 and (name N \ or name CA or name C or name O or name CB )) or resid 422 through 462 or (resid \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 616 or (resid 617 and (name N or name CA or name C or name O or name CB )) or \ resid 618 through 634 or (resid 635 and (name N or name CA or name C or name O o \ r name CB )) or resid 636 through 694 or (resid 695 and (name N or name CA or na \ me C or name O or name CB )) or resid 696 through 886 or (resid 887 and (name N \ or name CA or name C or name O or name CB )) or resid 888 through 896 or (resid \ 905 through 907 and (name N or name CA or name C or name O or name CB )) or resi \ d 908 through 939 or (resid 940 through 946 and (name N or name CA or name C or \ name O or name CB )) or resid 1028 through 1204)) } ncs_group { reference = chain 'C' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.310 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.004 0.057 13720 Z= 0.189 Angle : 0.685 8.244 18688 Z= 0.376 Chirality : 0.046 0.274 2224 Planarity : 0.005 0.042 2305 Dihedral : 12.747 108.986 4849 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.29 % Allowed : 2.96 % Favored : 96.75 % 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: -2.25 (0.18), residues: 1738 helix: -0.66 (0.15), residues: 932 sheet: -2.03 (0.42), residues: 100 loop : -2.51 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1083 TYR 0.020 0.002 TYR A 935 PHE 0.017 0.001 PHE B 847 TRP 0.015 0.002 TRP B 570 HIS 0.011 0.001 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00416 (13706) covalent geometry : angle 0.68121 (18652) SS BOND : bond 0.00543 ( 6) SS BOND : angle 1.42889 ( 12) hydrogen bonds : bond 0.11334 ( 799) hydrogen bonds : angle 5.42428 ( 2307) link_BETA1-4 : bond 0.00215 ( 4) link_BETA1-4 : angle 1.64024 ( 12) link_NAG-ASN : bond 0.00346 ( 4) link_NAG-ASN : angle 2.24978 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 421 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ILE cc_start: 0.9185 (mt) cc_final: 0.8984 (tt) REVERT: A 303 SER cc_start: 0.9185 (m) cc_final: 0.8975 (p) REVERT: A 334 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6738 (mtt180) REVERT: A 360 ASN cc_start: 0.7688 (m-40) cc_final: 0.7408 (p0) REVERT: A 499 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8202 (ttmt) REVERT: A 536 SER cc_start: 0.9398 (m) cc_final: 0.9117 (t) REVERT: A 551 ASN cc_start: 0.8103 (m-40) cc_final: 0.7552 (t0) REVERT: A 590 LEU cc_start: 0.8761 (mt) cc_final: 0.8516 (mt) REVERT: A 601 MET cc_start: 0.8868 (tpp) cc_final: 0.8661 (tpp) REVERT: A 628 TYR cc_start: 0.8229 (t80) cc_final: 0.8022 (t80) REVERT: A 707 GLN cc_start: 0.9296 (mm-40) cc_final: 0.9016 (mm110) REVERT: A 861 ASP cc_start: 0.7007 (m-30) cc_final: 0.6643 (m-30) REVERT: B 278 MET cc_start: 0.8579 (mmp) cc_final: 0.8096 (mmp) REVERT: B 372 TYR cc_start: 0.8182 (t80) cc_final: 0.7648 (t80) REVERT: B 381 ILE cc_start: 0.7907 (mt) cc_final: 0.7453 (mm) REVERT: B 445 VAL cc_start: 0.9489 (m) cc_final: 0.9222 (t) REVERT: B 523 ILE cc_start: 0.9220 (pt) cc_final: 0.8746 (tp) REVERT: B 536 SER cc_start: 0.9471 (m) cc_final: 0.9203 (p) REVERT: B 562 SER cc_start: 0.8845 (m) cc_final: 0.8575 (t) REVERT: B 573 LEU cc_start: 0.8858 (tp) cc_final: 0.8574 (mm) REVERT: B 590 LEU cc_start: 0.8560 (mt) cc_final: 0.8277 (mt) REVERT: B 601 MET cc_start: 0.8590 (tpp) cc_final: 0.8292 (tpp) REVERT: B 863 TRP cc_start: 0.8545 (m100) cc_final: 0.8008 (m100) REVERT: B 886 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8024 (ttm-80) REVERT: B 892 ILE cc_start: 0.9177 (mm) cc_final: 0.8925 (mp) outliers start: 4 outliers final: 2 residues processed: 424 average time/residue: 0.1131 time to fit residues: 70.2979 Evaluate side-chains 268 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 346 ASN A 613 GLN ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS B 133 GLN B 483 ASN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 ASN B 867 HIS B 881 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112216 restraints weight = 20458.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114586 restraints weight = 14677.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116159 restraints weight = 10257.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116124 restraints weight = 8215.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116525 restraints weight = 8013.623| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13720 Z= 0.128 Angle : 0.593 9.135 18688 Z= 0.302 Chirality : 0.042 0.237 2224 Planarity : 0.004 0.046 2305 Dihedral : 7.191 67.913 2021 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % 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 (0.20), residues: 1738 helix: 0.98 (0.17), residues: 960 sheet: -1.62 (0.45), residues: 100 loop : -1.73 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 891 TYR 0.023 0.001 TYR A 935 PHE 0.015 0.001 PHE A1073 TRP 0.014 0.002 TRP A 355 HIS 0.007 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00279 (13706) covalent geometry : angle 0.58385 (18652) SS BOND : bond 0.00615 ( 6) SS BOND : angle 2.96764 ( 12) hydrogen bonds : bond 0.04269 ( 799) hydrogen bonds : angle 4.39344 ( 2307) link_BETA1-4 : bond 0.00517 ( 4) link_BETA1-4 : angle 2.29087 ( 12) link_NAG-ASN : bond 0.00268 ( 4) link_NAG-ASN : angle 1.88221 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 351 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ILE cc_start: 0.9251 (mt) cc_final: 0.8971 (tt) REVERT: A 505 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7835 (ptmt) REVERT: A 536 SER cc_start: 0.9291 (m) cc_final: 0.9033 (t) REVERT: A 639 ILE cc_start: 0.8781 (tt) cc_final: 0.8553 (tt) REVERT: A 644 MET cc_start: 0.9100 (mtm) cc_final: 0.8597 (ttm) REVERT: A 1038 LYS cc_start: 0.9171 (tttt) cc_final: 0.8960 (ttmt) REVERT: B 108 LEU cc_start: 0.9261 (mt) cc_final: 0.9034 (mt) REVERT: B 372 TYR cc_start: 0.7832 (t80) cc_final: 0.7381 (t80) REVERT: B 381 ILE cc_start: 0.7409 (mt) cc_final: 0.6978 (mm) REVERT: B 397 TRP cc_start: 0.8294 (m100) cc_final: 0.8053 (m100) REVERT: B 445 VAL cc_start: 0.9427 (m) cc_final: 0.9132 (t) REVERT: B 523 ILE cc_start: 0.9181 (pt) cc_final: 0.8769 (tp) REVERT: B 536 SER cc_start: 0.9467 (m) cc_final: 0.8978 (p) REVERT: B 573 LEU cc_start: 0.8805 (tp) cc_final: 0.8383 (mm) REVERT: B 597 MET cc_start: 0.9322 (tpp) cc_final: 0.8843 (tpp) REVERT: B 644 MET cc_start: 0.8709 (mtp) cc_final: 0.7910 (ttp) REVERT: B 707 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7900 (mp10) REVERT: B 867 HIS cc_start: 0.6677 (OUTLIER) cc_final: 0.6452 (t-170) REVERT: B 886 ARG cc_start: 0.8262 (ttm-80) cc_final: 0.8022 (ttm-80) REVERT: B 892 ILE cc_start: 0.9285 (mm) cc_final: 0.9062 (mp) outliers start: 1 outliers final: 0 residues processed: 352 average time/residue: 0.1004 time to fit residues: 54.3014 Evaluate side-chains 248 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 140 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 149 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 376 ASN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 731 GLN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114517 restraints weight = 20766.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115752 restraints weight = 14769.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117001 restraints weight = 11606.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117724 restraints weight = 9622.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118125 restraints weight = 8740.805| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13720 Z= 0.144 Angle : 0.584 9.209 18688 Z= 0.298 Chirality : 0.042 0.167 2224 Planarity : 0.004 0.046 2305 Dihedral : 5.772 46.969 2021 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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 (0.21), residues: 1738 helix: 1.38 (0.17), residues: 964 sheet: -1.84 (0.43), residues: 134 loop : -1.39 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 886 TYR 0.012 0.001 TYR A 628 PHE 0.014 0.001 PHE B 775 TRP 0.010 0.001 TRP B 864 HIS 0.007 0.001 HIS B 915 Details of bonding type rmsd covalent geometry : bond 0.00328 (13706) covalent geometry : angle 0.57722 (18652) SS BOND : bond 0.00462 ( 6) SS BOND : angle 2.51516 ( 12) hydrogen bonds : bond 0.04068 ( 799) hydrogen bonds : angle 4.27031 ( 2307) link_BETA1-4 : bond 0.00476 ( 4) link_BETA1-4 : angle 2.20732 ( 12) link_NAG-ASN : bond 0.00176 ( 4) link_NAG-ASN : angle 1.67041 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8571 (mp) cc_final: 0.8221 (mp) REVERT: A 314 SER cc_start: 0.8618 (t) cc_final: 0.8282 (p) REVERT: A 453 ASN cc_start: 0.8616 (t0) cc_final: 0.8327 (t0) REVERT: A 505 LYS cc_start: 0.8314 (mmmt) cc_final: 0.7862 (ptmt) REVERT: A 597 MET cc_start: 0.8945 (tpp) cc_final: 0.8372 (tpp) REVERT: A 601 MET cc_start: 0.9103 (tpp) cc_final: 0.8552 (tpp) REVERT: A 644 MET cc_start: 0.9054 (mtm) cc_final: 0.8752 (ttm) REVERT: B 301 ILE cc_start: 0.9138 (mm) cc_final: 0.8915 (mm) REVERT: B 397 TRP cc_start: 0.8284 (m100) cc_final: 0.8037 (m100) REVERT: B 523 ILE cc_start: 0.9162 (pt) cc_final: 0.8778 (tp) REVERT: B 536 SER cc_start: 0.9495 (m) cc_final: 0.8913 (p) REVERT: B 573 LEU cc_start: 0.8800 (tp) cc_final: 0.8405 (mm) REVERT: B 590 LEU cc_start: 0.8441 (mt) cc_final: 0.8216 (mt) REVERT: B 892 ILE cc_start: 0.9272 (mm) cc_final: 0.9044 (mp) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.0922 time to fit residues: 46.2638 Evaluate side-chains 235 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 65 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 700 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.141787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110620 restraints weight = 20749.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112650 restraints weight = 15751.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113941 restraints weight = 10930.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114301 restraints weight = 9326.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114610 restraints weight = 8573.073| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13720 Z= 0.189 Angle : 0.638 8.485 18688 Z= 0.321 Chirality : 0.044 0.262 2224 Planarity : 0.004 0.036 2305 Dihedral : 4.897 26.942 2021 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.07 % Allowed : 3.47 % Favored : 96.46 % 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: 0.35 (0.21), residues: 1738 helix: 1.47 (0.17), residues: 964 sheet: -1.67 (0.42), residues: 130 loop : -1.27 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 886 TYR 0.012 0.001 TYR B 650 PHE 0.026 0.002 PHE B 775 TRP 0.021 0.001 TRP A 630 HIS 0.007 0.001 HIS B 790 Details of bonding type rmsd covalent geometry : bond 0.00435 (13706) covalent geometry : angle 0.63198 (18652) SS BOND : bond 0.00563 ( 6) SS BOND : angle 2.37668 ( 12) hydrogen bonds : bond 0.04168 ( 799) hydrogen bonds : angle 4.25507 ( 2307) link_BETA1-4 : bond 0.00231 ( 4) link_BETA1-4 : angle 2.05055 ( 12) link_NAG-ASN : bond 0.00420 ( 4) link_NAG-ASN : angle 1.68562 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.8650 (t) cc_final: 0.8244 (p) REVERT: A 453 ASN cc_start: 0.8725 (t0) cc_final: 0.8501 (t0) REVERT: A 505 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7945 (ptmt) REVERT: A 597 MET cc_start: 0.9041 (tpp) cc_final: 0.8637 (tpp) REVERT: A 601 MET cc_start: 0.9002 (tpp) cc_final: 0.8676 (tpp) REVERT: A 637 MET cc_start: 0.8996 (ttm) cc_final: 0.8095 (tmm) REVERT: A 864 TRP cc_start: 0.8226 (t60) cc_final: 0.7871 (t60) REVERT: B 397 TRP cc_start: 0.8296 (m100) cc_final: 0.8033 (m100) REVERT: B 436 LEU cc_start: 0.9082 (tp) cc_final: 0.8881 (tt) REVERT: B 523 ILE cc_start: 0.9184 (pt) cc_final: 0.8807 (tp) REVERT: B 536 SER cc_start: 0.9493 (m) cc_final: 0.8931 (p) REVERT: B 573 LEU cc_start: 0.8845 (tp) cc_final: 0.8470 (mm) REVERT: B 590 LEU cc_start: 0.8482 (mt) cc_final: 0.8221 (mt) REVERT: B 867 HIS cc_start: 0.6890 (OUTLIER) cc_final: 0.6425 (t-90) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.0976 time to fit residues: 45.7342 Evaluate side-chains 230 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 60 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114017 restraints weight = 20723.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116185 restraints weight = 15450.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117198 restraints weight = 10869.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117400 restraints weight = 9297.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118731 restraints weight = 8678.899| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13720 Z= 0.123 Angle : 0.567 8.955 18688 Z= 0.287 Chirality : 0.042 0.195 2224 Planarity : 0.003 0.040 2305 Dihedral : 4.401 21.265 2021 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 0.58 (0.21), residues: 1738 helix: 1.63 (0.17), residues: 978 sheet: -1.32 (0.44), residues: 130 loop : -1.23 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 454 TYR 0.016 0.001 TYR A 425 PHE 0.021 0.001 PHE B 775 TRP 0.031 0.001 TRP B 355 HIS 0.006 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00271 (13706) covalent geometry : angle 0.56305 (18652) SS BOND : bond 0.00357 ( 6) SS BOND : angle 1.62788 ( 12) hydrogen bonds : bond 0.03873 ( 799) hydrogen bonds : angle 4.15679 ( 2307) link_BETA1-4 : bond 0.00362 ( 4) link_BETA1-4 : angle 1.78814 ( 12) link_NAG-ASN : bond 0.00097 ( 4) link_NAG-ASN : angle 1.54904 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 314 SER cc_start: 0.8564 (t) cc_final: 0.8176 (p) REVERT: A 453 ASN cc_start: 0.8709 (t0) cc_final: 0.8466 (t0) REVERT: A 481 LEU cc_start: 0.8577 (mt) cc_final: 0.8244 (tt) REVERT: A 505 LYS cc_start: 0.8347 (mmmt) cc_final: 0.7933 (ptmt) REVERT: A 597 MET cc_start: 0.8992 (tpp) cc_final: 0.8644 (tpp) REVERT: A 601 MET cc_start: 0.8924 (tpp) cc_final: 0.8479 (tpp) REVERT: A 637 MET cc_start: 0.9028 (ttm) cc_final: 0.8053 (tmm) REVERT: A 644 MET cc_start: 0.9130 (mtp) cc_final: 0.8197 (ttm) REVERT: A 822 TRP cc_start: 0.8262 (p-90) cc_final: 0.7787 (p-90) REVERT: A 1067 ASP cc_start: 0.8492 (p0) cc_final: 0.8263 (p0) REVERT: B 397 TRP cc_start: 0.8252 (m100) cc_final: 0.7993 (m100) REVERT: B 436 LEU cc_start: 0.8982 (tp) cc_final: 0.8736 (tp) REVERT: B 470 ILE cc_start: 0.9106 (mt) cc_final: 0.8880 (mt) REVERT: B 523 ILE cc_start: 0.9169 (pt) cc_final: 0.8791 (tp) REVERT: B 536 SER cc_start: 0.9476 (m) cc_final: 0.8847 (p) REVERT: B 573 LEU cc_start: 0.8772 (tp) cc_final: 0.8362 (mm) REVERT: B 590 LEU cc_start: 0.8400 (mt) cc_final: 0.8161 (mt) REVERT: B 863 TRP cc_start: 0.8649 (m100) cc_final: 0.8328 (m100) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1040 time to fit residues: 49.3652 Evaluate side-chains 234 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 137 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 85 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 859 ASN B 867 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117538 restraints weight = 20860.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118575 restraints weight = 15106.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120280 restraints weight = 11424.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120903 restraints weight = 9493.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121261 restraints weight = 8648.217| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13720 Z= 0.143 Angle : 0.582 8.346 18688 Z= 0.295 Chirality : 0.042 0.193 2224 Planarity : 0.004 0.081 2305 Dihedral : 4.338 20.410 2021 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % 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 (0.21), residues: 1738 helix: 1.64 (0.17), residues: 984 sheet: -1.15 (0.44), residues: 130 loop : -1.08 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 886 TYR 0.012 0.001 TYR A 628 PHE 0.020 0.001 PHE B 775 TRP 0.027 0.001 TRP B 355 HIS 0.005 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00329 (13706) covalent geometry : angle 0.57807 (18652) SS BOND : bond 0.00406 ( 6) SS BOND : angle 1.97962 ( 12) hydrogen bonds : bond 0.03826 ( 799) hydrogen bonds : angle 4.14116 ( 2307) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 1.59893 ( 12) link_NAG-ASN : bond 0.00214 ( 4) link_NAG-ASN : angle 1.58515 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8554 (mp) cc_final: 0.8320 (mp) REVERT: A 314 SER cc_start: 0.8614 (t) cc_final: 0.8202 (p) REVERT: A 453 ASN cc_start: 0.8743 (t0) cc_final: 0.8464 (t0) REVERT: A 505 LYS cc_start: 0.8394 (mmmt) cc_final: 0.7983 (ptmt) REVERT: A 597 MET cc_start: 0.9045 (tpp) cc_final: 0.8597 (tpp) REVERT: A 601 MET cc_start: 0.8325 (tpp) cc_final: 0.8115 (tpp) REVERT: A 644 MET cc_start: 0.8712 (mtp) cc_final: 0.8477 (ttm) REVERT: A 822 TRP cc_start: 0.8347 (p-90) cc_final: 0.7945 (p-90) REVERT: B 397 TRP cc_start: 0.8238 (m100) cc_final: 0.7978 (m100) REVERT: B 436 LEU cc_start: 0.8992 (tp) cc_final: 0.8747 (tp) REVERT: B 470 ILE cc_start: 0.9064 (mt) cc_final: 0.8862 (mt) REVERT: B 523 ILE cc_start: 0.9196 (pt) cc_final: 0.8830 (tp) REVERT: B 536 SER cc_start: 0.9482 (m) cc_final: 0.8867 (p) REVERT: B 573 LEU cc_start: 0.8788 (tp) cc_final: 0.8392 (mm) REVERT: B 590 LEU cc_start: 0.8410 (mt) cc_final: 0.8177 (mt) REVERT: B 661 MET cc_start: 0.6929 (tmm) cc_final: 0.6627 (tmm) REVERT: B 863 TRP cc_start: 0.8688 (m100) cc_final: 0.8426 (m100) REVERT: B 867 HIS cc_start: 0.6887 (OUTLIER) cc_final: 0.6470 (t-90) outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.0969 time to fit residues: 44.5089 Evaluate side-chains 233 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 144 optimal weight: 0.0870 chunk 2 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 142 optimal weight: 0.0970 chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 106 optimal weight: 0.0470 chunk 82 optimal weight: 0.9990 overall best weight: 0.8458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.117577 restraints weight = 20655.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118972 restraints weight = 13187.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120484 restraints weight = 10476.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121827 restraints weight = 8393.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122021 restraints weight = 7803.628| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13720 Z= 0.119 Angle : 0.558 8.334 18688 Z= 0.282 Chirality : 0.041 0.149 2224 Planarity : 0.003 0.060 2305 Dihedral : 4.188 19.495 2021 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 0.87 (0.21), residues: 1738 helix: 1.76 (0.17), residues: 982 sheet: -0.83 (0.44), residues: 138 loop : -1.03 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 497 TYR 0.012 0.001 TYR A 628 PHE 0.024 0.001 PHE B 373 TRP 0.027 0.001 TRP A 630 HIS 0.006 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00268 (13706) covalent geometry : angle 0.55463 (18652) SS BOND : bond 0.00287 ( 6) SS BOND : angle 1.62062 ( 12) hydrogen bonds : bond 0.03662 ( 799) hydrogen bonds : angle 4.06294 ( 2307) link_BETA1-4 : bond 0.00363 ( 4) link_BETA1-4 : angle 1.42889 ( 12) link_NAG-ASN : bond 0.00070 ( 4) link_NAG-ASN : angle 1.56700 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 267 MET cc_start: 0.8502 (tpp) cc_final: 0.7976 (tpp) REVERT: A 314 SER cc_start: 0.8607 (t) cc_final: 0.8197 (p) REVERT: A 449 MET cc_start: 0.8544 (mmm) cc_final: 0.8078 (mmm) REVERT: A 505 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8069 (pttt) REVERT: A 597 MET cc_start: 0.9003 (tpp) cc_final: 0.8647 (tpp) REVERT: A 872 LEU cc_start: 0.8934 (mt) cc_final: 0.8378 (mt) REVERT: B 146 GLN cc_start: 0.8235 (tt0) cc_final: 0.7883 (tt0) REVERT: B 314 SER cc_start: 0.8910 (p) cc_final: 0.8676 (p) REVERT: B 372 TYR cc_start: 0.7743 (t80) cc_final: 0.7522 (t80) REVERT: B 436 LEU cc_start: 0.8941 (tp) cc_final: 0.8675 (tp) REVERT: B 523 ILE cc_start: 0.9212 (pt) cc_final: 0.8820 (tp) REVERT: B 536 SER cc_start: 0.9494 (m) cc_final: 0.8853 (p) REVERT: B 573 LEU cc_start: 0.8734 (tp) cc_final: 0.8330 (mm) REVERT: B 590 LEU cc_start: 0.8339 (mt) cc_final: 0.8104 (mt) REVERT: B 661 MET cc_start: 0.6996 (tmm) cc_final: 0.6677 (tmm) REVERT: B 863 TRP cc_start: 0.8700 (m100) cc_final: 0.8342 (m100) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1017 time to fit residues: 48.1461 Evaluate side-chains 239 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 154 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118114 restraints weight = 20340.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118927 restraints weight = 14242.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120355 restraints weight = 11299.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121399 restraints weight = 9319.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121517 restraints weight = 8339.885| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13720 Z= 0.133 Angle : 0.588 8.079 18688 Z= 0.295 Chirality : 0.042 0.167 2224 Planarity : 0.003 0.048 2305 Dihedral : 4.201 19.570 2021 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.07 % Allowed : 1.01 % Favored : 98.92 % 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: 0.83 (0.21), residues: 1738 helix: 1.72 (0.17), residues: 990 sheet: -0.85 (0.44), residues: 138 loop : -1.08 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 886 TYR 0.013 0.001 TYR A 372 PHE 0.019 0.001 PHE B 775 TRP 0.029 0.001 TRP A 630 HIS 0.006 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00303 (13706) covalent geometry : angle 0.58394 (18652) SS BOND : bond 0.00370 ( 6) SS BOND : angle 1.71967 ( 12) hydrogen bonds : bond 0.03702 ( 799) hydrogen bonds : angle 4.06258 ( 2307) link_BETA1-4 : bond 0.00362 ( 4) link_BETA1-4 : angle 1.41906 ( 12) link_NAG-ASN : bond 0.00197 ( 4) link_NAG-ASN : angle 1.65655 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8529 (tpp) cc_final: 0.8010 (tpp) REVERT: A 314 SER cc_start: 0.8582 (t) cc_final: 0.8175 (p) REVERT: A 449 MET cc_start: 0.8659 (mmm) cc_final: 0.8422 (tpp) REVERT: A 487 PHE cc_start: 0.8302 (m-80) cc_final: 0.7950 (m-80) REVERT: A 505 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8051 (pttt) REVERT: B 134 MET cc_start: 0.6868 (mtt) cc_final: 0.6652 (mtt) REVERT: B 146 GLN cc_start: 0.8287 (tt0) cc_final: 0.7953 (tt0) REVERT: B 372 TYR cc_start: 0.7793 (t80) cc_final: 0.7584 (t80) REVERT: B 436 LEU cc_start: 0.8966 (tp) cc_final: 0.8667 (tp) REVERT: B 470 ILE cc_start: 0.9047 (mt) cc_final: 0.8810 (mt) REVERT: B 518 PRO cc_start: 0.9052 (Cg_endo) cc_final: 0.8852 (Cg_exo) REVERT: B 523 ILE cc_start: 0.9235 (pt) cc_final: 0.8847 (tp) REVERT: B 536 SER cc_start: 0.9506 (m) cc_final: 0.8874 (p) REVERT: B 573 LEU cc_start: 0.8753 (tp) cc_final: 0.8363 (mm) REVERT: B 590 LEU cc_start: 0.8359 (mt) cc_final: 0.8150 (mt) REVERT: B 601 MET cc_start: 0.8820 (tpp) cc_final: 0.8171 (tpp) REVERT: B 661 MET cc_start: 0.7080 (tmm) cc_final: 0.6639 (tmm) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.0923 time to fit residues: 42.3270 Evaluate side-chains 231 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 129 optimal weight: 0.0030 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN ** B 790 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 = 0.3759 r_free = 0.3759 target = 0.151080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.120272 restraints weight = 20563.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122559 restraints weight = 13646.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123752 restraints weight = 10578.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124935 restraints weight = 8499.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125185 restraints weight = 7801.006| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13720 Z= 0.111 Angle : 0.578 8.720 18688 Z= 0.288 Chirality : 0.041 0.199 2224 Planarity : 0.003 0.039 2305 Dihedral : 4.142 18.423 2021 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 0.91 (0.21), residues: 1738 helix: 1.78 (0.17), residues: 990 sheet: -0.69 (0.45), residues: 138 loop : -1.05 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 886 TYR 0.011 0.001 TYR A 628 PHE 0.019 0.001 PHE B 775 TRP 0.031 0.001 TRP A 630 HIS 0.007 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00241 (13706) covalent geometry : angle 0.57506 (18652) SS BOND : bond 0.00276 ( 6) SS BOND : angle 1.61502 ( 12) hydrogen bonds : bond 0.03537 ( 799) hydrogen bonds : angle 4.03738 ( 2307) link_BETA1-4 : bond 0.00388 ( 4) link_BETA1-4 : angle 1.31016 ( 12) link_NAG-ASN : bond 0.00072 ( 4) link_NAG-ASN : angle 1.56502 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8583 (tpp) cc_final: 0.8015 (tpp) REVERT: A 487 PHE cc_start: 0.8254 (m-10) cc_final: 0.7900 (m-80) REVERT: A 505 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8021 (pttt) REVERT: A 644 MET cc_start: 0.7623 (ttp) cc_final: 0.7284 (ttp) REVERT: A 672 GLU cc_start: 0.8080 (tt0) cc_final: 0.7770 (tm-30) REVERT: B 109 THR cc_start: 0.8775 (m) cc_final: 0.8450 (t) REVERT: B 146 GLN cc_start: 0.8154 (tt0) cc_final: 0.7905 (tt0) REVERT: B 372 TYR cc_start: 0.7834 (t80) cc_final: 0.7631 (t80) REVERT: B 436 LEU cc_start: 0.8840 (tp) cc_final: 0.8565 (tp) REVERT: B 523 ILE cc_start: 0.9165 (pt) cc_final: 0.8808 (tp) REVERT: B 536 SER cc_start: 0.9493 (m) cc_final: 0.8890 (p) REVERT: B 573 LEU cc_start: 0.8718 (tp) cc_final: 0.8294 (mm) REVERT: B 601 MET cc_start: 0.8865 (tpp) cc_final: 0.8232 (tpp) REVERT: B 635 MET cc_start: 0.7899 (tpt) cc_final: 0.7519 (tpp) REVERT: B 661 MET cc_start: 0.7079 (tmm) cc_final: 0.6588 (tmm) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.0920 time to fit residues: 44.5485 Evaluate side-chains 239 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 24 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116456 restraints weight = 20591.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117688 restraints weight = 14381.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119139 restraints weight = 10963.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.119680 restraints weight = 9247.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120021 restraints weight = 8505.144| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13720 Z= 0.164 Angle : 0.617 9.155 18688 Z= 0.310 Chirality : 0.043 0.186 2224 Planarity : 0.004 0.037 2305 Dihedral : 4.261 20.086 2021 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.07 % Allowed : 0.29 % Favored : 99.64 % 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: 0.85 (0.21), residues: 1738 helix: 1.78 (0.17), residues: 986 sheet: -0.86 (0.44), residues: 138 loop : -1.11 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 693 TYR 0.010 0.001 TYR B 663 PHE 0.018 0.001 PHE A 221 TRP 0.028 0.001 TRP A 630 HIS 0.006 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00384 (13706) covalent geometry : angle 0.61414 (18652) SS BOND : bond 0.00319 ( 6) SS BOND : angle 1.70649 ( 12) hydrogen bonds : bond 0.03780 ( 799) hydrogen bonds : angle 4.09986 ( 2307) link_BETA1-4 : bond 0.00316 ( 4) link_BETA1-4 : angle 1.42743 ( 12) link_NAG-ASN : bond 0.00246 ( 4) link_NAG-ASN : angle 1.58569 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8619 (tpp) cc_final: 0.8025 (tpp) REVERT: A 487 PHE cc_start: 0.8346 (m-10) cc_final: 0.7990 (m-80) REVERT: A 505 LYS cc_start: 0.8479 (mmmt) cc_final: 0.8080 (pttt) REVERT: B 146 GLN cc_start: 0.8301 (tt0) cc_final: 0.7986 (tt0) REVERT: B 372 TYR cc_start: 0.7908 (t80) cc_final: 0.7667 (t80) REVERT: B 523 ILE cc_start: 0.9185 (pt) cc_final: 0.8818 (tp) REVERT: B 536 SER cc_start: 0.9514 (m) cc_final: 0.8943 (p) REVERT: B 573 LEU cc_start: 0.8782 (tp) cc_final: 0.8363 (mm) REVERT: B 590 LEU cc_start: 0.8449 (mt) cc_final: 0.8236 (mt) REVERT: B 601 MET cc_start: 0.8891 (tpp) cc_final: 0.8301 (tpp) REVERT: B 650 TYR cc_start: 0.7955 (p90) cc_final: 0.7732 (p90) REVERT: B 661 MET cc_start: 0.7127 (tmm) cc_final: 0.6613 (tmm) outliers start: 1 outliers final: 0 residues processed: 289 average time/residue: 0.0932 time to fit residues: 42.7459 Evaluate side-chains 231 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 19 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 166 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117404 restraints weight = 20499.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118472 restraints weight = 15423.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120118 restraints weight = 11610.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120647 restraints weight = 9992.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120885 restraints weight = 8766.969| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13720 Z= 0.145 Angle : 0.611 8.426 18688 Z= 0.304 Chirality : 0.043 0.189 2224 Planarity : 0.004 0.037 2305 Dihedral : 4.253 19.087 2021 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.14 % Allowed : 0.36 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.21), residues: 1738 helix: 1.81 (0.17), residues: 984 sheet: -0.87 (0.44), residues: 138 loop : -1.13 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 886 TYR 0.011 0.001 TYR B 650 PHE 0.018 0.001 PHE A 221 TRP 0.032 0.001 TRP A 630 HIS 0.005 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00336 (13706) covalent geometry : angle 0.60768 (18652) SS BOND : bond 0.00318 ( 6) SS BOND : angle 1.61320 ( 12) hydrogen bonds : bond 0.03719 ( 799) hydrogen bonds : angle 4.08224 ( 2307) link_BETA1-4 : bond 0.00287 ( 4) link_BETA1-4 : angle 1.34459 ( 12) link_NAG-ASN : bond 0.00157 ( 4) link_NAG-ASN : angle 1.50685 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.54 seconds wall clock time: 36 minutes 36.91 seconds (2196.91 seconds total)