Starting phenix.real_space_refine on Thu Jul 31 12:00:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5v_10704/07_2025/6y5v_10704.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5v_10704/07_2025/6y5v_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6y5v_10704/07_2025/6y5v_10704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5v_10704/07_2025/6y5v_10704.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5v_10704/07_2025/6y5v_10704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5v_10704/07_2025/6y5v_10704.cif" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 14, 'ARG:plan': 3} 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: 7.63, per 1000 atoms: 0.57 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.46 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: 4.29 Time building geometry restraints manager: 3.70 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 1093 or resid 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 1093 or resid 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.720 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.800 ------------------------------------------------------------------------------- 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 : 7.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (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 TRP 0.015 0.002 TRP B 570 HIS 0.011 0.001 HIS A 867 PHE 0.017 0.001 PHE B 847 TYR 0.020 0.002 TYR A 935 ARG 0.003 0.000 ARG A1083 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 4) link_NAG-ASN : angle 2.24978 ( 12) link_BETA1-4 : bond 0.00215 ( 4) link_BETA1-4 : angle 1.64024 ( 12) hydrogen bonds : bond 0.11334 ( 799) hydrogen bonds : angle 5.42428 ( 2307) SS BOND : bond 0.00543 ( 6) SS BOND : angle 1.42889 ( 12) covalent geometry : bond 0.00416 (13706) covalent geometry : angle 0.68121 (18652) *********************** 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 : 1.503 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: 0.8981 (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: 0.6742 (mtt180) REVERT: A 360 ASN cc_start: 0.7688 (m-40) cc_final: 0.7405 (p0) REVERT: A 536 SER cc_start: 0.9398 (m) cc_final: 0.9131 (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: 0.8494 (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: 0.8023 (t80) REVERT: A 707 GLN cc_start: 0.9296 (mm-40) cc_final: 0.9017 (mm110) REVERT: B 278 MET cc_start: 0.8579 (mmp) cc_final: 0.8098 (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: 0.7454 (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: 0.8747 (tp) REVERT: B 536 SER cc_start: 0.9471 (m) cc_final: 0.9205 (p) REVERT: B 562 SER cc_start: 0.8845 (m) cc_final: 0.8573 (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: 0.8589 (tpp) cc_final: 0.8290 (tpp) REVERT: B 863 TRP cc_start: 0.8545 (m100) cc_final: 0.8007 (m100) REVERT: B 886 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8023 (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: 0.2398 time to fit residues: 147.6471 Evaluate side-chains 269 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 267 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 136 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS A1040 ASN B 133 GLN B 483 ASN B 613 GLN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112529 restraints weight = 20442.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114918 restraints weight = 15608.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116137 restraints weight = 11638.273| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13720 Z= 0.137 Angle : 0.603 9.034 18688 Z= 0.307 Chirality : 0.042 0.245 2224 Planarity : 0.004 0.046 2305 Dihedral : 7.371 69.850 2021 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.14 % Allowed : 2.96 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1738 helix: 0.90 (0.16), residues: 960 sheet: -1.73 (0.44), residues: 100 loop : -1.70 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 355 HIS 0.006 0.001 HIS A 915 PHE 0.016 0.001 PHE A1073 TYR 0.021 0.001 TYR A 935 ARG 0.009 0.000 ARG A 497 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 4) link_NAG-ASN : angle 1.86999 ( 12) link_BETA1-4 : bond 0.00254 ( 4) link_BETA1-4 : angle 2.17462 ( 12) hydrogen bonds : bond 0.04297 ( 799) hydrogen bonds : angle 4.40416 ( 2307) SS BOND : bond 0.00455 ( 6) SS BOND : angle 3.11225 ( 12) covalent geometry : bond 0.00307 (13706) covalent geometry : angle 0.59370 (18652) *********************** 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 343 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 341 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ILE cc_start: 0.9275 (mt) cc_final: 0.8978 (tt) REVERT: A 505 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7856 (ptmt) REVERT: A 536 SER cc_start: 0.9326 (m) cc_final: 0.9068 (t) REVERT: A 590 LEU cc_start: 0.8673 (mt) cc_final: 0.8450 (mp) REVERT: A 601 MET cc_start: 0.9120 (tpp) cc_final: 0.8359 (tpp) REVERT: A 628 TYR cc_start: 0.8257 (t80) cc_final: 0.7975 (t80) REVERT: A 639 ILE cc_start: 0.8780 (tt) cc_final: 0.8486 (tt) REVERT: A 803 ASN cc_start: 0.8815 (p0) cc_final: 0.8247 (p0) REVERT: A 1038 LYS cc_start: 0.9177 (tttt) cc_final: 0.8976 (ttmt) REVERT: B 108 LEU cc_start: 0.9249 (mt) cc_final: 0.8989 (mt) REVERT: B 278 MET cc_start: 0.8528 (mmp) cc_final: 0.8058 (mmp) REVERT: B 372 TYR cc_start: 0.7879 (t80) cc_final: 0.7470 (t80) REVERT: B 381 ILE cc_start: 0.7440 (mt) cc_final: 0.7020 (mm) REVERT: B 445 VAL cc_start: 0.9453 (m) cc_final: 0.9155 (t) REVERT: B 523 ILE cc_start: 0.9174 (pt) cc_final: 0.8750 (tp) REVERT: B 536 SER cc_start: 0.9484 (m) cc_final: 0.9020 (p) REVERT: B 573 LEU cc_start: 0.8845 (tp) cc_final: 0.8443 (mm) REVERT: B 597 MET cc_start: 0.9314 (tpp) cc_final: 0.9044 (tpp) REVERT: B 707 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7970 (mp10) REVERT: B 867 HIS cc_start: 0.6715 (OUTLIER) cc_final: 0.6476 (t-170) REVERT: B 886 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7955 (ttm-80) REVERT: B 892 ILE cc_start: 0.9262 (mm) cc_final: 0.9040 (mp) outliers start: 2 outliers final: 0 residues processed: 343 average time/residue: 0.2456 time to fit residues: 127.9933 Evaluate side-chains 250 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 120 optimal weight: 5.9990 chunk 89 optimal weight: 0.0870 chunk 132 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS B 915 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112092 restraints weight = 20790.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113124 restraints weight = 14734.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114471 restraints weight = 11034.919| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13720 Z= 0.123 Angle : 0.569 9.335 18688 Z= 0.289 Chirality : 0.042 0.176 2224 Planarity : 0.004 0.068 2305 Dihedral : 5.731 47.206 2021 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1738 helix: 1.42 (0.17), residues: 968 sheet: -1.81 (0.43), residues: 134 loop : -1.42 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 864 HIS 0.007 0.001 HIS B 915 PHE 0.012 0.001 PHE B 555 TYR 0.015 0.001 TYR A 935 ARG 0.006 0.000 ARG A 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 4) link_NAG-ASN : angle 1.77572 ( 12) link_BETA1-4 : bond 0.00639 ( 4) link_BETA1-4 : angle 2.21812 ( 12) hydrogen bonds : bond 0.03955 ( 799) hydrogen bonds : angle 4.24536 ( 2307) SS BOND : bond 0.00590 ( 6) SS BOND : angle 2.38219 ( 12) covalent geometry : bond 0.00263 (13706) covalent geometry : angle 0.56126 (18652) *********************** 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 323 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 321 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8493 (mp) cc_final: 0.8263 (mp) REVERT: A 314 SER cc_start: 0.8640 (t) cc_final: 0.8274 (p) REVERT: A 453 ASN cc_start: 0.8630 (t0) cc_final: 0.8342 (t0) REVERT: A 505 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7851 (ptmt) REVERT: A 536 SER cc_start: 0.9342 (m) cc_final: 0.9106 (t) REVERT: A 597 MET cc_start: 0.8834 (tpp) cc_final: 0.8479 (tpp) REVERT: A 601 MET cc_start: 0.9131 (tpp) cc_final: 0.8677 (tpp) REVERT: A 637 MET cc_start: 0.9157 (ttm) cc_final: 0.8092 (tmm) REVERT: A 724 ARG cc_start: 0.8278 (mmp-170) cc_final: 0.7952 (mmp-170) REVERT: A 766 LEU cc_start: 0.9088 (tp) cc_final: 0.8873 (tp) REVERT: A 1057 MET cc_start: 0.8126 (mtm) cc_final: 0.7601 (ptm) REVERT: A 1071 MET cc_start: 0.8436 (tpt) cc_final: 0.8183 (tpp) REVERT: B 172 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7614 (mt) REVERT: B 301 ILE cc_start: 0.9160 (mm) cc_final: 0.8923 (mm) REVERT: B 312 ILE cc_start: 0.8694 (mm) cc_final: 0.8390 (pt) REVERT: B 381 ILE cc_start: 0.7470 (mt) cc_final: 0.6993 (mm) REVERT: B 523 ILE cc_start: 0.9140 (pt) cc_final: 0.8771 (tp) REVERT: B 536 SER cc_start: 0.9473 (m) cc_final: 0.8890 (p) REVERT: B 573 LEU cc_start: 0.8791 (tp) cc_final: 0.8400 (mm) REVERT: B 590 LEU cc_start: 0.8399 (mt) cc_final: 0.8181 (mt) REVERT: B 707 GLN cc_start: 0.8478 (mm-40) cc_final: 0.7932 (mp10) REVERT: B 892 ILE cc_start: 0.9304 (mm) cc_final: 0.9059 (mp) outliers start: 2 outliers final: 0 residues processed: 322 average time/residue: 0.2048 time to fit residues: 102.3919 Evaluate side-chains 247 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 148 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 110 optimal weight: 0.4980 chunk 82 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 290 ASN ** 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 = 0.3660 r_free = 0.3660 target = 0.142508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110980 restraints weight = 20666.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112176 restraints weight = 16152.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113323 restraints weight = 12236.408| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13720 Z= 0.188 Angle : 0.620 8.210 18688 Z= 0.315 Chirality : 0.044 0.165 2224 Planarity : 0.004 0.036 2305 Dihedral : 4.874 26.849 2021 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.07 % Allowed : 3.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1738 helix: 1.52 (0.17), residues: 962 sheet: -1.72 (0.42), residues: 130 loop : -1.27 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 864 HIS 0.006 0.001 HIS A 802 PHE 0.014 0.001 PHE B 555 TYR 0.013 0.001 TYR A 628 ARG 0.006 0.001 ARG B 886 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 4) link_NAG-ASN : angle 1.78140 ( 12) link_BETA1-4 : bond 0.00254 ( 4) link_BETA1-4 : angle 2.07619 ( 12) hydrogen bonds : bond 0.04145 ( 799) hydrogen bonds : angle 4.27181 ( 2307) SS BOND : bond 0.00296 ( 6) SS BOND : angle 2.33524 ( 12) covalent geometry : bond 0.00434 (13706) covalent geometry : angle 0.61400 (18652) *********************** 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 309 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8624 (mp) cc_final: 0.8299 (mp) REVERT: A 314 SER cc_start: 0.8614 (t) cc_final: 0.8223 (p) REVERT: A 453 ASN cc_start: 0.8635 (t0) cc_final: 0.8372 (t0) REVERT: A 505 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8018 (ptmt) REVERT: A 601 MET cc_start: 0.9178 (tpp) cc_final: 0.8931 (tpp) REVERT: A 637 MET cc_start: 0.9212 (ttm) cc_final: 0.8047 (tmm) REVERT: A 766 LEU cc_start: 0.9092 (tp) cc_final: 0.8891 (tp) REVERT: A 822 TRP cc_start: 0.8625 (p-90) cc_final: 0.7261 (p-90) REVERT: A 1071 MET cc_start: 0.8475 (tpt) cc_final: 0.8151 (tpp) REVERT: B 312 ILE cc_start: 0.8630 (mm) cc_final: 0.8424 (pt) REVERT: B 523 ILE cc_start: 0.9177 (pt) cc_final: 0.8809 (tp) REVERT: B 536 SER cc_start: 0.9521 (m) cc_final: 0.8959 (p) REVERT: B 573 LEU cc_start: 0.8853 (tp) cc_final: 0.8476 (mm) REVERT: B 590 LEU cc_start: 0.8469 (mt) cc_final: 0.8222 (mt) REVERT: B 597 MET cc_start: 0.9386 (tpt) cc_final: 0.9053 (tpp) REVERT: B 867 HIS cc_start: 0.6902 (OUTLIER) cc_final: 0.6414 (t-90) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.2183 time to fit residues: 103.4485 Evaluate side-chains 227 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 113 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 120 optimal weight: 0.0170 chunk 108 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** B 107 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113092 restraints weight = 20675.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114226 restraints weight = 15674.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115598 restraints weight = 11878.705| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13720 Z= 0.141 Angle : 0.574 9.326 18688 Z= 0.291 Chirality : 0.042 0.206 2224 Planarity : 0.003 0.033 2305 Dihedral : 4.421 22.273 2021 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1738 helix: 1.63 (0.17), residues: 974 sheet: -1.45 (0.43), residues: 130 loop : -1.25 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 630 HIS 0.005 0.001 HIS A 915 PHE 0.014 0.001 PHE B 848 TYR 0.013 0.001 TYR B 650 ARG 0.003 0.000 ARG A 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 4) link_NAG-ASN : angle 1.62009 ( 12) link_BETA1-4 : bond 0.00402 ( 4) link_BETA1-4 : angle 1.76269 ( 12) hydrogen bonds : bond 0.03905 ( 799) hydrogen bonds : angle 4.15828 ( 2307) SS BOND : bond 0.00275 ( 6) SS BOND : angle 1.80696 ( 12) covalent geometry : bond 0.00324 (13706) covalent geometry : angle 0.56977 (18652) *********************** 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 300 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8559 (mp) cc_final: 0.8167 (mp) REVERT: A 314 SER cc_start: 0.8586 (t) cc_final: 0.8178 (p) REVERT: A 449 MET cc_start: 0.8441 (mmm) cc_final: 0.8196 (mmt) REVERT: A 453 ASN cc_start: 0.8706 (t0) cc_final: 0.8383 (t0) REVERT: A 505 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8044 (pttt) REVERT: A 601 MET cc_start: 0.9118 (tpp) cc_final: 0.8704 (tpp) REVERT: A 637 MET cc_start: 0.9167 (ttm) cc_final: 0.8018 (tmm) REVERT: A 822 TRP cc_start: 0.8275 (p-90) cc_final: 0.7793 (p-90) REVERT: A 864 TRP cc_start: 0.8220 (t60) cc_final: 0.7867 (t60) REVERT: A 1071 MET cc_start: 0.8426 (tpt) cc_final: 0.8065 (tpp) REVERT: B 381 ILE cc_start: 0.7798 (mm) cc_final: 0.7403 (mm) REVERT: B 396 LEU cc_start: 0.9054 (mt) cc_final: 0.8816 (mt) REVERT: B 470 ILE cc_start: 0.9128 (mt) cc_final: 0.8911 (mt) REVERT: B 523 ILE cc_start: 0.9203 (pt) cc_final: 0.8826 (tp) REVERT: B 536 SER cc_start: 0.9500 (m) cc_final: 0.8893 (p) REVERT: B 573 LEU cc_start: 0.8820 (tp) cc_final: 0.8434 (mm) REVERT: B 590 LEU cc_start: 0.8404 (mt) cc_final: 0.8175 (mt) REVERT: B 601 MET cc_start: 0.8958 (tpp) cc_final: 0.8252 (tpp) REVERT: B 661 MET cc_start: 0.6946 (tmm) cc_final: 0.6510 (tmm) REVERT: B 863 TRP cc_start: 0.8686 (m100) cc_final: 0.8357 (m100) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2020 time to fit residues: 94.3957 Evaluate side-chains 236 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 125 optimal weight: 0.4980 chunk 159 optimal weight: 0.0070 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 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 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 = 0.3746 r_free = 0.3746 target = 0.149726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117580 restraints weight = 20744.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120118 restraints weight = 15218.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121591 restraints weight = 10745.623| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3459 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= 0.117 Angle : 0.568 9.007 18688 Z= 0.284 Chirality : 0.042 0.199 2224 Planarity : 0.003 0.053 2305 Dihedral : 4.257 19.577 2021 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.07 % Allowed : 1.16 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1738 helix: 1.80 (0.17), residues: 976 sheet: -1.20 (0.44), residues: 130 loop : -1.21 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 630 HIS 0.006 0.001 HIS A 790 PHE 0.012 0.001 PHE B 555 TYR 0.011 0.001 TYR B 372 ARG 0.004 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 4) link_NAG-ASN : angle 1.58151 ( 12) link_BETA1-4 : bond 0.00378 ( 4) link_BETA1-4 : angle 1.50898 ( 12) hydrogen bonds : bond 0.03698 ( 799) hydrogen bonds : angle 4.07491 ( 2307) SS BOND : bond 0.00437 ( 6) SS BOND : angle 1.90231 ( 12) covalent geometry : bond 0.00260 (13706) covalent geometry : angle 0.56371 (18652) *********************** 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 302 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.8557 (t) cc_final: 0.8147 (p) REVERT: A 453 ASN cc_start: 0.8692 (t0) cc_final: 0.8393 (t0) REVERT: A 505 LYS cc_start: 0.8434 (mmmt) cc_final: 0.7995 (ptmt) REVERT: A 553 ILE cc_start: 0.8529 (mt) cc_final: 0.8304 (mt) REVERT: A 601 MET cc_start: 0.9121 (tpp) cc_final: 0.8744 (tpp) REVERT: A 822 TRP cc_start: 0.8304 (p-90) cc_final: 0.7860 (p-90) REVERT: A 1067 ASP cc_start: 0.8458 (p0) cc_final: 0.8175 (p0) REVERT: A 1071 MET cc_start: 0.8426 (tpt) cc_final: 0.8183 (tpp) REVERT: B 381 ILE cc_start: 0.7737 (mm) cc_final: 0.7527 (mm) REVERT: B 470 ILE cc_start: 0.9113 (mt) cc_final: 0.8904 (mt) REVERT: B 523 ILE cc_start: 0.9179 (pt) cc_final: 0.8814 (tp) REVERT: B 536 SER cc_start: 0.9508 (m) cc_final: 0.8924 (p) REVERT: B 573 LEU cc_start: 0.8748 (tp) cc_final: 0.8343 (mm) REVERT: B 590 LEU cc_start: 0.8327 (mt) cc_final: 0.8122 (mt) REVERT: B 601 MET cc_start: 0.8963 (tpp) cc_final: 0.8195 (tpp) REVERT: B 644 MET cc_start: 0.8692 (ttm) cc_final: 0.8073 (ttm) REVERT: B 863 TRP cc_start: 0.8635 (m100) cc_final: 0.8351 (m100) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.2110 time to fit residues: 99.2978 Evaluate side-chains 244 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 47 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 143 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.143654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112027 restraints weight = 21027.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112741 restraints weight = 15265.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114446 restraints weight = 11747.944| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13720 Z= 0.141 Angle : 0.576 7.965 18688 Z= 0.291 Chirality : 0.042 0.163 2224 Planarity : 0.003 0.032 2305 Dihedral : 4.215 20.245 2021 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1738 helix: 1.79 (0.17), residues: 986 sheet: -1.07 (0.44), residues: 130 loop : -1.21 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 630 HIS 0.005 0.001 HIS B 115 PHE 0.014 0.001 PHE B 555 TYR 0.010 0.001 TYR A 628 ARG 0.007 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 4) link_NAG-ASN : angle 1.61793 ( 12) link_BETA1-4 : bond 0.00360 ( 4) link_BETA1-4 : angle 1.47500 ( 12) hydrogen bonds : bond 0.03758 ( 799) hydrogen bonds : angle 4.05768 ( 2307) SS BOND : bond 0.00347 ( 6) SS BOND : angle 1.75753 ( 12) covalent geometry : bond 0.00327 (13706) covalent geometry : angle 0.57241 (18652) *********************** 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 296 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.8593 (t) cc_final: 0.8189 (p) REVERT: A 449 MET cc_start: 0.8547 (mmp) cc_final: 0.8261 (mmp) REVERT: A 453 ASN cc_start: 0.8679 (t0) cc_final: 0.8449 (t0) REVERT: A 505 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8080 (pttt) REVERT: A 553 ILE cc_start: 0.8630 (mt) cc_final: 0.8416 (mt) REVERT: A 601 MET cc_start: 0.8739 (tpp) cc_final: 0.8488 (tpp) REVERT: A 1078 THR cc_start: 0.8445 (t) cc_final: 0.8176 (t) REVERT: B 523 ILE cc_start: 0.9236 (pt) cc_final: 0.8834 (tp) REVERT: B 536 SER cc_start: 0.9516 (m) cc_final: 0.8931 (p) REVERT: B 573 LEU cc_start: 0.8792 (tp) cc_final: 0.8401 (mm) REVERT: B 590 LEU cc_start: 0.8395 (mt) cc_final: 0.8163 (mt) REVERT: B 601 MET cc_start: 0.8946 (tpp) cc_final: 0.8223 (tpp) REVERT: B 644 MET cc_start: 0.8668 (ttm) cc_final: 0.8101 (ttm) REVERT: B 661 MET cc_start: 0.6980 (tmm) cc_final: 0.6554 (tmm) REVERT: B 863 TRP cc_start: 0.8742 (m100) cc_final: 0.8365 (m100) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2232 time to fit residues: 100.9415 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 : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 104 optimal weight: 0.0770 chunk 145 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 141 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN 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 B1056 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119863 restraints weight = 20436.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122509 restraints weight = 12992.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123870 restraints weight = 10362.026| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13720 Z= 0.112 Angle : 0.571 8.647 18688 Z= 0.286 Chirality : 0.042 0.200 2224 Planarity : 0.003 0.031 2305 Dihedral : 4.135 19.158 2021 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.14 % Allowed : 1.23 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1738 helix: 1.78 (0.17), residues: 1000 sheet: -0.86 (0.46), residues: 130 loop : -1.11 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 630 HIS 0.006 0.001 HIS B 115 PHE 0.018 0.001 PHE A 605 TYR 0.012 0.001 TYR A 372 ARG 0.004 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 4) link_NAG-ASN : angle 1.58366 ( 12) link_BETA1-4 : bond 0.00425 ( 4) link_BETA1-4 : angle 1.35606 ( 12) hydrogen bonds : bond 0.03607 ( 799) hydrogen bonds : angle 4.02970 ( 2307) SS BOND : bond 0.00330 ( 6) SS BOND : angle 1.59300 ( 12) covalent geometry : bond 0.00247 (13706) covalent geometry : angle 0.56725 (18652) *********************** 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 302 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 300 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8865 (ttm) cc_final: 0.8610 (ttm) REVERT: A 314 SER cc_start: 0.8564 (t) cc_final: 0.8149 (p) REVERT: A 449 MET cc_start: 0.8477 (mmp) cc_final: 0.8195 (mmp) REVERT: A 481 LEU cc_start: 0.8548 (mt) cc_final: 0.8222 (tt) REVERT: A 505 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8023 (ptmt) REVERT: A 601 MET cc_start: 0.8897 (tpp) cc_final: 0.8217 (tpp) REVERT: B 523 ILE cc_start: 0.9185 (pt) cc_final: 0.8846 (tp) REVERT: B 536 SER cc_start: 0.9493 (m) cc_final: 0.8864 (p) REVERT: B 573 LEU cc_start: 0.8719 (tp) cc_final: 0.8317 (mm) REVERT: B 590 LEU cc_start: 0.8302 (mt) cc_final: 0.8091 (mt) REVERT: B 601 MET cc_start: 0.8909 (tpp) cc_final: 0.8123 (tpp) REVERT: B 661 MET cc_start: 0.6926 (tmm) cc_final: 0.6529 (tmm) outliers start: 2 outliers final: 1 residues processed: 301 average time/residue: 0.2101 time to fit residues: 97.6787 Evaluate side-chains 239 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 159 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 168 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 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 882 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117724 restraints weight = 20437.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120006 restraints weight = 13219.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121200 restraints weight = 10508.779| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3910 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= 0.131 Angle : 0.594 9.509 18688 Z= 0.299 Chirality : 0.042 0.189 2224 Planarity : 0.003 0.035 2305 Dihedral : 4.161 19.462 2021 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1738 helix: 1.75 (0.17), residues: 1000 sheet: -0.83 (0.47), residues: 130 loop : -1.05 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 630 HIS 0.006 0.001 HIS A 915 PHE 0.015 0.001 PHE A 605 TYR 0.015 0.001 TYR B 372 ARG 0.005 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00096 ( 4) link_NAG-ASN : angle 1.55260 ( 12) link_BETA1-4 : bond 0.00516 ( 4) link_BETA1-4 : angle 1.42797 ( 12) hydrogen bonds : bond 0.03672 ( 799) hydrogen bonds : angle 4.07753 ( 2307) SS BOND : bond 0.00373 ( 6) SS BOND : angle 1.86001 ( 12) covalent geometry : bond 0.00300 (13706) covalent geometry : angle 0.59039 (18652) *********************** 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 299 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.8570 (t) cc_final: 0.8141 (p) REVERT: A 487 PHE cc_start: 0.8344 (m-80) cc_final: 0.8031 (m-80) REVERT: A 505 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8101 (pttt) REVERT: A 601 MET cc_start: 0.8907 (tpp) cc_final: 0.8586 (tpp) REVERT: B 523 ILE cc_start: 0.9190 (pt) cc_final: 0.8830 (tp) REVERT: B 536 SER cc_start: 0.9518 (m) cc_final: 0.8905 (p) REVERT: B 573 LEU cc_start: 0.8777 (tp) cc_final: 0.8345 (mm) REVERT: B 601 MET cc_start: 0.8908 (tpp) cc_final: 0.8299 (tpp) REVERT: B 661 MET cc_start: 0.7026 (tmm) cc_final: 0.6570 (tmm) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2061 time to fit residues: 96.5740 Evaluate side-chains 237 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 122 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 143 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** 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 483 ASN ** 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 = 0.3709 r_free = 0.3709 target = 0.146527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114668 restraints weight = 20824.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116319 restraints weight = 15214.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117552 restraints weight = 11513.618| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3955 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= 0.177 Angle : 0.638 8.437 18688 Z= 0.322 Chirality : 0.044 0.183 2224 Planarity : 0.003 0.032 2305 Dihedral : 4.315 21.185 2021 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.07 % Allowed : 0.22 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.21), residues: 1738 helix: 1.65 (0.17), residues: 998 sheet: -1.09 (0.45), residues: 130 loop : -1.09 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 630 HIS 0.006 0.001 HIS A 802 PHE 0.022 0.002 PHE A 605 TYR 0.013 0.001 TYR B 372 ARG 0.004 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 4) link_NAG-ASN : angle 1.53713 ( 12) link_BETA1-4 : bond 0.00325 ( 4) link_BETA1-4 : angle 1.45621 ( 12) hydrogen bonds : bond 0.03909 ( 799) hydrogen bonds : angle 4.18989 ( 2307) SS BOND : bond 0.00438 ( 6) SS BOND : angle 1.99225 ( 12) covalent geometry : bond 0.00414 (13706) covalent geometry : angle 0.63433 (18652) ********************** 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 293 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 PHE cc_start: 0.8332 (m-80) cc_final: 0.7986 (m-80) REVERT: A 505 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8090 (ptmt) REVERT: A 601 MET cc_start: 0.8885 (tpp) cc_final: 0.8576 (tpp) REVERT: B 523 ILE cc_start: 0.9197 (pt) cc_final: 0.8843 (tp) REVERT: B 536 SER cc_start: 0.9515 (m) cc_final: 0.8941 (p) REVERT: B 573 LEU cc_start: 0.8808 (tp) cc_final: 0.8413 (mm) REVERT: B 590 LEU cc_start: 0.8458 (mt) cc_final: 0.8240 (mt) REVERT: B 601 MET cc_start: 0.8994 (tpp) cc_final: 0.8499 (tpp) REVERT: B 650 TYR cc_start: 0.7951 (p90) cc_final: 0.7729 (p90) REVERT: B 661 MET cc_start: 0.7070 (tmm) cc_final: 0.6622 (tmm) outliers start: 1 outliers final: 1 residues processed: 292 average time/residue: 0.2178 time to fit residues: 97.9857 Evaluate side-chains 229 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 46 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 119 optimal weight: 0.2980 chunk 167 optimal weight: 2.9990 chunk 124 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** 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** B 859 ASN B1056 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119792 restraints weight = 20692.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122734 restraints weight = 12991.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123524 restraints weight = 10306.185| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4156 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= 0.115 Angle : 0.591 8.553 18688 Z= 0.296 Chirality : 0.042 0.196 2224 Planarity : 0.003 0.033 2305 Dihedral : 4.129 18.977 2021 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1738 helix: 1.75 (0.17), residues: 998 sheet: -0.86 (0.46), residues: 130 loop : -1.07 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 630 HIS 0.006 0.001 HIS A 915 PHE 0.022 0.001 PHE A 221 TYR 0.015 0.001 TYR B 650 ARG 0.005 0.000 ARG B 886 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 4) link_NAG-ASN : angle 1.44920 ( 12) link_BETA1-4 : bond 0.00409 ( 4) link_BETA1-4 : angle 1.27793 ( 12) hydrogen bonds : bond 0.03628 ( 799) hydrogen bonds : angle 4.08231 ( 2307) SS BOND : bond 0.00325 ( 6) SS BOND : angle 1.67402 ( 12) covalent geometry : bond 0.00255 (13706) covalent geometry : angle 0.58777 (18652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4184.23 seconds wall clock time: 74 minutes 26.82 seconds (4466.82 seconds total)