Starting phenix.real_space_refine on Sat Sep 12 03:32:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y5v_10704/09_2026/6y5v_10704.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5v_10704/09_2026/6y5v_10704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y5v_10704/09_2026/6y5v_10704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5v_10704/09_2026/6y5v_10704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y5v_10704/09_2026/6y5v_10704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5v_10704/09_2026/6y5v_10704.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6y5v_10704/09_2026/6y5v_10704.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y5v_10704/09_2026/6y5v_10704.cif" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 8728 2.51 5 N 2215 2.21 5 O 2365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13400 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 6641 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 3, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 106 Chain: "B" Number of atoms: 6653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 6653 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 14, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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 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 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 chiralities: 1 Time building chain proxies: 3.26, per 1000 atoms: 0.24 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: 0.93 Conformation dependent library (CDL) restraints added in 635.2 milliseconds 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3232 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 6 sheets defined 62.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.536A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 156 through 193 removed outlier: 6.493A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 243 removed outlier: 3.651A pdb=" N MET A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.716A pdb=" N VAL A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 removed outlier: 3.621A pdb=" N GLY A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.685A pdb=" N VAL A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 376' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.854A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.650A pdb=" N SER A 452 " --> pdb=" O MET A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 491 Proline residue: A 466 - end of helix removed outlier: 3.836A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.965A pdb=" N LEU A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 550 removed outlier: 4.277A pdb=" N ILE A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Proline residue: A 541 - end of helix removed outlier: 3.520A pdb=" N ASP A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.872A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 584 removed outlier: 3.577A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 616 Proline residue: A 593 - end of helix removed outlier: 3.745A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 675 removed outlier: 3.607A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N TYR A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 removed outlier: 3.612A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.186A pdb=" N LEU A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 751 Processing helix chain 'A' and resid 752 through 770 Processing helix chain 'A' and resid 783 through 795 removed outlier: 3.937A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 881 Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 906 through 917 removed outlier: 3.745A pdb=" N PHE A 912 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 931 No H-bonds generated for 'chain 'A' and resid 929 through 931' Processing helix chain 'A' and resid 932 through 946 removed outlier: 4.052A pdb=" N GLU A 938 " --> pdb=" O ALA A 934 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 946 " --> pdb=" O MET A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1048 Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1066 through 1078 Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.567A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.540A pdb=" N CYS B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 156 through 193 removed outlier: 6.320A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 243 removed outlier: 3.615A pdb=" N MET B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 261 through 284 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.712A pdb=" N VAL B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 removed outlier: 3.530A pdb=" N GLY B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.637A pdb=" N VAL B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.849A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 460 through 489 Proline residue: B 466 - end of helix removed outlier: 3.667A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 517 through 550 removed outlier: 4.210A pdb=" N ILE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Proline residue: B 541 - end of helix removed outlier: 3.502A pdb=" N ASP B 550 " --> pdb=" O ALA B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 removed outlier: 3.998A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 584 Processing helix chain 'B' and resid 587 through 616 Proline residue: B 593 - end of helix removed outlier: 3.728A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 675 removed outlier: 3.795A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TYR B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 696 removed outlier: 3.669A pdb=" N GLU B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 3.996A pdb=" N LEU B 726 " --> pdb=" O HIS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 751 Processing helix chain 'B' and resid 752 through 770 Processing helix chain 'B' and resid 783 through 795 removed outlier: 3.879A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 835 removed outlier: 3.722A pdb=" N LYS B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 881 removed outlier: 4.065A pdb=" N LEU B 872 " --> pdb=" O ASP B 868 " (cutoff:3.500A) Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 884 through 886 No H-bonds generated for 'chain 'B' and resid 884 through 886' Processing helix chain 'B' and resid 906 through 917 removed outlier: 3.518A pdb=" N ALA B 910 " --> pdb=" O LYS B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 931 No H-bonds generated for 'chain 'B' and resid 929 through 931' Processing helix chain 'B' and resid 932 through 946 removed outlier: 3.954A pdb=" N GLU B 938 " --> pdb=" O ALA B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1048 Processing helix chain 'B' and resid 1066 through 1078 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA3, first strand: chain 'A' and resid 775 through 781 removed outlier: 6.463A pdb=" N LEU A 708 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLY A 742 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 805 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA A 842 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET A 807 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU A1054 " --> pdb=" O ASN A 859 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP A 861 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ASN A1056 " --> pdb=" O ASP A 861 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TRP A 863 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 921 " --> pdb=" O ILE A 890 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA5, first strand: chain 'B' and resid 342 through 345 Processing sheet with id=AA6, first strand: chain 'B' and resid 775 through 781 removed outlier: 6.534A pdb=" N LEU B 708 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY B 742 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 805 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ALA B 842 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N MET B 807 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B1054 " --> pdb=" O ASN B 859 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP B 861 " --> pdb=" O LEU B1054 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN B1056 " --> pdb=" O ASP B 861 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N TRP B 863 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N GLU B 921 " --> pdb=" O CYS B 888 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE B 890 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU B 923 " --> pdb=" O ILE B 890 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE B 892 " --> pdb=" O GLU B 923 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.23 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 - 13.79: 7140 13.79 - 27.58: 617 27.58 - 41.36: 140 41.36 - 55.15: 27 55.15 - 68.94: 11 Dihedral angle restraints: 7935 sinusoidal: 2904 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 7932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1778 0.055 - 0.110: 389 0.110 - 0.165: 54 0.165 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 2224 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE B 865 " pdb=" CA ILE B 865 " pdb=" CG1 ILE B 865 " pdb=" CG2 ILE B 865 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 2221 not shown) Planarity restraints: 2309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B1034 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C HIS B1034 " -0.073 2.00e-02 2.50e+03 pdb=" O HIS B1034 " 0.027 2.00e-02 2.50e+03 pdb=" N THR B1035 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 536 " -0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C SER A 536 " 0.071 2.00e-02 2.50e+03 pdb=" O SER A 536 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU A 537 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 536 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.17e+01 pdb=" C SER B 536 " 0.059 2.00e-02 2.50e+03 pdb=" O SER B 536 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 537 " -0.020 2.00e-02 2.50e+03 ... (remaining 2306 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2441 2.77 - 3.30: 13570 3.30 - 3.83: 22102 3.83 - 4.37: 25069 4.37 - 4.90: 43729 Nonbonded interactions: 106911 Sorted by model distance: nonbonded pdb=" O PRO A1058 " pdb=" OH TYR A1070 " model vdw 2.232 3.040 nonbonded pdb=" NH1 ARG A 680 " pdb=" O PRO B 698 " model vdw 2.241 3.120 nonbonded pdb=" OD1 ASN B 859 " pdb=" OG SER B 889 " model vdw 2.277 3.040 nonbonded pdb=" O SER A 789 " pdb=" NE2 GLN A 793 " model vdw 2.313 3.120 nonbonded pdb=" O PHE B 825 " pdb=" OG1 THR B 828 " model vdw 2.313 3.040 ... (remaining 106906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 102 through 312 or (resid 313 and (name N or name CA or na \ me C or name O or name CB )) or resid 314 through 341 or (resid 342 and (name N \ or name CA or name C or name O or name CB )) or resid 343 through 393 or (resid \ 394 and (name N or name CA or name C or name O or name CB )) or resid 395 throug \ h 491 or (resid 492 and (name N or name CA or name C or name O or name CB )) or \ resid 493 through 504 or (resid 505 and (name N or name CA or name C or name O o \ r name CB )) or resid 506 through 715 or (resid 716 and (name N or name CA or na \ me C or name O or name CB )) or resid 717 through 772 or (resid 773 and (name N \ or name CA or name C or name O or name CB )) or resid 774 through 856 or (resid \ 857 and (name N or name CA or name C or name O or name CB )) or resid 858 throug \ h 872 or (resid 873 and (name N or name CA or name C or name O or name CB )) or \ resid 874 through 882 or (resid 883 and (name N or name CA or name C or name O o \ r name CB )) or resid 884 through 913 or (resid 914 and (name N or name CA or na \ me C or name O or name CB )) or resid 915 through 918 or (resid 919 through 920 \ and (name N or name CA or name C or name O or name CB )) or resid 921 through 92 \ 6 or (resid 927 and (name N or name CA or name C or name O or name CB )) or resi \ d 928 through 937 or (resid 938 through 946 and (name N or name CA or name C or \ name O or name CB )) or resid 1028 or (resid 1029 and (name N or name CA or name \ C or name O or name CB )) or resid 1030 through 1045 or (resid 1046 and (name N \ or name CA or name C or name O or name CB )) or resid 1047 through 1078 or (res \ id 1079 and (name N or name CA or name C or name O or name CB )) or resid 1080 t \ hrough 1081 or (resid 1082 and (name N or name CA or name C or name O or name CB \ )) or resid 1083 through 1204)) selection = (chain 'B' and (resid 102 through 112 or (resid 113 through 114 and (name N or n \ ame CA or name C or name O or name CB )) or resid 115 through 116 or (resid 117 \ through 121 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 3 through 211 or (resid 212 and (name N or name CA or name C or name O or name C \ B )) or resid 213 through 286 or (resid 287 and (name N or name CA or name C or \ name O or name CB )) or resid 288 through 290 or (resid 291 and (name N or name \ CA or name C or name O or name CB )) or resid 292 through 346 or (resid 347 thro \ ugh 348 and (name N or name CA or name C or name O or name CB )) or resid 349 th \ rough 364 or (resid 365 through 367 and (name N or name CA or name C or name O o \ r name CB )) or resid 368 through 417 or (resid 418 and (name N or name CA or na \ me C or name O or name CB )) or resid 419 through 420 or (resid 421 and (name N \ or name CA or name C or name O or name CB )) or resid 422 through 462 or (resid \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 616 or (resid 617 and (name N or name CA or name C or name O or name CB )) or \ resid 618 through 634 or (resid 635 and (name N or name CA or name C or name O o \ r name CB )) or resid 636 through 694 or (resid 695 and (name N or name CA or na \ me C or name O or name CB )) or resid 696 through 886 or (resid 887 and (name N \ or name CA or name C or name O or name CB )) or resid 888 through 896 or (resid \ 905 through 907 and (name N or name CA or name C or name O or name CB )) or resi \ d 908 through 939 or (resid 940 through 946 and (name N or name CA or name C or \ name O or name CB )) or resid 1028 through 1204)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.600 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 11.347 68.937 4685 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.29 % Allowed : 2.96 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.18), residues: 1738 helix: -0.66 (0.15), residues: 932 sheet: -2.03 (0.42), residues: 100 loop : -2.51 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1083 TYR 0.020 0.002 TYR A 935 PHE 0.017 0.001 PHE B 847 TRP 0.015 0.002 TRP B 570 HIS 0.011 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (13706) covalent geometry : angle 0.68121 / 0.38 (18652) SS BOND : bond 0.00543 / 0.28 ( 6) SS BOND : angle 1.42889 / 0.76 ( 12) hydrogen bonds : bond 0.11334 / 7.52 ( 799) hydrogen bonds : angle 5.42428 / 3.84 ( 2307) link_BETA1-4 : bond 0.00215 / 0.11 ( 4) link_BETA1-4 : angle 1.64024 / 0.85 ( 12) link_NAG-ASN : bond 0.00346 / 0.18 ( 4) link_NAG-ASN : angle 2.24978 / 1.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 421 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ILE cc_start: 0.9185 (mt) cc_final: 0.8984 (tt) REVERT: A 303 SER cc_start: 0.9185 (m) cc_final: 0.8975 (p) REVERT: A 334 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6738 (mtt180) REVERT: A 360 ASN cc_start: 0.7688 (m-40) cc_final: 0.7408 (p0) REVERT: A 499 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8202 (ttmt) REVERT: A 536 SER cc_start: 0.9398 (m) cc_final: 0.9117 (t) REVERT: A 551 ASN cc_start: 0.8103 (m-40) cc_final: 0.7552 (t0) REVERT: A 590 LEU cc_start: 0.8761 (mt) cc_final: 0.8516 (mt) REVERT: A 601 MET cc_start: 0.8868 (tpp) cc_final: 0.8661 (tpp) REVERT: A 628 TYR cc_start: 0.8229 (t80) cc_final: 0.8022 (t80) REVERT: A 707 GLN cc_start: 0.9296 (mm-40) cc_final: 0.9016 (mm110) REVERT: A 861 ASP cc_start: 0.7007 (m-30) cc_final: 0.6643 (m-30) REVERT: B 278 MET cc_start: 0.8579 (mmp) cc_final: 0.8096 (mmp) REVERT: B 372 TYR cc_start: 0.8182 (t80) cc_final: 0.7648 (t80) REVERT: B 381 ILE cc_start: 0.7907 (mt) cc_final: 0.7453 (mm) REVERT: B 445 VAL cc_start: 0.9489 (m) cc_final: 0.9222 (t) REVERT: B 523 ILE cc_start: 0.9220 (pt) cc_final: 0.8746 (tp) REVERT: B 536 SER cc_start: 0.9471 (m) cc_final: 0.9203 (p) REVERT: B 562 SER cc_start: 0.8845 (m) cc_final: 0.8575 (t) REVERT: B 573 LEU cc_start: 0.8858 (tp) cc_final: 0.8574 (mm) REVERT: B 590 LEU cc_start: 0.8560 (mt) cc_final: 0.8277 (mt) REVERT: B 601 MET cc_start: 0.8590 (tpp) cc_final: 0.8292 (tpp) REVERT: B 863 TRP cc_start: 0.8545 (m100) cc_final: 0.8008 (m100) REVERT: B 886 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8024 (ttm-80) REVERT: B 892 ILE cc_start: 0.9177 (mm) cc_final: 0.8925 (mp) outliers start: 4 outliers final: 2 residues processed: 424 average time/residue: 0.1029 time to fit residues: 64.3102 Evaluate side-chains 268 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN A 346 ASN ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS B 133 GLN B 483 ASN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 ASN B 867 HIS B 881 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111659 restraints weight = 20453.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114224 restraints weight = 14504.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115619 restraints weight = 9878.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116353 restraints weight = 7997.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116549 restraints weight = 7890.418| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2105 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= 0.125 Angle : 0.585 9.407 18688 Z= 0.300 Chirality : 0.042 0.254 2224 Planarity : 0.004 0.045 2305 Dihedral : 4.181 24.190 1857 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.07 % Allowed : 3.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1738 helix: 0.99 (0.16), residues: 960 sheet: -1.94 (0.41), residues: 132 loop : -1.68 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 891 TYR 0.021 0.001 TYR A 935 PHE 0.016 0.001 PHE A1073 TRP 0.012 0.001 TRP A 355 HIS 0.007 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (13706) covalent geometry : angle 0.57800 / 0.30 (18652) SS BOND : bond 0.00306 / 0.17 ( 6) SS BOND : angle 2.82713 / 1.48 ( 12) hydrogen bonds : bond 0.04186 / 2.78 ( 799) hydrogen bonds : angle 4.37368 / 3.10 ( 2307) link_BETA1-4 : bond 0.00261 / 0.13 ( 4) link_BETA1-4 : angle 1.55093 / 0.79 ( 12) link_NAG-ASN : bond 0.00316 / 0.16 ( 4) link_NAG-ASN : angle 1.97010 / 0.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ILE cc_start: 0.9251 (mt) cc_final: 0.8965 (tt) REVERT: A 505 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7869 (ptmt) REVERT: A 536 SER cc_start: 0.9286 (m) cc_final: 0.9047 (t) REVERT: A 549 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8362 (mtpt) REVERT: A 590 LEU cc_start: 0.8668 (mt) cc_final: 0.8467 (mt) REVERT: A 628 TYR cc_start: 0.8212 (t80) cc_final: 0.7997 (t80) REVERT: A 639 ILE cc_start: 0.8788 (tt) cc_final: 0.8569 (tt) REVERT: A 1038 LYS cc_start: 0.9189 (tttt) cc_final: 0.8974 (ttmt) REVERT: B 108 LEU cc_start: 0.9261 (mt) cc_final: 0.9038 (mt) REVERT: B 278 MET cc_start: 0.8563 (mmp) cc_final: 0.8090 (mmp) REVERT: B 372 TYR cc_start: 0.7880 (t80) cc_final: 0.7405 (t80) REVERT: B 381 ILE cc_start: 0.7434 (mt) cc_final: 0.6992 (mm) REVERT: B 397 TRP cc_start: 0.8302 (m100) cc_final: 0.8058 (m100) REVERT: B 445 VAL cc_start: 0.9422 (m) cc_final: 0.9132 (t) REVERT: B 523 ILE cc_start: 0.9180 (pt) cc_final: 0.8767 (tp) REVERT: B 536 SER cc_start: 0.9457 (m) cc_final: 0.8972 (p) REVERT: B 573 LEU cc_start: 0.8807 (tp) cc_final: 0.8386 (mm) REVERT: B 597 MET cc_start: 0.9323 (tpp) cc_final: 0.8845 (tpp) REVERT: B 644 MET cc_start: 0.8704 (mtp) cc_final: 0.7919 (ttp) REVERT: B 707 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7894 (mp10) REVERT: B 867 HIS cc_start: 0.6683 (OUTLIER) cc_final: 0.6454 (t-170) REVERT: B 886 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.8029 (ttm-80) REVERT: B 892 ILE cc_start: 0.9250 (mm) cc_final: 0.9027 (mp) outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.0919 time to fit residues: 50.1899 Evaluate side-chains 245 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 140 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 360 ASN A 376 ASN A 613 GLN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112071 restraints weight = 20807.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113355 restraints weight = 14793.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114771 restraints weight = 11304.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115267 restraints weight = 9221.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115452 restraints weight = 8499.136| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13720 Z= 0.174 Angle : 0.602 8.848 18688 Z= 0.310 Chirality : 0.042 0.177 2224 Planarity : 0.004 0.056 2305 Dihedral : 4.200 25.461 1857 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1738 helix: 1.34 (0.17), residues: 960 sheet: -1.91 (0.42), residues: 134 loop : -1.43 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 886 TYR 0.012 0.001 TYR A 935 PHE 0.017 0.001 PHE B 775 TRP 0.010 0.001 TRP B 864 HIS 0.006 0.001 HIS B 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (13706) covalent geometry : angle 0.59682 / 0.31 (18652) SS BOND : bond 0.00384 / 0.21 ( 6) SS BOND : angle 2.41436 / 1.27 ( 12) hydrogen bonds : bond 0.04159 / 2.76 ( 799) hydrogen bonds : angle 4.31352 / 3.07 ( 2307) link_BETA1-4 : bond 0.00394 / 0.20 ( 4) link_BETA1-4 : angle 1.55837 / 0.81 ( 12) link_NAG-ASN : bond 0.00315 / 0.16 ( 4) link_NAG-ASN : angle 1.72799 / 0.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8591 (mp) cc_final: 0.8373 (mp) REVERT: A 314 SER cc_start: 0.8661 (t) cc_final: 0.8305 (p) REVERT: A 331 LEU cc_start: 0.8782 (mt) cc_final: 0.8568 (mt) REVERT: A 453 ASN cc_start: 0.8577 (t0) cc_final: 0.8247 (t0) REVERT: A 505 LYS cc_start: 0.8369 (mmmt) cc_final: 0.7887 (ptmt) REVERT: A 601 MET cc_start: 0.9113 (tpp) cc_final: 0.8694 (tpp) REVERT: A 628 TYR cc_start: 0.8292 (t80) cc_final: 0.7962 (t80) REVERT: A 637 MET cc_start: 0.9175 (ttm) cc_final: 0.8116 (tmm) REVERT: A 766 LEU cc_start: 0.9084 (tp) cc_final: 0.8876 (tp) REVERT: A 822 TRP cc_start: 0.8550 (p-90) cc_final: 0.8063 (p-90) REVERT: A 1057 MET cc_start: 0.8127 (mtm) cc_final: 0.7881 (ptm) REVERT: A 1071 MET cc_start: 0.8735 (tpt) cc_final: 0.8390 (tpp) REVERT: B 301 ILE cc_start: 0.9160 (mm) cc_final: 0.8956 (mm) REVERT: B 397 TRP cc_start: 0.8317 (m100) cc_final: 0.8049 (m100) REVERT: B 523 ILE cc_start: 0.9178 (pt) cc_final: 0.8805 (tp) REVERT: B 536 SER cc_start: 0.9494 (m) cc_final: 0.8940 (p) REVERT: B 573 LEU cc_start: 0.8824 (tp) cc_final: 0.8435 (mm) REVERT: B 590 LEU cc_start: 0.8499 (mt) cc_final: 0.8255 (mt) REVERT: B 892 ILE cc_start: 0.9262 (mm) cc_final: 0.9029 (mp) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.0904 time to fit residues: 44.4429 Evaluate side-chains 238 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 65 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 700 HIS ** 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 = 0.3676 r_free = 0.3676 target = 0.143832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112540 restraints weight = 20597.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113943 restraints weight = 15778.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115155 restraints weight = 11331.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115321 restraints weight = 9600.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117896 restraints weight = 8961.154| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13720 Z= 0.145 Angle : 0.577 8.661 18688 Z= 0.294 Chirality : 0.042 0.269 2224 Planarity : 0.004 0.034 2305 Dihedral : 4.118 24.732 1857 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.21), residues: 1738 helix: 1.62 (0.17), residues: 960 sheet: -1.66 (0.42), residues: 130 loop : -1.30 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 886 TYR 0.012 0.001 TYR A 425 PHE 0.021 0.001 PHE B 775 TRP 0.022 0.001 TRP A 630 HIS 0.006 0.001 HIS B 790 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (13706) covalent geometry : angle 0.57195 / 0.29 (18652) SS BOND : bond 0.00208 / 0.10 ( 6) SS BOND : angle 2.16008 / 1.14 ( 12) hydrogen bonds : bond 0.03992 / 2.62 ( 799) hydrogen bonds : angle 4.17924 / 2.96 ( 2307) link_BETA1-4 : bond 0.00328 / 0.16 ( 4) link_BETA1-4 : angle 1.43943 / 0.74 ( 12) link_NAG-ASN : bond 0.00310 / 0.15 ( 4) link_NAG-ASN : angle 1.65774 / 0.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.8638 (t) cc_final: 0.8234 (p) REVERT: A 449 MET cc_start: 0.8475 (mmm) cc_final: 0.8049 (mmm) REVERT: A 453 ASN cc_start: 0.8711 (t0) cc_final: 0.8472 (t0) REVERT: A 505 LYS cc_start: 0.8361 (mmmt) cc_final: 0.7899 (ptmt) REVERT: A 549 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8351 (mtpt) REVERT: A 601 MET cc_start: 0.8859 (tpp) cc_final: 0.8547 (tpp) REVERT: A 628 TYR cc_start: 0.8276 (t80) cc_final: 0.7918 (t80) REVERT: A 637 MET cc_start: 0.9188 (ttm) cc_final: 0.8073 (tmm) REVERT: A 822 TRP cc_start: 0.8518 (p-90) cc_final: 0.7204 (p-90) REVERT: A 864 TRP cc_start: 0.8116 (t60) cc_final: 0.7775 (t60) REVERT: A 871 MET cc_start: 0.8402 (tpp) cc_final: 0.8057 (tpp) REVERT: A 1057 MET cc_start: 0.8261 (mtm) cc_final: 0.8042 (ptm) REVERT: A 1071 MET cc_start: 0.8590 (tpt) cc_final: 0.8266 (tpp) REVERT: B 381 ILE cc_start: 0.7754 (mm) cc_final: 0.7270 (mm) REVERT: B 397 TRP cc_start: 0.8280 (m100) cc_final: 0.7999 (m100) REVERT: B 523 ILE cc_start: 0.9148 (pt) cc_final: 0.8765 (tp) REVERT: B 536 SER cc_start: 0.9472 (m) cc_final: 0.8876 (p) REVERT: B 573 LEU cc_start: 0.8807 (tp) cc_final: 0.8422 (mm) REVERT: B 590 LEU cc_start: 0.8432 (mt) cc_final: 0.8213 (mt) REVERT: B 597 MET cc_start: 0.9262 (tpp) cc_final: 0.8665 (tpp) REVERT: B 601 MET cc_start: 0.9147 (tpp) cc_final: 0.8840 (tpp) REVERT: B 863 TRP cc_start: 0.8675 (m100) cc_final: 0.8407 (m100) REVERT: B 867 HIS cc_start: 0.6794 (OUTLIER) cc_final: 0.6373 (t-170) outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.0918 time to fit residues: 45.3806 Evaluate side-chains 231 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 60 optimal weight: 0.0970 chunk 167 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113167 restraints weight = 20908.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113262 restraints weight = 15939.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114651 restraints weight = 12241.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115133 restraints weight = 10661.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115425 restraints weight = 9509.552| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13720 Z= 0.170 Angle : 0.599 9.280 18688 Z= 0.305 Chirality : 0.043 0.193 2224 Planarity : 0.004 0.048 2305 Dihedral : 4.118 21.417 1857 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.21), residues: 1738 helix: 1.56 (0.17), residues: 984 sheet: -1.48 (0.42), residues: 130 loop : -1.31 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 454 TYR 0.015 0.001 TYR A 425 PHE 0.026 0.001 PHE B 775 TRP 0.022 0.001 TRP A 630 HIS 0.006 0.001 HIS B 790 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (13706) covalent geometry : angle 0.59572 / 0.30 (18652) SS BOND : bond 0.00633 / 0.33 ( 6) SS BOND : angle 1.79377 / 0.95 ( 12) hydrogen bonds : bond 0.04018 / 2.63 ( 799) hydrogen bonds : angle 4.18392 / 2.97 ( 2307) link_BETA1-4 : bond 0.00330 / 0.16 ( 4) link_BETA1-4 : angle 1.46714 / 0.76 ( 12) link_NAG-ASN : bond 0.00288 / 0.15 ( 4) link_NAG-ASN : angle 1.55556 / 0.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8812 (ttm) cc_final: 0.8369 (ttm) REVERT: A 314 SER cc_start: 0.8625 (t) cc_final: 0.8230 (p) REVERT: A 449 MET cc_start: 0.8620 (mmm) cc_final: 0.8366 (mmp) REVERT: A 453 ASN cc_start: 0.8708 (t0) cc_final: 0.8484 (t0) REVERT: A 505 LYS cc_start: 0.8445 (mmmt) cc_final: 0.7976 (ptmt) REVERT: A 601 MET cc_start: 0.8843 (tpp) cc_final: 0.8520 (tpp) REVERT: A 628 TYR cc_start: 0.8344 (t80) cc_final: 0.7897 (t80) REVERT: A 637 MET cc_start: 0.9202 (ttm) cc_final: 0.8050 (tmm) REVERT: A 822 TRP cc_start: 0.8217 (p-90) cc_final: 0.7789 (p-90) REVERT: A 1067 ASP cc_start: 0.8521 (p0) cc_final: 0.8307 (p0) REVERT: B 397 TRP cc_start: 0.8261 (m100) cc_final: 0.8007 (m100) REVERT: B 523 ILE cc_start: 0.9213 (pt) cc_final: 0.8832 (tp) REVERT: B 536 SER cc_start: 0.9492 (m) cc_final: 0.8905 (p) REVERT: B 573 LEU cc_start: 0.8830 (tp) cc_final: 0.8450 (mm) REVERT: B 590 LEU cc_start: 0.8416 (mt) cc_final: 0.8186 (mt) REVERT: B 661 MET cc_start: 0.6991 (tmm) cc_final: 0.6669 (tmm) REVERT: B 863 TRP cc_start: 0.8813 (m100) cc_final: 0.8402 (m100) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.0910 time to fit residues: 41.8337 Evaluate side-chains 221 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 137 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS B1048 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 = 0.149476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118780 restraints weight = 20529.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120202 restraints weight = 14638.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121575 restraints weight = 11197.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122575 restraints weight = 8940.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.122687 restraints weight = 8043.838| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13720 Z= 0.125 Angle : 0.574 9.102 18688 Z= 0.290 Chirality : 0.042 0.189 2224 Planarity : 0.003 0.036 2305 Dihedral : 4.035 19.262 1857 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.07 % Allowed : 2.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1738 helix: 1.68 (0.17), residues: 982 sheet: -1.15 (0.44), residues: 130 loop : -1.24 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 454 TYR 0.012 0.001 TYR A1070 PHE 0.017 0.001 PHE B 775 TRP 0.025 0.001 TRP A 630 HIS 0.006 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (13706) covalent geometry : angle 0.57022 / 0.29 (18652) SS BOND : bond 0.00262 / 0.15 ( 6) SS BOND : angle 1.96980 / 1.01 ( 12) hydrogen bonds : bond 0.03839 / 2.50 ( 799) hydrogen bonds : angle 4.12603 / 2.94 ( 2307) link_BETA1-4 : bond 0.00368 / 0.18 ( 4) link_BETA1-4 : angle 1.34134 / 0.69 ( 12) link_NAG-ASN : bond 0.00139 / 0.07 ( 4) link_NAG-ASN : angle 1.51025 / 0.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.8586 (t) cc_final: 0.8201 (p) REVERT: A 481 LEU cc_start: 0.8538 (mt) cc_final: 0.8209 (tt) REVERT: A 505 LYS cc_start: 0.8405 (mmmt) cc_final: 0.7970 (ptmt) REVERT: A 601 MET cc_start: 0.8795 (tpp) cc_final: 0.8425 (tpp) REVERT: A 822 TRP cc_start: 0.8283 (p-90) cc_final: 0.7759 (p-90) REVERT: A 1067 ASP cc_start: 0.8469 (p0) cc_final: 0.8047 (p0) REVERT: A 1078 THR cc_start: 0.8410 (t) cc_final: 0.8086 (t) REVERT: B 396 LEU cc_start: 0.8926 (mt) cc_final: 0.8711 (mt) REVERT: B 523 ILE cc_start: 0.9175 (pt) cc_final: 0.8813 (tp) REVERT: B 536 SER cc_start: 0.9483 (m) cc_final: 0.8867 (p) REVERT: B 573 LEU cc_start: 0.8763 (tp) cc_final: 0.8373 (mm) REVERT: B 601 MET cc_start: 0.8851 (tpp) cc_final: 0.8182 (tpp) REVERT: B 661 MET cc_start: 0.7044 (tmm) cc_final: 0.6558 (tmm) REVERT: B 867 HIS cc_start: 0.6863 (OUTLIER) cc_final: 0.6404 (t-90) outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.0891 time to fit residues: 42.1673 Evaluate side-chains 231 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 144 optimal weight: 0.2980 chunk 2 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 142 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 106 optimal weight: 0.0170 chunk 82 optimal weight: 0.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 859 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116832 restraints weight = 20714.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119683 restraints weight = 13256.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120844 restraints weight = 10326.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122144 restraints weight = 8155.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122357 restraints weight = 7719.832| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13720 Z= 0.117 Angle : 0.566 8.192 18688 Z= 0.287 Chirality : 0.041 0.168 2224 Planarity : 0.004 0.071 2305 Dihedral : 3.986 19.125 1857 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.21), residues: 1738 helix: 1.75 (0.17), residues: 988 sheet: -0.79 (0.44), residues: 138 loop : -1.10 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 886 TYR 0.009 0.001 TYR A 668 PHE 0.029 0.001 PHE A 645 TRP 0.015 0.001 TRP A 630 HIS 0.006 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13706) covalent geometry : angle 0.56254 / 0.29 (18652) SS BOND : bond 0.00306 / 0.18 ( 6) SS BOND : angle 1.78887 / 0.95 ( 12) hydrogen bonds : bond 0.03653 / 2.39 ( 799) hydrogen bonds : angle 4.07371 / 2.88 ( 2307) link_BETA1-4 : bond 0.00390 / 0.20 ( 4) link_BETA1-4 : angle 1.30055 / 0.67 ( 12) link_NAG-ASN : bond 0.00076 / 0.04 ( 4) link_NAG-ASN : angle 1.54188 / 0.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8470 (tpp) cc_final: 0.7983 (tpp) REVERT: A 314 SER cc_start: 0.8626 (t) cc_final: 0.8197 (p) REVERT: A 481 LEU cc_start: 0.8579 (mt) cc_final: 0.8276 (tt) REVERT: A 505 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8049 (pttt) REVERT: A 601 MET cc_start: 0.8978 (tpp) cc_final: 0.8604 (tpp) REVERT: A 822 TRP cc_start: 0.8275 (p-90) cc_final: 0.7721 (p-90) REVERT: A 871 MET cc_start: 0.8488 (tpp) cc_final: 0.8194 (tpp) REVERT: A 1067 ASP cc_start: 0.8443 (p0) cc_final: 0.8046 (p0) REVERT: A 1071 MET cc_start: 0.8618 (tpt) cc_final: 0.7775 (tpt) REVERT: B 523 ILE cc_start: 0.9220 (pt) cc_final: 0.8824 (tp) REVERT: B 536 SER cc_start: 0.9495 (m) cc_final: 0.8871 (p) REVERT: B 573 LEU cc_start: 0.8742 (tp) cc_final: 0.8345 (mm) REVERT: B 590 LEU cc_start: 0.8326 (mt) cc_final: 0.8099 (mt) REVERT: B 601 MET cc_start: 0.8832 (tpp) cc_final: 0.8181 (tpp) REVERT: B 661 MET cc_start: 0.7046 (tmm) cc_final: 0.6560 (tmm) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.0873 time to fit residues: 42.3258 Evaluate side-chains 235 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 154 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 0.0040 chunk 38 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 104 optimal weight: 0.0670 chunk 145 optimal weight: 0.8980 overall best weight: 0.5932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS B1056 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121522 restraints weight = 20181.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122517 restraints weight = 14111.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124176 restraints weight = 10989.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125225 restraints weight = 8850.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125405 restraints weight = 8131.437| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13720 Z= 0.112 Angle : 0.563 8.069 18688 Z= 0.283 Chirality : 0.041 0.180 2224 Planarity : 0.003 0.058 2305 Dihedral : 3.942 18.912 1857 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.14 % Allowed : 0.80 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1738 helix: 1.84 (0.17), residues: 988 sheet: -0.67 (0.44), residues: 138 loop : -1.05 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 497 TYR 0.017 0.001 TYR B 372 PHE 0.020 0.001 PHE A 645 TRP 0.016 0.001 TRP A 630 HIS 0.006 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13706) covalent geometry : angle 0.55946 / 0.28 (18652) SS BOND : bond 0.00317 / 0.18 ( 6) SS BOND : angle 1.71386 / 0.92 ( 12) hydrogen bonds : bond 0.03557 / 2.34 ( 799) hydrogen bonds : angle 4.02950 / 2.86 ( 2307) link_BETA1-4 : bond 0.00389 / 0.20 ( 4) link_BETA1-4 : angle 1.27731 / 0.65 ( 12) link_NAG-ASN : bond 0.00104 / 0.05 ( 4) link_NAG-ASN : angle 1.58798 / 0.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8419 (tpp) cc_final: 0.7973 (tpp) REVERT: A 314 SER cc_start: 0.8552 (t) cc_final: 0.8161 (p) REVERT: A 505 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8022 (pttt) REVERT: A 601 MET cc_start: 0.8772 (tpp) cc_final: 0.8400 (tpp) REVERT: A 1067 ASP cc_start: 0.8417 (p0) cc_final: 0.8132 (p0) REVERT: B 518 PRO cc_start: 0.9010 (Cg_endo) cc_final: 0.8794 (Cg_exo) REVERT: B 523 ILE cc_start: 0.9220 (pt) cc_final: 0.8820 (tp) REVERT: B 536 SER cc_start: 0.9503 (m) cc_final: 0.8888 (p) REVERT: B 573 LEU cc_start: 0.8742 (tp) cc_final: 0.8313 (mm) REVERT: B 590 LEU cc_start: 0.8294 (mt) cc_final: 0.8090 (mt) REVERT: B 601 MET cc_start: 0.8829 (tpp) cc_final: 0.8237 (tpp) REVERT: B 661 MET cc_start: 0.7046 (tmm) cc_final: 0.6501 (tmm) outliers start: 2 outliers final: 0 residues processed: 301 average time/residue: 0.0847 time to fit residues: 40.6853 Evaluate side-chains 235 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 129 optimal weight: 0.0770 chunk 28 optimal weight: 0.0170 chunk 39 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 ASN A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121583 restraints weight = 20455.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122720 restraints weight = 14080.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124163 restraints weight = 11128.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124506 restraints weight = 9327.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124894 restraints weight = 8709.293| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4030 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= 0.113 Angle : 0.574 7.991 18688 Z= 0.287 Chirality : 0.041 0.187 2224 Planarity : 0.003 0.050 2305 Dihedral : 3.951 18.249 1857 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.21), residues: 1738 helix: 1.87 (0.17), residues: 988 sheet: -0.57 (0.44), residues: 138 loop : -1.07 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 497 TYR 0.014 0.001 TYR A 372 PHE 0.016 0.001 PHE A 221 TRP 0.017 0.001 TRP A 630 HIS 0.007 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13706) covalent geometry : angle 0.57039 / 0.29 (18652) SS BOND : bond 0.00266 / 0.16 ( 6) SS BOND : angle 1.64092 / 0.88 ( 12) hydrogen bonds : bond 0.03495 / 2.29 ( 799) hydrogen bonds : angle 4.02799 / 2.86 ( 2307) link_BETA1-4 : bond 0.00398 / 0.20 ( 4) link_BETA1-4 : angle 1.25334 / 0.65 ( 12) link_NAG-ASN : bond 0.00069 / 0.03 ( 4) link_NAG-ASN : angle 1.56121 / 0.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8517 (tpp) cc_final: 0.7840 (tpp) REVERT: A 314 SER cc_start: 0.8574 (t) cc_final: 0.8155 (p) REVERT: A 487 PHE cc_start: 0.8306 (m-10) cc_final: 0.7975 (m-80) REVERT: A 505 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8023 (pttt) REVERT: A 601 MET cc_start: 0.8761 (tpp) cc_final: 0.8457 (tpp) REVERT: A 871 MET cc_start: 0.8689 (tpp) cc_final: 0.8282 (tpp) REVERT: A 1067 ASP cc_start: 0.8446 (p0) cc_final: 0.8133 (p0) REVERT: B 523 ILE cc_start: 0.9154 (pt) cc_final: 0.8802 (tp) REVERT: B 536 SER cc_start: 0.9507 (m) cc_final: 0.8868 (p) REVERT: B 573 LEU cc_start: 0.8745 (tp) cc_final: 0.8314 (mm) REVERT: B 601 MET cc_start: 0.8809 (tpp) cc_final: 0.8154 (tpp) REVERT: B 635 MET cc_start: 0.7934 (tpt) cc_final: 0.7536 (tpp) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.0832 time to fit residues: 40.0376 Evaluate side-chains 246 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 24 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.0020 chunk 71 optimal weight: 5.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121657 restraints weight = 20426.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123949 restraints weight = 14315.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125143 restraints weight = 10278.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125692 restraints weight = 8502.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126040 restraints weight = 7763.291| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13720 Z= 0.113 Angle : 0.584 8.197 18688 Z= 0.290 Chirality : 0.041 0.193 2224 Planarity : 0.003 0.042 2305 Dihedral : 3.907 18.067 1857 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.07 % Allowed : 0.36 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1738 helix: 1.92 (0.17), residues: 988 sheet: -0.49 (0.45), residues: 138 loop : -1.10 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 886 TYR 0.012 0.001 TYR B 372 PHE 0.017 0.001 PHE A 221 TRP 0.019 0.001 TRP A 630 HIS 0.007 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (13706) covalent geometry : angle 0.58063 / 0.29 (18652) SS BOND : bond 0.00302 / 0.17 ( 6) SS BOND : angle 1.58856 / 0.85 ( 12) hydrogen bonds : bond 0.03484 / 2.29 ( 799) hydrogen bonds : angle 4.00670 / 2.84 ( 2307) link_BETA1-4 : bond 0.00416 / 0.21 ( 4) link_BETA1-4 : angle 1.24577 / 0.64 ( 12) link_NAG-ASN : bond 0.00085 / 0.04 ( 4) link_NAG-ASN : angle 1.54408 / 0.70 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8562 (tpp) cc_final: 0.7972 (tpp) REVERT: A 314 SER cc_start: 0.8517 (t) cc_final: 0.8136 (p) REVERT: A 487 PHE cc_start: 0.8296 (m-10) cc_final: 0.7963 (m-80) REVERT: A 505 LYS cc_start: 0.8370 (mmmt) cc_final: 0.8008 (pttt) REVERT: A 601 MET cc_start: 0.8781 (tpp) cc_final: 0.8424 (tpp) REVERT: A 871 MET cc_start: 0.8695 (tpp) cc_final: 0.8342 (tpp) REVERT: A 1067 ASP cc_start: 0.8414 (p0) cc_final: 0.8095 (p0) REVERT: B 134 MET cc_start: 0.6837 (mtt) cc_final: 0.6590 (mtt) REVERT: B 523 ILE cc_start: 0.9178 (pt) cc_final: 0.8804 (tp) REVERT: B 573 LEU cc_start: 0.8720 (tp) cc_final: 0.8292 (mm) REVERT: B 601 MET cc_start: 0.8713 (tpp) cc_final: 0.8079 (tpp) REVERT: B 635 MET cc_start: 0.7924 (tpt) cc_final: 0.7509 (tpp) REVERT: B 661 MET cc_start: 0.6830 (tmm) cc_final: 0.6475 (tmm) REVERT: B 863 TRP cc_start: 0.8562 (m100) cc_final: 0.8355 (m100) REVERT: B 1039 LEU cc_start: 0.8546 (mt) cc_final: 0.8293 (mt) outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.0862 time to fit residues: 41.4978 Evaluate side-chains 241 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 19 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 15 optimal weight: 0.0050 chunk 116 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.151966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121152 restraints weight = 20382.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122523 restraints weight = 14286.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.123823 restraints weight = 11151.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124168 restraints weight = 9155.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124593 restraints weight = 8703.236| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13720 Z= 0.113 Angle : 0.574 8.145 18688 Z= 0.287 Chirality : 0.041 0.189 2224 Planarity : 0.003 0.037 2305 Dihedral : 3.890 18.040 1857 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.21), residues: 1738 helix: 1.94 (0.17), residues: 986 sheet: -0.49 (0.45), residues: 138 loop : -1.10 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 886 TYR 0.012 0.001 TYR B 650 PHE 0.015 0.001 PHE B 555 TRP 0.018 0.001 TRP A 630 HIS 0.007 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (13706) covalent geometry : angle 0.57151 / 0.29 (18652) SS BOND : bond 0.00301 / 0.17 ( 6) SS BOND : angle 1.52962 / 0.82 ( 12) hydrogen bonds : bond 0.03474 / 2.29 ( 799) hydrogen bonds : angle 4.01581 / 2.84 ( 2307) link_BETA1-4 : bond 0.00353 / 0.18 ( 4) link_BETA1-4 : angle 1.21147 / 0.62 ( 12) link_NAG-ASN : bond 0.00054 / 0.03 ( 4) link_NAG-ASN : angle 1.53604 / 0.70 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1952.90 seconds wall clock time: 34 minutes 39.37 seconds (2079.37 seconds total)