Starting phenix.real_space_refine on Wed Nov 19 14:21:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x58_6703/11_2025/5x58_6703.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x58_6703/11_2025/5x58_6703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5x58_6703/11_2025/5x58_6703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x58_6703/11_2025/5x58_6703.map" model { file = "/net/cci-nas-00/data/ceres_data/5x58_6703/11_2025/5x58_6703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x58_6703/11_2025/5x58_6703.cif" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.012 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 132 5.16 5 C 16102 2.51 5 N 4127 2.21 5 O 4904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25265 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 8234 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1001} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8226 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1000} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Restraints were copied for chains: C Time building chain proxies: 11.86, per 1000 atoms: 0.47 Number of scatterers: 25265 At special positions: 0 Unit cell: (149.5, 139.1, 159.9, 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 132 16.00 O 4904 8.00 N 4127 7.00 C 16102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.04 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.04 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 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=3, symmetry=0 Links applied NAG-ASN " NAG A1302 " - " ASN A 691 " " NAG A1303 " - " ASN A 699 " " NAG A1304 " - " ASN A 783 " " NAG A1305 " - " ASN A1056 " " NAG A1306 " - " ASN A 357 " " NAG A1307 " - " ASN A 330 " " NAG A1308 " - " ASN A 318 " " NAG A1309 " - " ASN A 269 " " NAG A1310 " - " ASN A 227 " " NAG A1311 " - " ASN A 158 " " NAG A1312 " - " ASN A 119 " " NAG A1313 " - " ASN A 65 " " NAG B1301 " - " ASN B 602 " " NAG B1302 " - " ASN B 691 " " NAG B1303 " - " ASN B 699 " " NAG B1304 " - " ASN B 783 " " NAG B1305 " - " ASN B1056 " " NAG B1306 " - " ASN B 357 " " NAG B1307 " - " ASN B 330 " " NAG B1308 " - " ASN B 318 " " NAG B1309 " - " ASN B 269 " " NAG B1310 " - " ASN B 227 " " NAG B1311 " - " ASN B 158 " " NAG B1312 " - " ASN B 119 " " NAG B1313 " - " ASN B 65 " " NAG C1301 " - " ASN C 602 " " NAG C1302 " - " ASN C 691 " " NAG C1303 " - " ASN C 699 " " NAG C1304 " - " ASN C 783 " " NAG C1305 " - " ASN C1056 " " NAG C1306 " - " ASN C 357 " " NAG C1307 " - " ASN C 330 " " NAG C1308 " - " ASN C 318 " " NAG C1309 " - " ASN C 269 " " NAG C1310 " - " ASN C 227 " " NAG C1311 " - " ASN C 158 " " NAG C1312 " - " ASN C 119 " " NAG C1313 " - " ASN C 65 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 45 sheets defined 22.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 327 removed outlier: 3.852A pdb=" N GLU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 327' Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.192A pdb=" N ARG A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.964A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.583A pdb=" N GLY A 726 " --> pdb=" O MET A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 744 through 765 removed outlier: 4.108A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 807 removed outlier: 3.810A pdb=" N LYS A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 Processing helix chain 'A' and resid 868 through 873 removed outlier: 3.547A pdb=" N ALA A 872 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 removed outlier: 3.694A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.959A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 4.170A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 3.933A pdb=" N LYS A 929 " --> pdb=" O THR A 925 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.646A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1014 removed outlier: 3.645A pdb=" N ASP A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 327 removed outlier: 3.851A pdb=" N GLU B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 324 through 327' Processing helix chain 'B' and resid 390 through 397 removed outlier: 4.192A pdb=" N ARG B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.965A pdb=" N ALA B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 removed outlier: 3.582A pdb=" N GLY B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 744 through 765 removed outlier: 4.109A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 807 removed outlier: 3.810A pdb=" N LYS B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 868 through 873 removed outlier: 3.547A pdb=" N ALA B 872 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 892 removed outlier: 3.693A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.959A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 removed outlier: 4.171A pdb=" N THR B 921 " --> pdb=" O GLN B 917 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 3.932A pdb=" N LYS B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 964 removed outlier: 3.646A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1014 removed outlier: 3.644A pdb=" N ASP B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 981 " --> pdb=" O ARG B 977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 988 " --> pdb=" O GLN B 984 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B1003 " --> pdb=" O GLU B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 327 removed outlier: 3.851A pdb=" N GLU C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 327' Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.192A pdb=" N ARG C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.964A pdb=" N ALA C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 726 removed outlier: 3.584A pdb=" N GLY C 726 " --> pdb=" O MET C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 744 through 765 removed outlier: 4.108A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 807 removed outlier: 3.811A pdb=" N LYS C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 868 through 873 removed outlier: 3.547A pdb=" N ALA C 872 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 892 removed outlier: 3.693A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 removed outlier: 3.959A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 923 removed outlier: 4.171A pdb=" N THR C 921 " --> pdb=" O GLN C 917 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 3.933A pdb=" N LYS C 929 " --> pdb=" O THR C 925 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 964 removed outlier: 3.646A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 1014 removed outlier: 3.644A pdb=" N ASP C 976 " --> pdb=" O GLU C 972 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 988 " --> pdb=" O GLN C 984 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.523A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR A 71 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 250 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG A 38 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N LEU A 216 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48 removed outlier: 5.700A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.744A pdb=" N ASP A 57 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 5.597A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 147 through 150 removed outlier: 7.137A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 298 through 299 Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 312 removed outlier: 7.409A pdb=" N SER A 310 " --> pdb=" O ASN A 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.242A pdb=" N ASN A 321 " --> pdb=" O VAL A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.961A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 537 through 540 removed outlier: 5.701A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 640 through 641 removed outlier: 5.596A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 652 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 683 through 685 Processing sheet with id=AB4, first strand: chain 'A' and resid 693 through 697 removed outlier: 3.546A pdb=" N ILE A 696 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A1083 " --> pdb=" O ASN A1080 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 704 through 710 removed outlier: 6.889A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 704 through 710 Processing sheet with id=AB7, first strand: chain 'A' and resid 769 through 771 removed outlier: 6.097A pdb=" N MET A 770 " --> pdb=" O SER C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1071 through 1072 removed outlier: 3.539A pdb=" N PHE A1071 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.524A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 71 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 186 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG B 38 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N LEU B 216 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.743A pdb=" N ASP B 57 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 5.598A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 147 through 150 removed outlier: 7.137A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 298 through 299 Processing sheet with id=AC5, first strand: chain 'B' and resid 310 through 312 removed outlier: 7.409A pdb=" N SER B 310 " --> pdb=" O ASN B 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.242A pdb=" N ASN B 321 " --> pdb=" O VAL B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.961A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 537 through 540 removed outlier: 5.701A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 641 removed outlier: 5.596A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 652 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 683 through 685 Processing sheet with id=AD2, first strand: chain 'B' and resid 693 through 697 removed outlier: 3.545A pdb=" N ILE B 696 " --> pdb=" O ARG B1055 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B1083 " --> pdb=" O ASN B1080 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 704 through 710 removed outlier: 6.889A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 704 through 710 Processing sheet with id=AD5, first strand: chain 'B' and resid 1071 through 1072 removed outlier: 3.539A pdb=" N PHE B1071 " --> pdb=" O PHE B1103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.523A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR C 71 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA C 250 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 186 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG C 38 " --> pdb=" O ASN C 214 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N LEU C 216 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.744A pdb=" N ASP C 57 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 5.597A pdb=" N VAL C 123 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 147 through 150 removed outlier: 7.137A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AE2, first strand: chain 'C' and resid 310 through 312 removed outlier: 7.409A pdb=" N SER C 310 " --> pdb=" O ASN C 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.242A pdb=" N ASN C 321 " --> pdb=" O VAL C 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.962A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 640 through 641 removed outlier: 5.596A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 652 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 693 through 697 removed outlier: 3.545A pdb=" N ILE C 696 " --> pdb=" O ARG C1055 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C1083 " --> pdb=" O ASN C1080 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 704 through 710 removed outlier: 6.889A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 704 through 710 Processing sheet with id=AE9, first strand: chain 'C' and resid 1071 through 1072 removed outlier: 3.539A pdb=" N PHE C1071 " --> pdb=" O PHE C1103 " (cutoff:3.500A) 811 hydrogen bonds defined for protein. 2244 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: 5.82 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7870 1.34 - 1.46: 5722 1.46 - 1.58: 12087 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 25859 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C ASP B 790 " pdb=" N PRO B 791 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.66e+01 bond pdb=" C ASP A 790 " pdb=" N PRO A 791 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.64e+01 ... (remaining 25854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 34611 3.62 - 7.25: 513 7.25 - 10.87: 42 10.87 - 14.50: 15 14.50 - 18.12: 9 Bond angle restraints: 35190 Sorted by residual: angle pdb=" N ARG A 306 " pdb=" CA ARG A 306 " pdb=" C ARG A 306 " ideal model delta sigma weight residual 110.91 120.17 -9.26 1.17e+00 7.31e-01 6.27e+01 angle pdb=" N ARG C 306 " pdb=" CA ARG C 306 " pdb=" C ARG C 306 " ideal model delta sigma weight residual 110.91 120.13 -9.22 1.17e+00 7.31e-01 6.21e+01 angle pdb=" N ARG B 306 " pdb=" CA ARG B 306 " pdb=" C ARG B 306 " ideal model delta sigma weight residual 110.91 120.12 -9.21 1.17e+00 7.31e-01 6.20e+01 angle pdb=" N VAL B 354 " pdb=" CA VAL B 354 " pdb=" C VAL B 354 " ideal model delta sigma weight residual 110.72 103.92 6.80 1.01e+00 9.80e-01 4.53e+01 angle pdb=" N VAL C 354 " pdb=" CA VAL C 354 " pdb=" C VAL C 354 " ideal model delta sigma weight residual 110.72 103.94 6.78 1.01e+00 9.80e-01 4.51e+01 ... (remaining 35185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 15197 21.67 - 43.34: 425 43.34 - 65.01: 102 65.01 - 86.68: 39 86.68 - 108.34: 90 Dihedral angle restraints: 15853 sinusoidal: 6631 harmonic: 9222 Sorted by residual: dihedral pdb=" CA THR B 616 " pdb=" C THR B 616 " pdb=" N PRO B 617 " pdb=" CA PRO B 617 " ideal model delta harmonic sigma weight residual 180.00 132.11 47.89 0 5.00e+00 4.00e-02 9.17e+01 dihedral pdb=" CA THR C 616 " pdb=" C THR C 616 " pdb=" N PRO C 617 " pdb=" CA PRO C 617 " ideal model delta harmonic sigma weight residual 180.00 132.17 47.83 0 5.00e+00 4.00e-02 9.15e+01 dihedral pdb=" CA THR A 616 " pdb=" C THR A 616 " pdb=" N PRO A 617 " pdb=" CA PRO A 617 " ideal model delta harmonic sigma weight residual 180.00 132.18 47.82 0 5.00e+00 4.00e-02 9.15e+01 ... (remaining 15850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3462 0.084 - 0.168: 551 0.168 - 0.252: 48 0.252 - 0.336: 17 0.336 - 0.420: 10 Chirality restraints: 4088 Sorted by residual: chirality pdb=" CB ILE B 787 " pdb=" CA ILE B 787 " pdb=" CG1 ILE B 787 " pdb=" CG2 ILE B 787 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CB ILE A 787 " pdb=" CA ILE A 787 " pdb=" CG1 ILE A 787 " pdb=" CG2 ILE A 787 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CB ILE C 787 " pdb=" CA ILE C 787 " pdb=" CG1 ILE C 787 " pdb=" CG2 ILE C 787 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.34e+00 ... (remaining 4085 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 616 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO C 617 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 617 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 617 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 616 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO A 617 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 616 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO B 617 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 617 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 617 " -0.042 5.00e-02 4.00e+02 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6567 2.80 - 3.32: 22850 3.32 - 3.85: 42174 3.85 - 4.37: 49285 4.37 - 4.90: 82893 Nonbonded interactions: 203769 Sorted by model distance: nonbonded pdb=" O GLU A 647 " pdb=" OH TYR A 677 " model vdw 2.272 3.040 nonbonded pdb=" O GLU C 647 " pdb=" OH TYR C 677 " model vdw 2.273 3.040 nonbonded pdb=" O GLU B 647 " pdb=" OH TYR B 677 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR A 738 " pdb=" OD1 ASP A 976 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR B 738 " pdb=" OD1 ASP B 976 " model vdw 2.314 3.040 ... (remaining 203764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 662 or resid 673 through 809 or resid 831 throu \ gh 1301)) selection = (chain 'B' and (resid 18 through 662 or resid 673 through 1314)) selection = chain 'C' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 30.710 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 : 0.007 0.090 25918 Z= 0.334 Angle : 1.211 18.125 35340 Z= 0.665 Chirality : 0.066 0.420 4088 Planarity : 0.006 0.075 4498 Dihedral : 14.958 108.345 9865 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 0.44 % Allowed : 4.82 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 5.88 % Twisted General : 0.10 % 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: -4.64 (0.12), residues: 3135 helix: -4.02 (0.11), residues: 609 sheet: -2.43 (0.18), residues: 614 loop : -3.11 (0.12), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1089 TYR 0.034 0.003 TYR B 481 PHE 0.024 0.003 PHE C 870 TRP 0.028 0.003 TRP C 423 HIS 0.013 0.002 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00726 (25859) covalent geometry : angle 1.17267 (35190) SS BOND : bond 0.00976 ( 18) SS BOND : angle 2.28457 ( 36) hydrogen bonds : bond 0.28529 ( 793) hydrogen bonds : angle 11.62957 ( 2244) Misc. bond : bond 0.00374 ( 3) link_NAG-ASN : bond 0.00903 ( 38) link_NAG-ASN : angle 5.34023 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 692 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8744 (t0) cc_final: 0.8308 (m-30) REVERT: A 84 LYS cc_start: 0.8654 (mmpt) cc_final: 0.8444 (tppt) REVERT: A 109 ASN cc_start: 0.7042 (p0) cc_final: 0.6251 (t0) REVERT: A 130 PHE cc_start: 0.7489 (m-80) cc_final: 0.6445 (m-80) REVERT: A 131 GLU cc_start: 0.6027 (tt0) cc_final: 0.5675 (pt0) REVERT: A 184 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8151 (mp0) REVERT: A 189 ASN cc_start: 0.8134 (t0) cc_final: 0.7691 (t0) REVERT: A 256 TYR cc_start: 0.8241 (m-80) cc_final: 0.8004 (m-80) REVERT: A 411 LYS cc_start: 0.7307 (tptm) cc_final: 0.6861 (tppt) REVERT: A 640 GLU cc_start: 0.8080 (tt0) cc_final: 0.7866 (tp30) REVERT: A 692 ASN cc_start: 0.8774 (m-40) cc_final: 0.8518 (p0) REVERT: A 707 GLU cc_start: 0.9144 (tt0) cc_final: 0.8920 (tt0) REVERT: A 733 ASN cc_start: 0.8794 (t160) cc_final: 0.8453 (m-40) REVERT: A 745 LEU cc_start: 0.8469 (tm) cc_final: 0.8115 (tp) REVERT: A 755 GLU cc_start: 0.8039 (pp20) cc_final: 0.7588 (mm-30) REVERT: A 762 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7894 (mm-30) REVERT: A 768 LYS cc_start: 0.8727 (tttp) cc_final: 0.8518 (tppt) REVERT: A 769 GLN cc_start: 0.8809 (pm20) cc_final: 0.8571 (pm20) REVERT: A 796 LYS cc_start: 0.7857 (mtmm) cc_final: 0.7526 (mmtm) REVERT: A 833 CYS cc_start: 0.6335 (m) cc_final: 0.5736 (p) REVERT: A 851 MET cc_start: 0.8887 (mtt) cc_final: 0.8641 (mtm) REVERT: A 918 GLU cc_start: 0.8987 (tt0) cc_final: 0.8761 (mm-30) REVERT: A 963 LEU cc_start: 0.8200 (mm) cc_final: 0.7925 (mt) REVERT: A 970 GLU cc_start: 0.8255 (tt0) cc_final: 0.8002 (tm-30) REVERT: A 972 GLU cc_start: 0.8453 (tt0) cc_final: 0.7826 (pp20) REVERT: A 1055 ARG cc_start: 0.8512 (mmm160) cc_final: 0.8265 (ttm-80) REVERT: A 1071 PHE cc_start: 0.8032 (m-80) cc_final: 0.7759 (m-80) REVERT: B 57 ASP cc_start: 0.8731 (t0) cc_final: 0.8173 (m-30) REVERT: B 78 ASN cc_start: 0.7872 (p0) cc_final: 0.7662 (p0) REVERT: B 109 ASN cc_start: 0.7048 (p0) cc_final: 0.6204 (t0) REVERT: B 130 PHE cc_start: 0.7360 (m-80) cc_final: 0.7065 (m-80) REVERT: B 131 GLU cc_start: 0.5948 (tt0) cc_final: 0.5677 (pt0) REVERT: B 132 LEU cc_start: 0.6054 (mm) cc_final: 0.5692 (mm) REVERT: B 184 GLU cc_start: 0.8710 (mt-10) cc_final: 0.7916 (mp0) REVERT: B 260 THR cc_start: 0.8990 (m) cc_final: 0.8767 (p) REVERT: B 410 TYR cc_start: 0.7792 (t80) cc_final: 0.7196 (t80) REVERT: B 447 LYS cc_start: 0.6739 (mttt) cc_final: 0.6497 (mmtm) REVERT: B 689 TYR cc_start: 0.7845 (t80) cc_final: 0.7641 (t80) REVERT: B 692 ASN cc_start: 0.8514 (m-40) cc_final: 0.8290 (p0) REVERT: B 693 THR cc_start: 0.8777 (p) cc_final: 0.8318 (p) REVERT: B 733 ASN cc_start: 0.8850 (t160) cc_final: 0.8473 (m-40) REVERT: B 745 LEU cc_start: 0.8634 (tm) cc_final: 0.7995 (mt) REVERT: B 746 ASN cc_start: 0.8705 (t0) cc_final: 0.8492 (t0) REVERT: B 755 GLU cc_start: 0.8148 (pp20) cc_final: 0.7731 (mm-30) REVERT: B 762 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8185 (mm-30) REVERT: B 796 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7399 (tppt) REVERT: B 851 MET cc_start: 0.8917 (mtt) cc_final: 0.8670 (mtm) REVERT: B 884 MET cc_start: 0.8788 (mmm) cc_final: 0.8463 (tpt) REVERT: B 886 TYR cc_start: 0.9018 (t80) cc_final: 0.8761 (t80) REVERT: B 897 VAL cc_start: 0.9092 (t) cc_final: 0.8875 (m) REVERT: B 918 GLU cc_start: 0.9112 (tt0) cc_final: 0.8863 (mm-30) REVERT: B 972 GLU cc_start: 0.8579 (tt0) cc_final: 0.7986 (pt0) REVERT: B 1049 TYR cc_start: 0.8758 (t80) cc_final: 0.8486 (t80) REVERT: B 1054 GLU cc_start: 0.8820 (pm20) cc_final: 0.8282 (pm20) REVERT: B 1055 ARG cc_start: 0.8658 (mmm160) cc_final: 0.8442 (ttm-80) REVERT: C 57 ASP cc_start: 0.8714 (t0) cc_final: 0.8253 (m-30) REVERT: C 101 TRP cc_start: 0.7736 (m-90) cc_final: 0.7500 (m-90) REVERT: C 109 ASN cc_start: 0.6946 (p0) cc_final: 0.6331 (t0) REVERT: C 131 GLU cc_start: 0.5825 (tt0) cc_final: 0.5220 (pt0) REVERT: C 132 LEU cc_start: 0.5754 (mm) cc_final: 0.5217 (mm) REVERT: C 184 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8357 (mp0) REVERT: C 207 ARG cc_start: 0.6166 (ptm160) cc_final: 0.5796 (mmt-90) REVERT: C 260 THR cc_start: 0.8946 (m) cc_final: 0.8598 (p) REVERT: C 340 TRP cc_start: 0.6175 (p-90) cc_final: 0.5553 (p-90) REVERT: C 411 LYS cc_start: 0.7242 (tptm) cc_final: 0.6839 (tppt) REVERT: C 518 ASP cc_start: 0.7451 (t70) cc_final: 0.7226 (p0) REVERT: C 560 ASP cc_start: 0.8526 (t70) cc_final: 0.8321 (t0) REVERT: C 733 ASN cc_start: 0.8678 (t160) cc_final: 0.8354 (m110) REVERT: C 745 LEU cc_start: 0.8476 (tm) cc_final: 0.8176 (mt) REVERT: C 746 ASN cc_start: 0.8739 (t0) cc_final: 0.8478 (t0) REVERT: C 755 GLU cc_start: 0.7836 (pp20) cc_final: 0.7505 (mm-30) REVERT: C 762 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8036 (mm-30) REVERT: C 768 LYS cc_start: 0.8611 (tttp) cc_final: 0.8334 (ttmm) REVERT: C 769 GLN cc_start: 0.8694 (pm20) cc_final: 0.8327 (pm20) REVERT: C 796 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7428 (mmtm) REVERT: C 900 GLU cc_start: 0.8735 (tt0) cc_final: 0.8495 (tt0) REVERT: C 918 GLU cc_start: 0.8972 (tt0) cc_final: 0.8757 (tm-30) REVERT: C 963 LEU cc_start: 0.8077 (mm) cc_final: 0.7733 (mt) REVERT: C 970 GLU cc_start: 0.8366 (tt0) cc_final: 0.8146 (tm-30) REVERT: C 972 GLU cc_start: 0.8633 (tt0) cc_final: 0.8130 (tm-30) REVERT: C 1055 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8550 (ttm-80) REVERT: C 1071 PHE cc_start: 0.8060 (m-80) cc_final: 0.7773 (m-10) outliers start: 12 outliers final: 4 residues processed: 704 average time/residue: 0.1779 time to fit residues: 194.8502 Evaluate side-chains 409 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 405 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 920 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.0010 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 112 GLN A 135 ASN A 201 GLN A 409 ASN A 522 ASN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 599 GLN A 614 GLN A 632 GLN A 733 ASN A 766 GLN A 883 GLN A 904 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN A 937 ASN A 984 GLN A1090 ASN B 70 HIS B 129 ASN B 135 ASN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 409 ASN B 522 ASN B 526 ASN B 528 ASN B 599 GLN B 614 GLN B 632 GLN B 733 ASN B 766 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN B 889 ASN B 904 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 GLN B 937 ASN B 984 GLN B1053 GLN B1090 ASN C 70 HIS C 135 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 409 ASN C 492 GLN C 522 ASN ** C 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN C 599 GLN C 614 GLN C 632 GLN C 733 ASN C 766 GLN C 835 GLN C 883 GLN C 896 ASN C 904 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 GLN C 937 ASN C 984 GLN C1065 HIS C1090 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.178383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144791 restraints weight = 39631.487| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.58 r_work: 0.3499 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 25918 Z= 0.142 Angle : 0.759 13.350 35340 Z= 0.373 Chirality : 0.050 0.351 4088 Planarity : 0.005 0.073 4498 Dihedral : 12.977 82.328 4286 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.37 % Allowed : 10.33 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.92 % 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: -3.36 (0.13), residues: 3135 helix: -1.60 (0.18), residues: 608 sheet: -1.73 (0.19), residues: 619 loop : -2.75 (0.12), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 453 TYR 0.036 0.002 TYR A 481 PHE 0.024 0.002 PHE A 460 TRP 0.017 0.001 TRP B 340 HIS 0.003 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00321 (25859) covalent geometry : angle 0.73491 (35190) SS BOND : bond 0.00303 ( 18) SS BOND : angle 0.82858 ( 36) hydrogen bonds : bond 0.04388 ( 793) hydrogen bonds : angle 6.59487 ( 2244) Misc. bond : bond 0.00113 ( 3) link_NAG-ASN : bond 0.00687 ( 38) link_NAG-ASN : angle 3.41182 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 489 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.7277 (m-80) cc_final: 0.6611 (m-80) REVERT: A 132 LEU cc_start: 0.6893 (mm) cc_final: 0.6622 (mm) REVERT: A 316 PHE cc_start: 0.6977 (t80) cc_final: 0.6470 (t80) REVERT: A 342 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7085 (ttm-80) REVERT: A 385 ASP cc_start: 0.7700 (m-30) cc_final: 0.7101 (m-30) REVERT: A 411 LYS cc_start: 0.7781 (tptm) cc_final: 0.7580 (tptp) REVERT: A 652 ILE cc_start: 0.8269 (mt) cc_final: 0.7998 (mt) REVERT: A 693 THR cc_start: 0.8065 (p) cc_final: 0.7834 (p) REVERT: A 736 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8986 (tt) REVERT: A 972 GLU cc_start: 0.8143 (tt0) cc_final: 0.7882 (pt0) REVERT: B 130 PHE cc_start: 0.7407 (m-80) cc_final: 0.7042 (m-80) REVERT: B 260 THR cc_start: 0.8833 (m) cc_final: 0.8513 (p) REVERT: B 316 PHE cc_start: 0.7245 (t80) cc_final: 0.6923 (t80) REVERT: B 342 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7890 (ttm-80) REVERT: B 385 ASP cc_start: 0.7728 (m-30) cc_final: 0.7468 (m-30) REVERT: B 447 LYS cc_start: 0.6718 (mttt) cc_final: 0.6482 (mmtm) REVERT: B 539 THR cc_start: 0.8428 (m) cc_final: 0.8098 (p) REVERT: B 689 TYR cc_start: 0.7126 (t80) cc_final: 0.6842 (t80) REVERT: B 693 THR cc_start: 0.8348 (p) cc_final: 0.7860 (p) REVERT: B 961 ASP cc_start: 0.7534 (m-30) cc_final: 0.7277 (m-30) REVERT: B 1054 GLU cc_start: 0.7981 (pm20) cc_final: 0.7623 (pm20) REVERT: B 1071 PHE cc_start: 0.7652 (m-80) cc_final: 0.7114 (m-80) REVERT: C 78 ASN cc_start: 0.7821 (p0) cc_final: 0.7568 (p0) REVERT: C 99 ARG cc_start: 0.6020 (ptp90) cc_final: 0.5807 (ptp-170) REVERT: C 260 THR cc_start: 0.8858 (m) cc_final: 0.8541 (p) REVERT: C 305 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6453 (m-80) REVERT: C 316 PHE cc_start: 0.7370 (t80) cc_final: 0.7085 (t80) REVERT: C 338 TYR cc_start: 0.7510 (p90) cc_final: 0.6843 (p90) REVERT: C 411 LYS cc_start: 0.7643 (tptm) cc_final: 0.7240 (tptp) REVERT: C 539 THR cc_start: 0.8298 (m) cc_final: 0.7968 (p) REVERT: C 961 ASP cc_start: 0.7591 (m-30) cc_final: 0.7319 (m-30) REVERT: C 1071 PHE cc_start: 0.7484 (m-80) cc_final: 0.7063 (m-80) outliers start: 65 outliers final: 41 residues processed: 533 average time/residue: 0.1717 time to fit residues: 145.5202 Evaluate side-chains 410 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 367 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 58 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 312 optimal weight: 0.2980 chunk 131 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN A 526 ASN A 883 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 492 GLN B 692 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 GLN ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 ASN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.178746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140323 restraints weight = 39574.778| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.74 r_work: 0.3560 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 25918 Z= 0.166 Angle : 0.738 14.446 35340 Z= 0.360 Chirality : 0.049 0.337 4088 Planarity : 0.004 0.069 4498 Dihedral : 10.722 69.412 4278 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 3.29 % Allowed : 12.08 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % 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: -2.71 (0.14), residues: 3135 helix: -0.25 (0.20), residues: 614 sheet: -1.49 (0.19), residues: 646 loop : -2.57 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 207 TYR 0.025 0.002 TYR B 442 PHE 0.022 0.001 PHE A 220 TRP 0.016 0.002 TRP B 868 HIS 0.005 0.001 HIS A1040 Details of bonding type rmsd covalent geometry : bond 0.00383 (25859) covalent geometry : angle 0.71509 (35190) SS BOND : bond 0.00310 ( 18) SS BOND : angle 0.87336 ( 36) hydrogen bonds : bond 0.04053 ( 793) hydrogen bonds : angle 6.01692 ( 2244) Misc. bond : bond 0.00063 ( 3) link_NAG-ASN : bond 0.00636 ( 38) link_NAG-ASN : angle 3.26361 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 385 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7186 (mm) cc_final: 0.6894 (mm) REVERT: A 184 GLU cc_start: 0.8186 (mp0) cc_final: 0.7581 (mp0) REVERT: A 316 PHE cc_start: 0.6787 (t80) cc_final: 0.6245 (t80) REVERT: A 342 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7733 (ttm-80) REVERT: A 453 ARG cc_start: 0.5518 (OUTLIER) cc_final: 0.4041 (pmt100) REVERT: A 539 THR cc_start: 0.8421 (m) cc_final: 0.7965 (p) REVERT: A 972 GLU cc_start: 0.8190 (tt0) cc_final: 0.7748 (pt0) REVERT: A 1022 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8694 (p) REVERT: A 1054 GLU cc_start: 0.8126 (pm20) cc_final: 0.7816 (pm20) REVERT: A 1071 PHE cc_start: 0.7660 (m-80) cc_final: 0.7423 (m-80) REVERT: B 87 ILE cc_start: 0.8604 (pt) cc_final: 0.8391 (mt) REVERT: B 130 PHE cc_start: 0.7340 (m-80) cc_final: 0.6898 (m-80) REVERT: B 316 PHE cc_start: 0.7004 (t80) cc_final: 0.6609 (t80) REVERT: B 340 TRP cc_start: 0.7124 (p-90) cc_final: 0.6839 (p-90) REVERT: B 342 ARG cc_start: 0.8089 (ttm-80) cc_final: 0.7852 (ttm-80) REVERT: B 390 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6171 (tttt) REVERT: B 410 TYR cc_start: 0.7063 (t80) cc_final: 0.6647 (t80) REVERT: B 447 LYS cc_start: 0.6925 (mttt) cc_final: 0.6366 (mmtm) REVERT: B 481 TYR cc_start: 0.6431 (t80) cc_final: 0.5176 (t80) REVERT: B 539 THR cc_start: 0.8363 (m) cc_final: 0.7930 (p) REVERT: B 599 GLN cc_start: 0.6032 (OUTLIER) cc_final: 0.5807 (mp10) REVERT: B 689 TYR cc_start: 0.7329 (t80) cc_final: 0.7109 (t80) REVERT: B 745 LEU cc_start: 0.8503 (tm) cc_final: 0.8010 (tt) REVERT: B 746 ASN cc_start: 0.8019 (t0) cc_final: 0.7801 (t0) REVERT: B 749 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8225 (pt) REVERT: B 961 ASP cc_start: 0.7390 (m-30) cc_final: 0.7091 (m-30) REVERT: B 1054 GLU cc_start: 0.8014 (pm20) cc_final: 0.7565 (pm20) REVERT: C 109 ASN cc_start: 0.7310 (p0) cc_final: 0.6620 (t0) REVERT: C 260 THR cc_start: 0.8841 (m) cc_final: 0.8452 (p) REVERT: C 305 PHE cc_start: 0.7007 (OUTLIER) cc_final: 0.6311 (m-80) REVERT: C 316 PHE cc_start: 0.6997 (t80) cc_final: 0.6672 (t80) REVERT: C 338 TYR cc_start: 0.7494 (p90) cc_final: 0.6184 (p90) REVERT: C 340 TRP cc_start: 0.8012 (p-90) cc_final: 0.6943 (p-90) REVERT: C 390 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6666 (tttt) REVERT: C 410 TYR cc_start: 0.7469 (t80) cc_final: 0.7217 (t80) REVERT: C 411 LYS cc_start: 0.7530 (tptm) cc_final: 0.7218 (tptp) REVERT: C 442 TYR cc_start: 0.6453 (p90) cc_final: 0.6131 (p90) REVERT: C 453 ARG cc_start: 0.5326 (OUTLIER) cc_final: 0.4547 (pmt100) REVERT: C 539 THR cc_start: 0.8266 (m) cc_final: 0.7801 (p) REVERT: C 745 LEU cc_start: 0.8592 (tm) cc_final: 0.8222 (tt) REVERT: C 746 ASN cc_start: 0.8037 (t0) cc_final: 0.7819 (t0) REVERT: C 749 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8185 (pt) REVERT: C 961 ASP cc_start: 0.7460 (m-30) cc_final: 0.7068 (m-30) REVERT: C 969 VAL cc_start: 0.8357 (m) cc_final: 0.7921 (p) REVERT: C 1071 PHE cc_start: 0.7623 (m-80) cc_final: 0.7301 (m-80) outliers start: 90 outliers final: 64 residues processed: 452 average time/residue: 0.1638 time to fit residues: 119.6402 Evaluate side-chains 395 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 322 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1022 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 297 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 283 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 60 optimal weight: 0.0470 chunk 249 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 201 GLN A 492 GLN A 614 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN A1090 ASN B 201 GLN B 614 GLN B 692 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN B 889 ASN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN B1095 GLN C 70 HIS C 280 GLN C 492 GLN C 599 GLN C 614 GLN C 661 HIS C 883 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.173363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.134877 restraints weight = 39050.268| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.57 r_work: 0.3465 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 25918 Z= 0.272 Angle : 0.796 15.915 35340 Z= 0.392 Chirality : 0.052 0.344 4088 Planarity : 0.005 0.065 4498 Dihedral : 9.956 63.252 4278 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 5.26 % Allowed : 12.30 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.27 % 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: -2.59 (0.14), residues: 3135 helix: 0.12 (0.21), residues: 617 sheet: -1.61 (0.19), residues: 651 loop : -2.53 (0.13), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 797 TYR 0.025 0.002 TYR A 598 PHE 0.023 0.002 PHE C 62 TRP 0.015 0.002 TRP A 423 HIS 0.010 0.001 HIS B1040 Details of bonding type rmsd covalent geometry : bond 0.00633 (25859) covalent geometry : angle 0.77289 (35190) SS BOND : bond 0.00620 ( 18) SS BOND : angle 1.13650 ( 36) hydrogen bonds : bond 0.04289 ( 793) hydrogen bonds : angle 5.92790 ( 2244) Misc. bond : bond 0.00065 ( 3) link_NAG-ASN : bond 0.00592 ( 38) link_NAG-ASN : angle 3.40168 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 359 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6403 (mm) REVERT: A 151 MET cc_start: -0.0346 (tmm) cc_final: -0.0608 (tmm) REVERT: A 184 GLU cc_start: 0.8281 (mp0) cc_final: 0.7909 (mp0) REVERT: A 294 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7882 (pt0) REVERT: A 316 PHE cc_start: 0.6858 (t80) cc_final: 0.6349 (t80) REVERT: A 451 PHE cc_start: 0.8355 (m-80) cc_final: 0.7978 (m-80) REVERT: A 453 ARG cc_start: 0.5907 (OUTLIER) cc_final: 0.4801 (pmt100) REVERT: A 514 LYS cc_start: 0.7994 (mtmm) cc_final: 0.7709 (mttp) REVERT: A 539 THR cc_start: 0.8386 (m) cc_final: 0.7989 (p) REVERT: A 961 ASP cc_start: 0.7831 (m-30) cc_final: 0.7532 (m-30) REVERT: A 1054 GLU cc_start: 0.8253 (pm20) cc_final: 0.7929 (pm20) REVERT: A 1071 PHE cc_start: 0.8061 (m-80) cc_final: 0.7709 (m-80) REVERT: B 130 PHE cc_start: 0.7491 (m-80) cc_final: 0.6845 (m-80) REVERT: B 263 MET cc_start: 0.8315 (ttt) cc_final: 0.8073 (ttt) REVERT: B 316 PHE cc_start: 0.7210 (t80) cc_final: 0.6773 (t80) REVERT: B 340 TRP cc_start: 0.7640 (p-90) cc_final: 0.7368 (p-90) REVERT: B 342 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7560 (ttm-80) REVERT: B 410 TYR cc_start: 0.7066 (t80) cc_final: 0.6563 (t80) REVERT: B 447 LYS cc_start: 0.6936 (mttt) cc_final: 0.6461 (mmtm) REVERT: B 481 TYR cc_start: 0.6268 (t80) cc_final: 0.5105 (t80) REVERT: B 539 THR cc_start: 0.8489 (m) cc_final: 0.8011 (p) REVERT: B 599 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.6365 (mp10) REVERT: B 745 LEU cc_start: 0.8616 (tm) cc_final: 0.8071 (mt) REVERT: B 749 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8531 (pt) REVERT: B 961 ASP cc_start: 0.7411 (m-30) cc_final: 0.7117 (m-30) REVERT: B 972 GLU cc_start: 0.7766 (pt0) cc_final: 0.7531 (pm20) REVERT: B 1054 GLU cc_start: 0.8073 (pm20) cc_final: 0.7643 (pm20) REVERT: C 262 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8574 (t80) REVERT: C 306 ARG cc_start: 0.6922 (mmm-85) cc_final: 0.6237 (mmm-85) REVERT: C 316 PHE cc_start: 0.7031 (t80) cc_final: 0.6598 (t80) REVERT: C 338 TYR cc_start: 0.7633 (p90) cc_final: 0.7236 (p90) REVERT: C 411 LYS cc_start: 0.7363 (tptm) cc_final: 0.6937 (tptp) REVERT: C 442 TYR cc_start: 0.6569 (p90) cc_final: 0.6258 (p90) REVERT: C 453 ARG cc_start: 0.5752 (OUTLIER) cc_final: 0.4910 (pmt100) REVERT: C 539 THR cc_start: 0.8357 (m) cc_final: 0.7843 (p) REVERT: C 614 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.6757 (mp10) REVERT: C 745 LEU cc_start: 0.8562 (tm) cc_final: 0.8072 (mt) REVERT: C 746 ASN cc_start: 0.8214 (t0) cc_final: 0.7887 (t0) REVERT: C 749 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8453 (pt) REVERT: C 972 GLU cc_start: 0.7825 (pt0) cc_final: 0.6995 (tm-30) REVERT: C 1071 PHE cc_start: 0.7960 (m-80) cc_final: 0.7683 (m-80) outliers start: 144 outliers final: 102 residues processed: 465 average time/residue: 0.1661 time to fit residues: 124.8167 Evaluate side-chains 434 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 324 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 950 SER Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 30 optimal weight: 0.0980 chunk 221 optimal weight: 8.9990 chunk 312 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 304 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 309 optimal weight: 0.6980 chunk 252 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 883 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN B 70 HIS B 280 GLN B 835 GLN B 883 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN B1090 ASN C 280 GLN C 546 GLN C 599 GLN C 883 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 984 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.178002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139630 restraints weight = 38800.490| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.54 r_work: 0.3544 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25918 Z= 0.129 Angle : 0.690 13.229 35340 Z= 0.337 Chirality : 0.048 0.315 4088 Planarity : 0.004 0.067 4498 Dihedral : 9.004 59.808 4278 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.02 % Allowed : 14.17 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % 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: -2.13 (0.15), residues: 3135 helix: 0.78 (0.22), residues: 625 sheet: -1.32 (0.19), residues: 644 loop : -2.34 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 342 TYR 0.020 0.001 TYR A 481 PHE 0.018 0.001 PHE C 870 TRP 0.012 0.001 TRP A 423 HIS 0.008 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00294 (25859) covalent geometry : angle 0.66557 (35190) SS BOND : bond 0.00234 ( 18) SS BOND : angle 1.65717 ( 36) hydrogen bonds : bond 0.03593 ( 793) hydrogen bonds : angle 5.46953 ( 2244) Misc. bond : bond 0.00053 ( 3) link_NAG-ASN : bond 0.00657 ( 38) link_NAG-ASN : angle 3.15753 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 366 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.2688 (mtp) cc_final: 0.2302 (mtt) REVERT: A 184 GLU cc_start: 0.8349 (mp0) cc_final: 0.8041 (mp0) REVERT: A 262 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8219 (t80) REVERT: A 316 PHE cc_start: 0.6656 (t80) cc_final: 0.6135 (t80) REVERT: A 442 TYR cc_start: 0.6047 (p90) cc_final: 0.5827 (p90) REVERT: A 451 PHE cc_start: 0.8215 (m-80) cc_final: 0.7934 (m-80) REVERT: A 453 ARG cc_start: 0.5737 (OUTLIER) cc_final: 0.4444 (pmt100) REVERT: A 514 LYS cc_start: 0.7963 (mtmm) cc_final: 0.7682 (mttp) REVERT: A 539 THR cc_start: 0.8368 (m) cc_final: 0.7990 (p) REVERT: A 961 ASP cc_start: 0.7823 (m-30) cc_final: 0.7429 (m-30) REVERT: A 1022 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8579 (p) REVERT: A 1054 GLU cc_start: 0.8209 (pm20) cc_final: 0.7922 (pm20) REVERT: B 263 MET cc_start: 0.8178 (ttt) cc_final: 0.7869 (ttt) REVERT: B 294 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7704 (mt-10) REVERT: B 306 ARG cc_start: 0.6626 (mmm-85) cc_final: 0.6199 (mmm160) REVERT: B 316 PHE cc_start: 0.6744 (t80) cc_final: 0.6327 (t80) REVERT: B 340 TRP cc_start: 0.7559 (p-90) cc_final: 0.6995 (p-90) REVERT: B 342 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7763 (ttm-80) REVERT: B 385 ASP cc_start: 0.7615 (m-30) cc_final: 0.6928 (m-30) REVERT: B 390 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6369 (pttt) REVERT: B 410 TYR cc_start: 0.7197 (t80) cc_final: 0.6825 (t80) REVERT: B 447 LYS cc_start: 0.6758 (mttt) cc_final: 0.6348 (mmtm) REVERT: B 481 TYR cc_start: 0.6377 (t80) cc_final: 0.5031 (t80) REVERT: B 539 THR cc_start: 0.8369 (m) cc_final: 0.7899 (p) REVERT: B 745 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7933 (tt) REVERT: B 749 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8173 (pt) REVERT: B 961 ASP cc_start: 0.7467 (m-30) cc_final: 0.7189 (m-30) REVERT: B 1049 TYR cc_start: 0.8481 (t80) cc_final: 0.8229 (t80) REVERT: B 1054 GLU cc_start: 0.7991 (pm20) cc_final: 0.7636 (pm20) REVERT: B 1071 PHE cc_start: 0.7688 (m-80) cc_final: 0.7347 (m-80) REVERT: C 99 ARG cc_start: 0.6027 (ptp90) cc_final: 0.5752 (ptp-170) REVERT: C 305 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6595 (m-10) REVERT: C 306 ARG cc_start: 0.6486 (mmm-85) cc_final: 0.5768 (mmm160) REVERT: C 316 PHE cc_start: 0.6728 (t80) cc_final: 0.6341 (t80) REVERT: C 338 TYR cc_start: 0.7538 (p90) cc_final: 0.7097 (p90) REVERT: C 411 LYS cc_start: 0.7416 (tptm) cc_final: 0.7146 (tptp) REVERT: C 442 TYR cc_start: 0.6578 (p90) cc_final: 0.6270 (p90) REVERT: C 453 ARG cc_start: 0.5177 (OUTLIER) cc_final: 0.3838 (pmt100) REVERT: C 539 THR cc_start: 0.8396 (m) cc_final: 0.7934 (p) outliers start: 110 outliers final: 77 residues processed: 444 average time/residue: 0.1597 time to fit residues: 115.0838 Evaluate side-chains 388 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 303 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 423 TRP Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 72 optimal weight: 0.8980 chunk 245 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 599 GLN A 661 HIS A 883 GLN A 931 GLN B 280 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN B 931 GLN C 280 GLN C 492 GLN C 883 GLN C 931 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.171491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127357 restraints weight = 38915.769| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.54 r_work: 0.3436 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 25918 Z= 0.321 Angle : 0.818 14.741 35340 Z= 0.403 Chirality : 0.053 0.340 4088 Planarity : 0.005 0.064 4498 Dihedral : 9.096 58.318 4278 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.07 % Allowed : 14.31 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.27 % 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: -2.36 (0.14), residues: 3135 helix: 0.40 (0.21), residues: 617 sheet: -1.28 (0.19), residues: 628 loop : -2.48 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 797 TYR 0.023 0.002 TYR C 689 PHE 0.022 0.002 PHE C 62 TRP 0.017 0.002 TRP A 423 HIS 0.008 0.001 HIS B1040 Details of bonding type rmsd covalent geometry : bond 0.00746 (25859) covalent geometry : angle 0.79328 (35190) SS BOND : bond 0.00623 ( 18) SS BOND : angle 1.63565 ( 36) hydrogen bonds : bond 0.04309 ( 793) hydrogen bonds : angle 5.82554 ( 2244) Misc. bond : bond 0.00044 ( 3) link_NAG-ASN : bond 0.00479 ( 38) link_NAG-ASN : angle 3.50006 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 325 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: -0.0498 (tmm) cc_final: -0.0993 (tmm) REVERT: A 184 GLU cc_start: 0.8259 (mp0) cc_final: 0.7788 (mp0) REVERT: A 306 ARG cc_start: 0.7235 (mmm-85) cc_final: 0.6433 (mmm160) REVERT: A 316 PHE cc_start: 0.6814 (t80) cc_final: 0.6353 (t80) REVERT: A 342 ARG cc_start: 0.8095 (ttm170) cc_final: 0.7864 (ttm170) REVERT: A 442 TYR cc_start: 0.6137 (p90) cc_final: 0.5880 (p90) REVERT: A 451 PHE cc_start: 0.8340 (m-80) cc_final: 0.8088 (m-80) REVERT: A 453 ARG cc_start: 0.5980 (OUTLIER) cc_final: 0.5092 (pmt100) REVERT: A 539 THR cc_start: 0.8370 (m) cc_final: 0.7947 (p) REVERT: A 958 VAL cc_start: 0.8529 (t) cc_final: 0.8248 (t) REVERT: A 961 ASP cc_start: 0.7923 (m-30) cc_final: 0.7502 (m-30) REVERT: A 1054 GLU cc_start: 0.8345 (pm20) cc_final: 0.7964 (pm20) REVERT: B 263 MET cc_start: 0.8356 (ttt) cc_final: 0.8127 (ttt) REVERT: B 306 ARG cc_start: 0.6923 (mmm-85) cc_final: 0.6305 (mmm160) REVERT: B 340 TRP cc_start: 0.7649 (p-90) cc_final: 0.6925 (p-90) REVERT: B 342 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7927 (ttm-80) REVERT: B 390 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6415 (pttt) REVERT: B 410 TYR cc_start: 0.7113 (t80) cc_final: 0.6458 (t80) REVERT: B 447 LYS cc_start: 0.6607 (mttt) cc_final: 0.6261 (mmtm) REVERT: B 514 LYS cc_start: 0.7748 (mtmm) cc_final: 0.7538 (mttp) REVERT: B 539 THR cc_start: 0.8496 (m) cc_final: 0.7940 (p) REVERT: B 599 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.6363 (mp10) REVERT: B 745 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8330 (mt) REVERT: B 749 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8679 (pp) REVERT: B 882 MET cc_start: 0.8400 (mtp) cc_final: 0.8177 (mtt) REVERT: B 961 ASP cc_start: 0.7652 (m-30) cc_final: 0.7368 (m-30) REVERT: B 1054 GLU cc_start: 0.8294 (pm20) cc_final: 0.7831 (pm20) REVERT: C 306 ARG cc_start: 0.7034 (mmm-85) cc_final: 0.6407 (mmm160) REVERT: C 313 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8354 (p) REVERT: C 316 PHE cc_start: 0.7004 (t80) cc_final: 0.6509 (t80) REVERT: C 411 LYS cc_start: 0.7357 (tptm) cc_final: 0.6974 (tptp) REVERT: C 442 TYR cc_start: 0.6467 (p90) cc_final: 0.6141 (p90) REVERT: C 453 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.5143 (pmt100) REVERT: C 539 THR cc_start: 0.8380 (m) cc_final: 0.7860 (p) outliers start: 139 outliers final: 106 residues processed: 430 average time/residue: 0.1641 time to fit residues: 113.6843 Evaluate side-chains 413 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 300 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 950 SER Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1078 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 217 optimal weight: 8.9990 chunk 293 optimal weight: 0.7980 chunk 255 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 157 optimal weight: 0.0370 chunk 228 optimal weight: 1.9990 chunk 245 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 835 GLN A 883 GLN A 984 GLN B 280 GLN B 614 GLN B 661 HIS B 733 ASN B 883 GLN C 280 GLN C 599 GLN C 835 GLN C 883 GLN C 984 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.176880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.139376 restraints weight = 38779.960| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.59 r_work: 0.3520 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25918 Z= 0.134 Angle : 0.695 13.351 35340 Z= 0.338 Chirality : 0.048 0.310 4088 Planarity : 0.004 0.064 4498 Dihedral : 8.416 58.546 4278 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.94 % Allowed : 15.48 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % 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: -2.05 (0.15), residues: 3135 helix: 0.86 (0.21), residues: 631 sheet: -1.23 (0.20), residues: 625 loop : -2.32 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 315 TYR 0.023 0.001 TYR A 367 PHE 0.017 0.001 PHE C 870 TRP 0.011 0.001 TRP A 423 HIS 0.002 0.000 HIS B1040 Details of bonding type rmsd covalent geometry : bond 0.00301 (25859) covalent geometry : angle 0.67251 (35190) SS BOND : bond 0.00248 ( 18) SS BOND : angle 1.16308 ( 36) hydrogen bonds : bond 0.03551 ( 793) hydrogen bonds : angle 5.39505 ( 2244) Misc. bond : bond 0.00043 ( 3) link_NAG-ASN : bond 0.00645 ( 38) link_NAG-ASN : angle 3.12239 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 342 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8371 (mp0) cc_final: 0.8006 (mp0) REVERT: A 262 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8161 (t80) REVERT: A 316 PHE cc_start: 0.6689 (t80) cc_final: 0.6210 (t80) REVERT: A 342 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7770 (ttm170) REVERT: A 387 PHE cc_start: 0.7950 (p90) cc_final: 0.7736 (p90) REVERT: A 411 LYS cc_start: 0.7620 (tptp) cc_final: 0.7052 (tppt) REVERT: A 451 PHE cc_start: 0.8306 (m-80) cc_final: 0.8077 (m-80) REVERT: A 453 ARG cc_start: 0.5744 (OUTLIER) cc_final: 0.4430 (pmt100) REVERT: A 539 THR cc_start: 0.8373 (m) cc_final: 0.8005 (p) REVERT: A 961 ASP cc_start: 0.7719 (m-30) cc_final: 0.7250 (m-30) REVERT: A 1022 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8615 (p) REVERT: A 1054 GLU cc_start: 0.8206 (pm20) cc_final: 0.7928 (pm20) REVERT: B 263 MET cc_start: 0.8187 (ttt) cc_final: 0.7923 (ttt) REVERT: B 294 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7742 (mt-10) REVERT: B 306 ARG cc_start: 0.6568 (mmm-85) cc_final: 0.6111 (mmm160) REVERT: B 340 TRP cc_start: 0.7559 (p-90) cc_final: 0.6965 (p-90) REVERT: B 342 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7887 (ttm110) REVERT: B 390 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6408 (pttt) REVERT: B 410 TYR cc_start: 0.7260 (t80) cc_final: 0.6732 (t80) REVERT: B 447 LYS cc_start: 0.6483 (mttt) cc_final: 0.6157 (mmtm) REVERT: B 514 LYS cc_start: 0.7520 (mtmm) cc_final: 0.7285 (mttp) REVERT: B 539 THR cc_start: 0.8373 (m) cc_final: 0.7876 (p) REVERT: B 745 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7822 (tt) REVERT: B 749 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8198 (pt) REVERT: B 961 ASP cc_start: 0.7574 (m-30) cc_final: 0.7282 (m-30) REVERT: B 1049 TYR cc_start: 0.8534 (t80) cc_final: 0.8319 (t80) REVERT: B 1054 GLU cc_start: 0.8039 (pm20) cc_final: 0.7689 (pm20) REVERT: B 1071 PHE cc_start: 0.7620 (m-80) cc_final: 0.7304 (m-10) REVERT: C 256 TYR cc_start: 0.7877 (m-80) cc_final: 0.7318 (m-80) REVERT: C 262 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8531 (t80) REVERT: C 306 ARG cc_start: 0.6741 (mmm-85) cc_final: 0.6149 (mmm160) REVERT: C 411 LYS cc_start: 0.7381 (tptm) cc_final: 0.6932 (tptp) REVERT: C 442 TYR cc_start: 0.6355 (p90) cc_final: 0.6055 (p90) REVERT: C 453 ARG cc_start: 0.5203 (OUTLIER) cc_final: 0.3861 (pmt100) REVERT: C 481 TYR cc_start: 0.5598 (t80) cc_final: 0.4687 (t80) REVERT: C 539 THR cc_start: 0.8449 (m) cc_final: 0.7997 (p) REVERT: C 614 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6867 (mp10) REVERT: C 961 ASP cc_start: 0.7574 (m-30) cc_final: 0.7214 (m-30) outliers start: 108 outliers final: 84 residues processed: 418 average time/residue: 0.1638 time to fit residues: 110.5071 Evaluate side-chains 412 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 319 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 132 optimal weight: 0.0170 chunk 80 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 223 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 35 optimal weight: 0.6980 chunk 278 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 GLN B 201 GLN C 835 GLN C 883 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.177039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135186 restraints weight = 39095.054| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.72 r_work: 0.3533 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25918 Z= 0.136 Angle : 0.686 13.713 35340 Z= 0.335 Chirality : 0.048 0.310 4088 Planarity : 0.004 0.062 4498 Dihedral : 8.053 55.344 4278 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.16 % Allowed : 16.17 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % 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: -1.87 (0.15), residues: 3135 helix: 1.11 (0.21), residues: 634 sheet: -1.12 (0.20), residues: 628 loop : -2.25 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 207 TYR 0.019 0.001 TYR B 442 PHE 0.016 0.001 PHE C 870 TRP 0.006 0.001 TRP A 423 HIS 0.003 0.000 HIS C1040 Details of bonding type rmsd covalent geometry : bond 0.00313 (25859) covalent geometry : angle 0.66474 (35190) SS BOND : bond 0.00241 ( 18) SS BOND : angle 1.13840 ( 36) hydrogen bonds : bond 0.03491 ( 793) hydrogen bonds : angle 5.30691 ( 2244) Misc. bond : bond 0.00033 ( 3) link_NAG-ASN : bond 0.00593 ( 38) link_NAG-ASN : angle 3.01100 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 347 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8353 (mp0) cc_final: 0.7943 (mp0) REVERT: A 262 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8153 (t80) REVERT: A 316 PHE cc_start: 0.6594 (t80) cc_final: 0.6106 (t80) REVERT: A 342 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7762 (ttm170) REVERT: A 411 LYS cc_start: 0.7512 (tptp) cc_final: 0.6969 (tppt) REVERT: A 451 PHE cc_start: 0.8176 (m-80) cc_final: 0.7912 (m-80) REVERT: A 453 ARG cc_start: 0.5728 (OUTLIER) cc_final: 0.4412 (pmt100) REVERT: A 539 THR cc_start: 0.8367 (m) cc_final: 0.7917 (p) REVERT: A 599 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6391 (mp10) REVERT: A 961 ASP cc_start: 0.7888 (m-30) cc_final: 0.7489 (m-30) REVERT: A 1022 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8559 (p) REVERT: A 1054 GLU cc_start: 0.8338 (pm20) cc_final: 0.7925 (pm20) REVERT: B 263 MET cc_start: 0.8215 (ttt) cc_final: 0.7925 (ttt) REVERT: B 294 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7729 (mt-10) REVERT: B 306 ARG cc_start: 0.6844 (mmm-85) cc_final: 0.6388 (mmm160) REVERT: B 340 TRP cc_start: 0.7555 (p-90) cc_final: 0.6968 (p-90) REVERT: B 342 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7902 (ttm110) REVERT: B 390 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6395 (pttt) REVERT: B 410 TYR cc_start: 0.7223 (t80) cc_final: 0.6809 (t80) REVERT: B 447 LYS cc_start: 0.6565 (mttt) cc_final: 0.6187 (mmtm) REVERT: B 599 GLN cc_start: 0.6359 (OUTLIER) cc_final: 0.5896 (mp10) REVERT: B 745 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7890 (mt) REVERT: B 749 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8153 (pt) REVERT: B 961 ASP cc_start: 0.7578 (m-30) cc_final: 0.7299 (m-30) REVERT: B 1049 TYR cc_start: 0.8563 (t80) cc_final: 0.8337 (t80) REVERT: B 1054 GLU cc_start: 0.8121 (pm20) cc_final: 0.7658 (pm20) REVERT: B 1071 PHE cc_start: 0.7559 (m-80) cc_final: 0.7284 (m-10) REVERT: C 256 TYR cc_start: 0.7754 (m-80) cc_final: 0.7130 (m-80) REVERT: C 262 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8562 (t80) REVERT: C 306 ARG cc_start: 0.6776 (mmm-85) cc_final: 0.5870 (mmm160) REVERT: C 411 LYS cc_start: 0.7417 (tptm) cc_final: 0.6984 (tptp) REVERT: C 442 TYR cc_start: 0.6393 (p90) cc_final: 0.6104 (p90) REVERT: C 453 ARG cc_start: 0.5385 (OUTLIER) cc_final: 0.4204 (pmt100) REVERT: C 481 TYR cc_start: 0.5573 (t80) cc_final: 0.4788 (t80) REVERT: C 551 PHE cc_start: 0.7690 (m-10) cc_final: 0.7428 (m-80) REVERT: C 614 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6831 (mp10) REVERT: C 961 ASP cc_start: 0.7551 (m-30) cc_final: 0.7154 (m-30) outliers start: 114 outliers final: 88 residues processed: 431 average time/residue: 0.1598 time to fit residues: 112.9550 Evaluate side-chains 409 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 310 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 599 GLN Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1078 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 288 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 599 GLN A 626 ASN A 883 GLN A 901 ASN A 915 GLN B 937 ASN C 883 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.177665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140683 restraints weight = 39160.807| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.59 r_work: 0.3544 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25918 Z= 0.135 Angle : 0.687 14.862 35340 Z= 0.335 Chirality : 0.048 0.308 4088 Planarity : 0.004 0.061 4498 Dihedral : 7.819 52.974 4278 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 4.16 % Allowed : 16.54 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % 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: -1.78 (0.15), residues: 3135 helix: 1.23 (0.21), residues: 637 sheet: -0.97 (0.20), residues: 614 loop : -2.24 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 207 TYR 0.019 0.001 TYR B 598 PHE 0.016 0.001 PHE A1071 TRP 0.005 0.001 TRP B 476 HIS 0.003 0.000 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00312 (25859) covalent geometry : angle 0.66514 (35190) SS BOND : bond 0.00307 ( 18) SS BOND : angle 1.28122 ( 36) hydrogen bonds : bond 0.03433 ( 793) hydrogen bonds : angle 5.23602 ( 2244) Misc. bond : bond 0.00032 ( 3) link_NAG-ASN : bond 0.00609 ( 38) link_NAG-ASN : angle 3.05757 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 338 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8081 (t0) cc_final: 0.7838 (t0) REVERT: A 262 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8049 (t80) REVERT: A 316 PHE cc_start: 0.6789 (t80) cc_final: 0.6281 (t80) REVERT: A 342 ARG cc_start: 0.7981 (ttm170) cc_final: 0.7736 (ttm170) REVERT: A 411 LYS cc_start: 0.7499 (tptp) cc_final: 0.6991 (tppt) REVERT: A 442 TYR cc_start: 0.6148 (p90) cc_final: 0.5896 (p90) REVERT: A 451 PHE cc_start: 0.8213 (m-80) cc_final: 0.7943 (m-80) REVERT: A 453 ARG cc_start: 0.5688 (OUTLIER) cc_final: 0.4369 (pmt100) REVERT: A 539 THR cc_start: 0.8356 (m) cc_final: 0.7940 (p) REVERT: A 907 ASN cc_start: 0.7924 (m110) cc_final: 0.7386 (m-40) REVERT: A 961 ASP cc_start: 0.7910 (m-30) cc_final: 0.7492 (m-30) REVERT: A 1022 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8535 (p) REVERT: A 1054 GLU cc_start: 0.8328 (pm20) cc_final: 0.7949 (pm20) REVERT: B 144 MET cc_start: -0.1186 (ptt) cc_final: -0.1721 (ptm) REVERT: B 263 MET cc_start: 0.8185 (ttt) cc_final: 0.7898 (ttt) REVERT: B 294 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7691 (mt-10) REVERT: B 306 ARG cc_start: 0.6875 (mmm-85) cc_final: 0.6478 (mmm160) REVERT: B 340 TRP cc_start: 0.7604 (p-90) cc_final: 0.7054 (p-90) REVERT: B 342 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7854 (ttm110) REVERT: B 390 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6972 (ttmt) REVERT: B 410 TYR cc_start: 0.7240 (t80) cc_final: 0.6844 (t80) REVERT: B 447 LYS cc_start: 0.6528 (mttt) cc_final: 0.6204 (mmtm) REVERT: B 494 TYR cc_start: 0.7249 (m-10) cc_final: 0.6987 (m-10) REVERT: B 599 GLN cc_start: 0.6360 (OUTLIER) cc_final: 0.5873 (mp10) REVERT: B 745 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7992 (mt) REVERT: B 749 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8164 (pt) REVERT: B 1049 TYR cc_start: 0.8544 (t80) cc_final: 0.8320 (t80) REVERT: B 1054 GLU cc_start: 0.8153 (pm20) cc_final: 0.7731 (pm20) REVERT: C 256 TYR cc_start: 0.7708 (m-80) cc_final: 0.7125 (m-80) REVERT: C 262 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8551 (t80) REVERT: C 306 ARG cc_start: 0.6875 (mmm-85) cc_final: 0.6275 (mmm160) REVERT: C 411 LYS cc_start: 0.7601 (tptm) cc_final: 0.7131 (tptp) REVERT: C 442 TYR cc_start: 0.6416 (p90) cc_final: 0.6126 (p90) REVERT: C 453 ARG cc_start: 0.5361 (OUTLIER) cc_final: 0.4177 (pmt100) REVERT: C 481 TYR cc_start: 0.5551 (t80) cc_final: 0.4739 (t80) REVERT: C 614 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6842 (mp10) REVERT: C 961 ASP cc_start: 0.7613 (m-30) cc_final: 0.7209 (m-30) outliers start: 114 outliers final: 91 residues processed: 416 average time/residue: 0.1618 time to fit residues: 109.4307 Evaluate side-chains 425 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 324 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1078 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 199 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 177 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 0.0980 chunk 136 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 309 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 GLN A 883 GLN B 492 GLN C 492 GLN C 883 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.176296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138811 restraints weight = 38881.211| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.53 r_work: 0.3531 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 25918 Z= 0.166 Angle : 0.702 14.631 35340 Z= 0.343 Chirality : 0.049 0.315 4088 Planarity : 0.004 0.061 4498 Dihedral : 7.712 54.174 4278 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.83 % Allowed : 17.01 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % 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: -1.79 (0.15), residues: 3135 helix: 1.22 (0.21), residues: 636 sheet: -1.04 (0.20), residues: 623 loop : -2.23 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 758 TYR 0.033 0.001 TYR B 598 PHE 0.021 0.001 PHE B1071 TRP 0.005 0.001 TRP A 619 HIS 0.004 0.001 HIS C1040 Details of bonding type rmsd covalent geometry : bond 0.00389 (25859) covalent geometry : angle 0.67992 (35190) SS BOND : bond 0.00290 ( 18) SS BOND : angle 1.23527 ( 36) hydrogen bonds : bond 0.03584 ( 793) hydrogen bonds : angle 5.28790 ( 2244) Misc. bond : bond 0.00027 ( 3) link_NAG-ASN : bond 0.00614 ( 38) link_NAG-ASN : angle 3.07806 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 318 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8168 (t0) cc_final: 0.7875 (t0) REVERT: A 256 TYR cc_start: 0.7548 (m-80) cc_final: 0.7344 (m-80) REVERT: A 262 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8167 (t80) REVERT: A 316 PHE cc_start: 0.6516 (t80) cc_final: 0.6077 (t80) REVERT: A 342 ARG cc_start: 0.7990 (ttm170) cc_final: 0.7696 (ttm170) REVERT: A 411 LYS cc_start: 0.7481 (tptp) cc_final: 0.6903 (tppt) REVERT: A 451 PHE cc_start: 0.8213 (m-80) cc_final: 0.7979 (m-80) REVERT: A 453 ARG cc_start: 0.5696 (OUTLIER) cc_final: 0.4387 (pmt100) REVERT: A 539 THR cc_start: 0.8270 (m) cc_final: 0.7857 (p) REVERT: A 599 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6575 (mm-40) REVERT: A 961 ASP cc_start: 0.7815 (m-30) cc_final: 0.7362 (m-30) REVERT: A 1054 GLU cc_start: 0.8362 (pm20) cc_final: 0.8056 (pm20) REVERT: B 144 MET cc_start: -0.1384 (ptt) cc_final: -0.1892 (ptm) REVERT: B 263 MET cc_start: 0.8265 (ttt) cc_final: 0.7985 (ttt) REVERT: B 294 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7684 (mt-10) REVERT: B 306 ARG cc_start: 0.6797 (mmm-85) cc_final: 0.6193 (mmm160) REVERT: B 340 TRP cc_start: 0.7613 (p-90) cc_final: 0.6989 (p-90) REVERT: B 342 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7804 (ttm110) REVERT: B 390 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6944 (ttmt) REVERT: B 410 TYR cc_start: 0.7158 (t80) cc_final: 0.6683 (t80) REVERT: B 447 LYS cc_start: 0.6563 (mttt) cc_final: 0.6176 (mmtm) REVERT: B 494 TYR cc_start: 0.7336 (m-10) cc_final: 0.7064 (m-80) REVERT: B 599 GLN cc_start: 0.6313 (OUTLIER) cc_final: 0.5922 (mp10) REVERT: B 745 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8064 (mt) REVERT: B 749 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8158 (pt) REVERT: B 1049 TYR cc_start: 0.8564 (t80) cc_final: 0.8306 (t80) REVERT: B 1054 GLU cc_start: 0.8149 (pm20) cc_final: 0.7671 (pm20) REVERT: C 256 TYR cc_start: 0.7720 (m-80) cc_final: 0.7096 (m-80) REVERT: C 306 ARG cc_start: 0.6937 (mmm-85) cc_final: 0.6335 (mmm160) REVERT: C 411 LYS cc_start: 0.7599 (tptm) cc_final: 0.7197 (tptp) REVERT: C 442 TYR cc_start: 0.6409 (p90) cc_final: 0.6119 (p90) REVERT: C 453 ARG cc_start: 0.5422 (OUTLIER) cc_final: 0.4260 (pmt100) REVERT: C 481 TYR cc_start: 0.5550 (t80) cc_final: 0.4924 (t80) REVERT: C 614 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6855 (mp10) REVERT: C 961 ASP cc_start: 0.7594 (m-30) cc_final: 0.7205 (m-30) REVERT: C 1032 MET cc_start: 0.8588 (ptp) cc_final: 0.8228 (ptp) outliers start: 105 outliers final: 91 residues processed: 395 average time/residue: 0.1634 time to fit residues: 104.8316 Evaluate side-chains 408 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 308 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 599 GLN Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 492 GLN Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1078 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 232 optimal weight: 40.0000 chunk 276 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 252 optimal weight: 10.0000 chunk 255 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 261 optimal weight: 0.8980 chunk 266 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 140 optimal weight: 10.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN C 883 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.176104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.138748 restraints weight = 39060.382| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.36 r_work: 0.3544 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.257 25918 Z= 0.238 Angle : 0.877 59.166 35340 Z= 0.473 Chirality : 0.052 0.920 4088 Planarity : 0.005 0.173 4498 Dihedral : 7.707 54.121 4278 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.76 % Allowed : 16.90 % Favored : 79.34 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % 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: -1.79 (0.15), residues: 3135 helix: 1.22 (0.21), residues: 636 sheet: -1.05 (0.20), residues: 623 loop : -2.23 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 758 TYR 0.026 0.002 TYR C 598 PHE 0.021 0.001 PHE B1071 TRP 0.005 0.001 TRP B 101 HIS 0.004 0.001 HIS C1040 Details of bonding type rmsd covalent geometry : bond 0.00532 (25859) covalent geometry : angle 0.85754 (35190) SS BOND : bond 0.01133 ( 18) SS BOND : angle 2.39447 ( 36) hydrogen bonds : bond 0.03679 ( 793) hydrogen bonds : angle 5.29368 ( 2244) Misc. bond : bond 0.00025 ( 3) link_NAG-ASN : bond 0.00605 ( 38) link_NAG-ASN : angle 3.07621 ( 114) =============================================================================== Job complete usr+sys time: 6642.30 seconds wall clock time: 114 minutes 40.24 seconds (6880.24 seconds total)