Starting phenix.real_space_refine on Sun Sep 13 17:33:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5x58_6703/09_2026/5x58_6703.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x58_6703/09_2026/5x58_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5x58_6703/09_2026/5x58_6703.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5x58_6703/09_2026/5x58_6703.cif" model { file = "/net/cci-nas-00/data/ceres_data/5x58_6703/09_2026/5x58_6703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x58_6703/09_2026/5x58_6703.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5x58_6703/09_2026/5x58_6703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x58_6703/09_2026/5x58_6703.map" } 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25265 Number of models: 1 Model: "" Number of chains: 6 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: "C" Number of atoms: 8217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8217 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 999} 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 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 chiralities: 14 Chain: "C" 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 chiralities: 14 Time building chain proxies: 5.63, per 1000 atoms: 0.22 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: 2.41 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: 1.08 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: 6.56 Time building geometry restraints manager: 3.10 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 - 16.57: 14245 16.57 - 33.13: 575 33.13 - 49.70: 106 49.70 - 66.27: 12 66.27 - 82.83: 33 Dihedral angle restraints: 14971 sinusoidal: 5749 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 14968 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.140 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 10.447 76.935 8983 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/Z covalent geometry : bond 0.00726 / 0.33 (25859) covalent geometry : angle 1.17267 / 0.66 (35190) SS BOND : bond 0.00976 / 0.64 ( 18) SS BOND : angle 2.28457 / 1.69 ( 36) hydrogen bonds : bond 0.28529 / 19.17 ( 793) hydrogen bonds : angle 11.62957 / 8.09 ( 2244) Misc. bond : bond 0.00374 / 0.19 ( 3) link_NAG-ASN : bond 0.00903 / 0.62 ( 38) link_NAG-ASN : angle 5.34023 / 3.86 ( 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 : 0.776 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: 0.1673 time to fit residues: 184.7142 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 : 0.892 ------------------------------------------------------------------------------- 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... 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 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: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.178830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.145284 restraints weight = 39738.426| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.48 r_work: 0.3506 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 25918 Z= 0.138 Angle : 0.734 13.511 35340 Z= 0.367 Chirality : 0.049 0.348 4088 Planarity : 0.005 0.073 4498 Dihedral : 6.839 41.110 3404 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.41 % Allowed : 10.37 % Favored : 87.22 % 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: -3.35 (0.13), residues: 3135 helix: -1.57 (0.18), residues: 607 sheet: -1.72 (0.19), residues: 619 loop : -2.75 (0.12), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 342 TYR 0.036 0.002 TYR A 481 PHE 0.023 0.002 PHE A 460 TRP 0.021 0.001 TRP B 340 HIS 0.003 0.001 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (25859) covalent geometry : angle 0.71080 / 0.36 (35190) SS BOND : bond 0.00295 / 0.20 ( 18) SS BOND : angle 0.79752 / 0.61 ( 36) hydrogen bonds : bond 0.04326 / 2.88 ( 793) hydrogen bonds : angle 6.58679 / 4.56 ( 2244) Misc. bond : bond 0.00107 / 0.05 ( 3) link_NAG-ASN : bond 0.00699 / 0.49 ( 38) link_NAG-ASN : angle 3.32452 / 2.29 ( 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 553 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 487 time to evaluate : 1.073 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: A 130 PHE cc_start: 0.7260 (m-80) cc_final: 0.6609 (m-80) REVERT: A 132 LEU cc_start: 0.6903 (mm) cc_final: 0.6642 (mm) REVERT: A 316 PHE cc_start: 0.6964 (t80) cc_final: 0.6461 (t80) REVERT: A 342 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7098 (ttm-80) REVERT: A 385 ASP cc_start: 0.7669 (m-30) cc_final: 0.7122 (m-30) REVERT: A 652 ILE cc_start: 0.8267 (mt) cc_final: 0.7990 (mt) REVERT: A 693 THR cc_start: 0.8066 (p) cc_final: 0.7830 (p) REVERT: A 736 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8972 (tt) REVERT: A 972 GLU cc_start: 0.8128 (tt0) cc_final: 0.7876 (pt0) REVERT: B 130 PHE cc_start: 0.7399 (m-80) cc_final: 0.7041 (m-80) REVERT: B 260 THR cc_start: 0.8831 (m) cc_final: 0.8508 (p) REVERT: B 316 PHE cc_start: 0.7228 (t80) cc_final: 0.6911 (t80) REVERT: B 342 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7898 (ttm-80) REVERT: B 385 ASP cc_start: 0.7692 (m-30) cc_final: 0.7446 (m-30) REVERT: B 447 LYS cc_start: 0.6690 (mttt) cc_final: 0.6483 (mmtm) REVERT: B 539 THR cc_start: 0.8421 (m) cc_final: 0.8097 (p) REVERT: B 689 TYR cc_start: 0.7128 (t80) cc_final: 0.6847 (t80) REVERT: B 693 THR cc_start: 0.8347 (p) cc_final: 0.7854 (p) REVERT: B 961 ASP cc_start: 0.7531 (m-30) cc_final: 0.7275 (m-30) REVERT: B 972 GLU cc_start: 0.7916 (tt0) cc_final: 0.7699 (pt0) REVERT: B 1054 GLU cc_start: 0.7985 (pm20) cc_final: 0.7624 (pm20) REVERT: B 1071 PHE cc_start: 0.7625 (m-80) cc_final: 0.7082 (m-80) REVERT: C 78 ASN cc_start: 0.7810 (p0) cc_final: 0.7558 (p0) REVERT: C 99 ARG cc_start: 0.6017 (ptp90) cc_final: 0.5811 (ptp-170) REVERT: C 260 THR cc_start: 0.8856 (m) cc_final: 0.8531 (p) REVERT: C 305 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6444 (m-80) REVERT: C 316 PHE cc_start: 0.7381 (t80) cc_final: 0.7095 (t80) REVERT: C 338 TYR cc_start: 0.7494 (p90) cc_final: 0.6837 (p90) REVERT: C 411 LYS cc_start: 0.7662 (tptm) cc_final: 0.7271 (tptp) REVERT: C 539 THR cc_start: 0.8298 (m) cc_final: 0.7968 (p) REVERT: C 961 ASP cc_start: 0.7389 (m-30) cc_final: 0.7126 (m-30) REVERT: C 963 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7329 (mt) REVERT: C 1071 PHE cc_start: 0.7471 (m-80) cc_final: 0.7057 (m-80) outliers start: 66 outliers final: 41 residues processed: 532 average time/residue: 0.1568 time to fit residues: 133.7275 Evaluate side-chains 409 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 365 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 729 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 963 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: 1.9990 chunk 208 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 312 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 129 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 492 GLN A 526 ASN A 883 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 201 GLN B 280 GLN B 492 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 936 GLN ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN C 70 HIS C 280 GLN C 526 ASN C 661 HIS C 883 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.175394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.137419 restraints weight = 39363.748| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.91 r_work: 0.3487 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 25918 Z= 0.249 Angle : 0.775 15.452 35340 Z= 0.386 Chirality : 0.051 0.346 4088 Planarity : 0.005 0.067 4498 Dihedral : 6.631 40.442 3396 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.87 % Allowed : 12.01 % Favored : 84.12 % 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: -2.84 (0.14), residues: 3135 helix: -0.39 (0.20), residues: 612 sheet: -1.55 (0.19), residues: 656 loop : -2.66 (0.13), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 207 TYR 0.028 0.002 TYR A 598 PHE 0.019 0.002 PHE A 220 TRP 0.019 0.002 TRP B 868 HIS 0.009 0.001 HIS A1040 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.25 (25859) covalent geometry : angle 0.75056 / 0.38 (35190) SS BOND : bond 0.00446 / 0.29 ( 18) SS BOND : angle 1.07615 / 0.82 ( 36) hydrogen bonds : bond 0.04397 / 2.94 ( 793) hydrogen bonds : angle 6.17280 / 4.29 ( 2244) Misc. bond : bond 0.00076 / 0.04 ( 3) link_NAG-ASN : bond 0.00617 / 0.43 ( 38) link_NAG-ASN : angle 3.41986 / 2.34 ( 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: 106 poor density : 369 time to evaluate : 0.836 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: A 132 LEU cc_start: 0.6777 (mm) cc_final: 0.6455 (mm) REVERT: A 316 PHE cc_start: 0.6939 (t80) cc_final: 0.6338 (t80) REVERT: A 342 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7627 (ttm-80) REVERT: A 407 ASP cc_start: 0.5080 (t0) cc_final: 0.4465 (t0) REVERT: A 411 LYS cc_start: 0.7809 (tptp) cc_final: 0.7173 (tppt) REVERT: A 451 PHE cc_start: 0.8234 (m-80) cc_final: 0.7815 (m-80) REVERT: A 453 ARG cc_start: 0.5672 (OUTLIER) cc_final: 0.4651 (pmt100) REVERT: A 972 GLU cc_start: 0.8231 (tt0) cc_final: 0.7842 (pt0) REVERT: A 1054 GLU cc_start: 0.8219 (pm20) cc_final: 0.7918 (pm20) REVERT: B 263 MET cc_start: 0.8289 (ttt) cc_final: 0.8017 (ttt) REVERT: B 316 PHE cc_start: 0.7155 (t80) cc_final: 0.6726 (t80) REVERT: B 340 TRP cc_start: 0.7433 (p-90) cc_final: 0.7029 (p-90) REVERT: B 342 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7882 (ttm-80) REVERT: B 410 TYR cc_start: 0.7216 (t80) cc_final: 0.6772 (t80) REVERT: B 447 LYS cc_start: 0.6784 (mttt) cc_final: 0.6354 (mmtm) REVERT: B 481 TYR cc_start: 0.6395 (t80) cc_final: 0.5290 (t80) REVERT: B 539 THR cc_start: 0.8464 (m) cc_final: 0.8013 (p) REVERT: B 551 PHE cc_start: 0.7441 (m-10) cc_final: 0.7110 (m-80) REVERT: B 599 GLN cc_start: 0.6099 (OUTLIER) cc_final: 0.5873 (mm-40) REVERT: B 689 TYR cc_start: 0.7464 (t80) cc_final: 0.7261 (t80) REVERT: B 745 LEU cc_start: 0.8596 (tm) cc_final: 0.8061 (mt) REVERT: B 749 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8458 (pt) REVERT: B 961 ASP cc_start: 0.7538 (m-30) cc_final: 0.7322 (m-30) REVERT: B 972 GLU cc_start: 0.8283 (tt0) cc_final: 0.8031 (tm-30) REVERT: B 1054 GLU cc_start: 0.8049 (pm20) cc_final: 0.7656 (pm20) REVERT: C 232 ARG cc_start: 0.7862 (ttp-110) cc_final: 0.7612 (mtp180) REVERT: C 260 THR cc_start: 0.8885 (m) cc_final: 0.8351 (p) REVERT: C 305 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6671 (m-10) REVERT: C 316 PHE cc_start: 0.7290 (t80) cc_final: 0.6898 (t80) REVERT: C 338 TYR cc_start: 0.7526 (p90) cc_final: 0.6348 (p90) REVERT: C 340 TRP cc_start: 0.8059 (p-90) cc_final: 0.6969 (p-90) REVERT: C 390 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6649 (tttt) REVERT: C 411 LYS cc_start: 0.7624 (tptm) cc_final: 0.7299 (tptp) REVERT: C 442 TYR cc_start: 0.6483 (p90) cc_final: 0.6163 (p90) REVERT: C 453 ARG cc_start: 0.5505 (OUTLIER) cc_final: 0.4986 (pmt100) REVERT: C 745 LEU cc_start: 0.8507 (tm) cc_final: 0.8015 (mt) REVERT: C 746 ASN cc_start: 0.8182 (t0) cc_final: 0.7896 (t0) REVERT: C 961 ASP cc_start: 0.7383 (m-30) cc_final: 0.7126 (m-30) REVERT: C 969 VAL cc_start: 0.8486 (m) cc_final: 0.8033 (p) REVERT: C 1071 PHE cc_start: 0.7807 (m-80) cc_final: 0.7493 (m-80) outliers start: 106 outliers final: 80 residues processed: 445 average time/residue: 0.1552 time to fit residues: 111.7599 Evaluate side-chains 411 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 325 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 313 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 594 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 969 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 102 VAL Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 305 PHE 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 524 CYS Chi-restraints excluded: chain B residue 525 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 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 749 LEU Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE 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 969 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU 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 151 MET 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 372 THR 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 500 SER 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 603 CYS 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 893 VAL Chi-restraints excluded: chain C residue 950 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 297 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 283 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 249 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 614 GLN A 883 GLN A 889 ASN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN A1090 ASN B 70 HIS B 614 GLN B 835 GLN B 883 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1090 ASN C 280 GLN C 492 GLN C 546 GLN C 614 GLN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.177266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.139410 restraints weight = 39072.555| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.74 r_work: 0.3529 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 25918 Z= 0.154 Angle : 0.694 14.106 35340 Z= 0.344 Chirality : 0.049 0.326 4088 Planarity : 0.004 0.066 4498 Dihedral : 6.280 38.209 3396 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.09 % Allowed : 12.52 % Favored : 83.39 % 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: -2.43 (0.14), residues: 3135 helix: 0.34 (0.21), residues: 621 sheet: -1.40 (0.19), residues: 657 loop : -2.51 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 342 TYR 0.022 0.001 TYR A 481 PHE 0.019 0.001 PHE C 870 TRP 0.012 0.001 TRP A 423 HIS 0.004 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (25859) covalent geometry : angle 0.67145 / 0.34 (35190) SS BOND : bond 0.00481 / 0.23 ( 18) SS BOND : angle 1.67389 / 1.17 ( 36) hydrogen bonds : bond 0.03810 / 2.54 ( 793) hydrogen bonds : angle 5.72741 / 3.98 ( 2244) Misc. bond : bond 0.00053 / 0.03 ( 3) link_NAG-ASN : bond 0.00619 / 0.43 ( 38) link_NAG-ASN : angle 3.06265 / 2.11 ( 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 474 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 362 time to evaluate : 0.991 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: A 132 LEU cc_start: 0.6762 (mm) cc_final: 0.6395 (mm) REVERT: A 262 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8261 (t80) REVERT: A 316 PHE cc_start: 0.6759 (t80) cc_final: 0.6289 (t80) REVERT: A 342 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7746 (ttm-80) REVERT: A 411 LYS cc_start: 0.7523 (tptp) cc_final: 0.7161 (tppt) REVERT: A 442 TYR cc_start: 0.6386 (p90) cc_final: 0.6118 (p90) REVERT: A 451 PHE cc_start: 0.8211 (m-80) cc_final: 0.7742 (m-80) REVERT: A 453 ARG cc_start: 0.5615 (OUTLIER) cc_final: 0.4190 (pmt100) REVERT: A 514 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7637 (mttp) REVERT: A 539 THR cc_start: 0.8366 (m) cc_final: 0.7986 (p) REVERT: A 961 ASP cc_start: 0.7780 (m-30) cc_final: 0.7485 (m-30) REVERT: A 972 GLU cc_start: 0.8195 (tt0) cc_final: 0.7757 (pt0) REVERT: A 1022 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8769 (p) REVERT: A 1054 GLU cc_start: 0.8172 (pm20) cc_final: 0.7878 (pm20) REVERT: B 263 MET cc_start: 0.8148 (ttt) cc_final: 0.7802 (ttt) REVERT: B 294 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7767 (mt-10) REVERT: B 306 ARG cc_start: 0.6827 (mmm-85) cc_final: 0.6511 (tpp80) REVERT: B 316 PHE cc_start: 0.6988 (t80) cc_final: 0.6581 (t80) REVERT: B 340 TRP cc_start: 0.7591 (p-90) cc_final: 0.7142 (p-90) REVERT: B 342 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7787 (ttm-80) REVERT: B 410 TYR cc_start: 0.7282 (t80) cc_final: 0.6911 (t80) REVERT: B 447 LYS cc_start: 0.6613 (mttt) cc_final: 0.6326 (mmtm) REVERT: B 481 TYR cc_start: 0.6301 (t80) cc_final: 0.5108 (t80) REVERT: B 539 THR cc_start: 0.8465 (m) cc_final: 0.8021 (p) REVERT: B 689 TYR cc_start: 0.7422 (t80) cc_final: 0.7199 (t80) REVERT: B 745 LEU cc_start: 0.8424 (tm) cc_final: 0.8020 (tt) REVERT: B 749 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8232 (pt) REVERT: B 961 ASP cc_start: 0.7423 (m-30) cc_final: 0.7102 (m-30) REVERT: B 972 GLU cc_start: 0.8188 (tt0) cc_final: 0.7987 (tm-30) REVERT: B 1054 GLU cc_start: 0.8031 (pm20) cc_final: 0.7642 (pm20) REVERT: C 106 THR cc_start: 0.7753 (p) cc_final: 0.7524 (t) REVERT: C 305 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6587 (m-80) REVERT: C 316 PHE cc_start: 0.6921 (t80) cc_final: 0.6549 (t80) REVERT: C 338 TYR cc_start: 0.7626 (p90) cc_final: 0.6398 (p90) REVERT: C 411 LYS cc_start: 0.7457 (tptm) cc_final: 0.7025 (tptp) REVERT: C 442 TYR cc_start: 0.6596 (p90) cc_final: 0.6286 (p90) REVERT: C 453 ARG cc_start: 0.5231 (OUTLIER) cc_final: 0.4051 (pmt100) REVERT: C 581 VAL cc_start: 0.9269 (t) cc_final: 0.9000 (t) REVERT: C 614 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: C 745 LEU cc_start: 0.8383 (tm) cc_final: 0.8071 (mt) REVERT: C 746 ASN cc_start: 0.8160 (t0) cc_final: 0.7917 (t0) REVERT: C 961 ASP cc_start: 0.7354 (m-30) cc_final: 0.7061 (m-30) REVERT: C 1071 PHE cc_start: 0.7687 (m-80) cc_final: 0.7482 (m-80) outliers start: 112 outliers final: 81 residues processed: 445 average time/residue: 0.1529 time to fit residues: 111.1770 Evaluate side-chains 409 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 321 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 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 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 922 THR 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 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 305 PHE 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 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 497 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 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 749 LEU Chi-restraints excluded: chain B residue 870 PHE 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 969 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1082 THR 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 151 MET 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 372 THR Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 546 GLN 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 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 893 VAL Chi-restraints excluded: chain C residue 1022 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 30 optimal weight: 0.0170 chunk 221 optimal weight: 6.9990 chunk 312 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 304 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 309 optimal weight: 0.9980 chunk 252 optimal weight: 10.0000 overall best weight: 2.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN A 883 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 492 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN C 883 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.175631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137994 restraints weight = 38839.461| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.53 r_work: 0.3520 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 25918 Z= 0.184 Angle : 0.695 14.730 35340 Z= 0.345 Chirality : 0.049 0.329 4088 Planarity : 0.004 0.067 4498 Dihedral : 6.157 38.592 3396 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 4.67 % Allowed : 13.36 % Favored : 81.96 % 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: -2.22 (0.14), residues: 3135 helix: 0.62 (0.22), residues: 621 sheet: -1.24 (0.20), residues: 639 loop : -2.43 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 207 TYR 0.019 0.001 TYR A 481 PHE 0.020 0.001 PHE A 220 TRP 0.013 0.001 TRP A 423 HIS 0.009 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (25859) covalent geometry : angle 0.67318 / 0.34 (35190) SS BOND : bond 0.00529 / 0.30 ( 18) SS BOND : angle 1.45231 / 0.97 ( 36) hydrogen bonds : bond 0.03799 / 2.53 ( 793) hydrogen bonds : angle 5.59533 / 3.90 ( 2244) Misc. bond : bond 0.00049 / 0.02 ( 3) link_NAG-ASN : bond 0.00577 / 0.41 ( 38) link_NAG-ASN : angle 3.03427 / 2.07 ( 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 466 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 338 time to evaluate : 0.907 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: 0.6771 (OUTLIER) cc_final: 0.6465 (mm) REVERT: A 232 ARG cc_start: 0.7825 (ttp-110) cc_final: 0.7512 (ttp80) REVERT: A 262 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8227 (t80) REVERT: A 316 PHE cc_start: 0.6762 (t80) cc_final: 0.6257 (t80) REVERT: A 411 LYS cc_start: 0.7548 (tptp) cc_final: 0.7247 (tppt) REVERT: A 442 TYR cc_start: 0.6108 (p90) cc_final: 0.5889 (p90) REVERT: A 451 PHE cc_start: 0.8221 (m-80) cc_final: 0.7816 (m-80) REVERT: A 453 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.4488 (pmt100) REVERT: A 539 THR cc_start: 0.8367 (m) cc_final: 0.7965 (p) REVERT: A 961 ASP cc_start: 0.7771 (m-30) cc_final: 0.7443 (m-30) REVERT: A 1054 GLU cc_start: 0.8186 (pm20) cc_final: 0.7869 (pm20) REVERT: B 263 MET cc_start: 0.8177 (ttt) cc_final: 0.7889 (ttt) REVERT: B 316 PHE cc_start: 0.7006 (t80) cc_final: 0.6543 (t80) REVERT: B 340 TRP cc_start: 0.7530 (p-90) cc_final: 0.6969 (p-90) REVERT: B 342 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7703 (ttm-80) REVERT: B 385 ASP cc_start: 0.7605 (m-30) cc_final: 0.6903 (m-30) REVERT: B 410 TYR cc_start: 0.7230 (t80) cc_final: 0.6881 (t80) REVERT: B 447 LYS cc_start: 0.6802 (mttt) cc_final: 0.6383 (mmtm) REVERT: B 481 TYR cc_start: 0.6349 (t80) cc_final: 0.5204 (t80) REVERT: B 539 THR cc_start: 0.8457 (m) cc_final: 0.7957 (p) REVERT: B 599 GLN cc_start: 0.6206 (OUTLIER) cc_final: 0.5716 (mm-40) REVERT: B 745 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8106 (mt) REVERT: B 749 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8242 (pt) REVERT: B 961 ASP cc_start: 0.7593 (m-30) cc_final: 0.7324 (m-30) REVERT: B 972 GLU cc_start: 0.8162 (tt0) cc_final: 0.7941 (tm-30) REVERT: B 1054 GLU cc_start: 0.8080 (pm20) cc_final: 0.7712 (pm20) REVERT: B 1071 PHE cc_start: 0.7897 (m-80) cc_final: 0.7564 (m-80) REVERT: C 99 ARG cc_start: 0.6216 (ptp-170) cc_final: 0.5920 (ptp-170) REVERT: C 262 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8408 (t80) REVERT: C 305 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6652 (m-10) REVERT: C 306 ARG cc_start: 0.6570 (mmm-85) cc_final: 0.5781 (mmm160) REVERT: C 316 PHE cc_start: 0.6883 (t80) cc_final: 0.6506 (t80) REVERT: C 338 TYR cc_start: 0.7544 (p90) cc_final: 0.7062 (p90) REVERT: C 411 LYS cc_start: 0.7439 (tptm) cc_final: 0.7145 (tptp) REVERT: C 442 TYR cc_start: 0.6577 (p90) cc_final: 0.6271 (p90) REVERT: C 453 ARG cc_start: 0.5446 (OUTLIER) cc_final: 0.4336 (pmt100) REVERT: C 581 VAL cc_start: 0.9250 (t) cc_final: 0.9024 (t) REVERT: C 614 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6745 (mp10) REVERT: C 961 ASP cc_start: 0.7537 (m-30) cc_final: 0.7249 (m-30) outliers start: 128 outliers final: 95 residues processed: 425 average time/residue: 0.1524 time to fit residues: 105.2133 Evaluate side-chains 411 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 306 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 423 TRP Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 525 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 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 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1042 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 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 181 HIS Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 305 PHE 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 412 LEU Chi-restraints excluded: chain B residue 423 TRP Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 497 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 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 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 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 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 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 385 ASP 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 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 601 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 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1063 ILE 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: 10.0000 chunk 140 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 181 optimal weight: 0.0970 chunk 7 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 overall best weight: 2.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS A 599 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN B 280 GLN B 492 GLN B 614 GLN B 931 GLN B 984 GLN C 129 ASN C 492 GLN C 883 GLN C 931 GLN C 984 GLN C 987 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.174449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.137051 restraints weight = 38993.418| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.60 r_work: 0.3508 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 25918 Z= 0.213 Angle : 0.712 14.589 35340 Z= 0.353 Chirality : 0.050 0.331 4088 Planarity : 0.005 0.065 4498 Dihedral : 6.150 37.478 3396 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 5.07 % Allowed : 13.47 % Favored : 81.45 % 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: -2.18 (0.14), residues: 3135 helix: 0.62 (0.21), residues: 627 sheet: -1.18 (0.20), residues: 640 loop : -2.40 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 207 TYR 0.018 0.002 TYR B 442 PHE 0.019 0.002 PHE A1071 TRP 0.014 0.001 TRP A 423 HIS 0.006 0.001 HIS A1040 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (25859) covalent geometry : angle 0.69016 / 0.35 (35190) SS BOND : bond 0.00400 / 0.26 ( 18) SS BOND : angle 1.27917 / 0.91 ( 36) hydrogen bonds : bond 0.03854 / 2.57 ( 793) hydrogen bonds : angle 5.55758 / 3.87 ( 2244) Misc. bond : bond 0.00050 / 0.03 ( 3) link_NAG-ASN : bond 0.00574 / 0.40 ( 38) link_NAG-ASN : angle 3.08525 / 2.08 ( 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 : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6314 (mm) REVERT: A 232 ARG cc_start: 0.7849 (ttp-110) cc_final: 0.7546 (ttp80) REVERT: A 262 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8579 (t80) REVERT: A 316 PHE cc_start: 0.6769 (t80) cc_final: 0.6276 (t80) REVERT: A 411 LYS cc_start: 0.7463 (tptp) cc_final: 0.7100 (tppt) REVERT: A 442 TYR cc_start: 0.6110 (p90) cc_final: 0.5878 (p90) REVERT: A 451 PHE cc_start: 0.8198 (m-80) cc_final: 0.7926 (m-80) REVERT: A 453 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.4559 (pmt100) REVERT: A 539 THR cc_start: 0.8338 (m) cc_final: 0.7917 (p) REVERT: A 961 ASP cc_start: 0.7889 (m-30) cc_final: 0.7485 (m-30) REVERT: A 1054 GLU cc_start: 0.8267 (pm20) cc_final: 0.7899 (pm20) REVERT: B 263 MET cc_start: 0.8282 (ttt) cc_final: 0.8001 (ttt) REVERT: B 294 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7787 (mt-10) REVERT: B 306 ARG cc_start: 0.6923 (mmm-85) cc_final: 0.6419 (mmt90) REVERT: B 316 PHE cc_start: 0.7013 (t80) cc_final: 0.6538 (t80) REVERT: B 340 TRP cc_start: 0.7489 (p-90) cc_final: 0.6962 (p-90) REVERT: B 342 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: B 385 ASP cc_start: 0.7711 (m-30) cc_final: 0.6974 (m-30) REVERT: B 410 TYR cc_start: 0.7113 (t80) cc_final: 0.6620 (t80) REVERT: B 447 LYS cc_start: 0.6382 (mttt) cc_final: 0.6088 (mmtm) REVERT: B 527 PHE cc_start: 0.8492 (p90) cc_final: 0.8161 (p90) REVERT: B 539 THR cc_start: 0.8456 (m) cc_final: 0.7940 (p) REVERT: B 745 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8136 (mt) REVERT: B 749 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8295 (pt) REVERT: B 946 LYS cc_start: 0.8737 (mtpm) cc_final: 0.8520 (mtpp) REVERT: B 961 ASP cc_start: 0.7601 (m-30) cc_final: 0.7320 (m-30) REVERT: B 972 GLU cc_start: 0.8222 (tt0) cc_final: 0.7893 (tm-30) REVERT: B 1054 GLU cc_start: 0.8210 (pm20) cc_final: 0.7816 (pm20) REVERT: B 1071 PHE cc_start: 0.7972 (m-80) cc_final: 0.7691 (m-80) REVERT: C 262 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8655 (t80) REVERT: C 305 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6998 (m-10) REVERT: C 306 ARG cc_start: 0.6853 (mmm-85) cc_final: 0.6170 (mmm160) REVERT: C 316 PHE cc_start: 0.6934 (t80) cc_final: 0.6524 (t80) REVERT: C 338 TYR cc_start: 0.7599 (p90) cc_final: 0.6916 (p90) REVERT: C 411 LYS cc_start: 0.7475 (tptm) cc_final: 0.6968 (tptp) REVERT: C 442 TYR cc_start: 0.6528 (p90) cc_final: 0.6212 (p90) REVERT: C 453 ARG cc_start: 0.5476 (OUTLIER) cc_final: 0.4473 (pmt100) REVERT: C 961 ASP cc_start: 0.7545 (m-30) cc_final: 0.7242 (m-30) REVERT: C 969 VAL cc_start: 0.8404 (m) cc_final: 0.8032 (p) REVERT: C 972 GLU cc_start: 0.7929 (pt0) cc_final: 0.6983 (tm-30) outliers start: 139 outliers final: 101 residues processed: 429 average time/residue: 0.1491 time to fit residues: 105.1115 Evaluate side-chains 421 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 312 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 262 PHE Chi-restraints excluded: chain A residue 263 MET 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 423 TRP Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 525 VAL 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 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 870 PHE 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 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1042 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 211 SER 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 305 PHE 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 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 497 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 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 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 262 PHE Chi-restraints excluded: chain C residue 302 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 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 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 601 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 891 ILE Chi-restraints excluded: chain C residue 893 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: 10.0000 chunk 293 optimal weight: 4.9990 chunk 255 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 228 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN A 661 HIS A 915 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 614 GLN C 883 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.179254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.145121 restraints weight = 38628.399| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 3.21 r_work: 0.3567 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 25918 Z= 0.191 Angle : 0.701 13.971 35340 Z= 0.347 Chirality : 0.049 0.327 4088 Planarity : 0.004 0.064 4498 Dihedral : 6.067 36.474 3396 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.71 % Allowed : 14.17 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % Twisted General : 0.03 % 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: -2.11 (0.15), residues: 3135 helix: 0.73 (0.21), residues: 623 sheet: -1.22 (0.20), residues: 648 loop : -2.34 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 315 TYR 0.021 0.002 TYR A 163 PHE 0.019 0.002 PHE B 130 TRP 0.012 0.001 TRP A 423 HIS 0.005 0.001 HIS A1040 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (25859) covalent geometry : angle 0.67930 / 0.34 (35190) SS BOND : bond 0.00355 / 0.23 ( 18) SS BOND : angle 1.79498 / 1.26 ( 36) hydrogen bonds : bond 0.03772 / 2.51 ( 793) hydrogen bonds : angle 5.51195 / 3.84 ( 2244) Misc. bond : bond 0.00039 / 0.02 ( 3) link_NAG-ASN : bond 0.00592 / 0.42 ( 38) link_NAG-ASN : angle 3.00273 / 2.04 ( 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 458 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 329 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7649 (ttp80) REVERT: A 262 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8615 (t80) REVERT: A 316 PHE cc_start: 0.6796 (t80) cc_final: 0.6323 (t80) REVERT: A 411 LYS cc_start: 0.7501 (tptp) cc_final: 0.7136 (tppt) REVERT: A 451 PHE cc_start: 0.8386 (m-80) cc_final: 0.8124 (m-80) REVERT: A 453 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.4631 (pmt100) REVERT: A 539 THR cc_start: 0.8448 (m) cc_final: 0.8041 (p) REVERT: A 599 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.7072 (mm-40) REVERT: A 961 ASP cc_start: 0.7973 (m-30) cc_final: 0.7583 (m-30) REVERT: A 1054 GLU cc_start: 0.8254 (pm20) cc_final: 0.7897 (pm20) REVERT: B 263 MET cc_start: 0.8120 (ttt) cc_final: 0.7899 (ttt) REVERT: B 294 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7789 (mt-10) REVERT: B 306 ARG cc_start: 0.6669 (mmm-85) cc_final: 0.6353 (mmt90) REVERT: B 316 PHE cc_start: 0.6860 (t80) cc_final: 0.6425 (t80) REVERT: B 340 TRP cc_start: 0.7705 (p-90) cc_final: 0.7095 (p-90) REVERT: B 342 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.8001 (ttm-80) REVERT: B 390 LYS cc_start: 0.7201 (ttmt) cc_final: 0.6530 (pttt) REVERT: B 410 TYR cc_start: 0.7290 (t80) cc_final: 0.6783 (t80) REVERT: B 527 PHE cc_start: 0.8531 (p90) cc_final: 0.8270 (p90) REVERT: B 539 THR cc_start: 0.8513 (m) cc_final: 0.8002 (p) REVERT: B 745 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8177 (mt) REVERT: B 749 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8267 (pt) REVERT: B 961 ASP cc_start: 0.7546 (m-30) cc_final: 0.7263 (m-30) REVERT: B 1049 TYR cc_start: 0.8590 (t80) cc_final: 0.8339 (t80) REVERT: B 1054 GLU cc_start: 0.8102 (pm20) cc_final: 0.7777 (pm20) REVERT: B 1071 PHE cc_start: 0.7711 (m-80) cc_final: 0.7465 (m-80) REVERT: C 99 ARG cc_start: 0.6186 (ptp-170) cc_final: 0.5936 (ptp-170) REVERT: C 262 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8603 (t80) REVERT: C 306 ARG cc_start: 0.6876 (mmm-85) cc_final: 0.6305 (mmm160) REVERT: C 338 TYR cc_start: 0.7709 (p90) cc_final: 0.7048 (p90) REVERT: C 411 LYS cc_start: 0.7561 (tptm) cc_final: 0.7085 (tptp) REVERT: C 442 TYR cc_start: 0.6560 (p90) cc_final: 0.6255 (p90) REVERT: C 453 ARG cc_start: 0.5590 (OUTLIER) cc_final: 0.4417 (pmt100) REVERT: C 481 TYR cc_start: 0.5585 (t80) cc_final: 0.4730 (t80) REVERT: C 551 PHE cc_start: 0.7829 (m-10) cc_final: 0.7586 (m-80) REVERT: C 614 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6973 (mp10) REVERT: C 961 ASP cc_start: 0.7639 (m-30) cc_final: 0.7362 (m-30) outliers start: 129 outliers final: 106 residues processed: 427 average time/residue: 0.1529 time to fit residues: 106.5480 Evaluate side-chains 421 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 307 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 388 VAL Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 525 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 599 GLN Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 652 ILE 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 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 1042 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 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 211 SER 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 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 497 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 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 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 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 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 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 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 601 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 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 1078 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 132 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 278 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 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 = 0.4243 r_free = 0.4243 target = 0.176419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.138884 restraints weight = 38821.301| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.60 r_work: 0.3542 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25918 Z= 0.146 Angle : 0.676 13.698 35340 Z= 0.334 Chirality : 0.049 0.319 4088 Planarity : 0.004 0.063 4498 Dihedral : 5.892 36.411 3396 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.60 % Allowed : 14.60 % Favored : 80.80 % 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: -1.96 (0.15), residues: 3135 helix: 0.90 (0.21), residues: 630 sheet: -1.21 (0.20), residues: 644 loop : -2.24 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 315 TYR 0.019 0.001 TYR B 442 PHE 0.017 0.001 PHE A1071 TRP 0.006 0.001 TRP A 423 HIS 0.003 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (25859) covalent geometry : angle 0.65640 / 0.33 (35190) SS BOND : bond 0.00273 / 0.18 ( 18) SS BOND : angle 1.37646 / 0.97 ( 36) hydrogen bonds : bond 0.03529 / 2.36 ( 793) hydrogen bonds : angle 5.36392 / 3.73 ( 2244) Misc. bond : bond 0.00035 / 0.02 ( 3) link_NAG-ASN : bond 0.00619 / 0.44 ( 38) link_NAG-ASN : angle 2.83199 / 1.92 ( 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 473 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 347 time to evaluate : 0.703 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 232 ARG cc_start: 0.7703 (ttp-110) cc_final: 0.7464 (ttp80) REVERT: A 262 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8535 (t80) REVERT: A 294 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7884 (pt0) REVERT: A 316 PHE cc_start: 0.6630 (t80) cc_final: 0.6154 (t80) REVERT: A 342 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7578 (ttm170) REVERT: A 411 LYS cc_start: 0.7249 (tptp) cc_final: 0.6967 (tppt) REVERT: A 451 PHE cc_start: 0.8124 (m-80) cc_final: 0.7840 (m-80) REVERT: A 453 ARG cc_start: 0.5620 (OUTLIER) cc_final: 0.4347 (pmt100) REVERT: A 539 THR cc_start: 0.8340 (m) cc_final: 0.7895 (p) REVERT: A 599 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6983 (mm-40) REVERT: A 961 ASP cc_start: 0.7735 (m-30) cc_final: 0.7328 (m-30) REVERT: A 1022 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8678 (p) REVERT: A 1054 GLU cc_start: 0.8273 (pm20) cc_final: 0.7901 (pm20) REVERT: B 256 TYR cc_start: 0.8027 (m-80) cc_final: 0.7819 (m-80) REVERT: B 263 MET cc_start: 0.8262 (ttt) cc_final: 0.7997 (ttt) REVERT: B 294 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7731 (mt-10) REVERT: B 306 ARG cc_start: 0.6789 (mmm-85) cc_final: 0.6276 (mmt90) REVERT: B 316 PHE cc_start: 0.6777 (t80) cc_final: 0.6311 (t80) REVERT: B 340 TRP cc_start: 0.7541 (p-90) cc_final: 0.6958 (p-90) REVERT: B 342 ARG cc_start: 0.8128 (ttm-80) cc_final: 0.7841 (ttm110) REVERT: B 390 LYS cc_start: 0.7079 (ttmt) cc_final: 0.6418 (tttt) REVERT: B 410 TYR cc_start: 0.7223 (t80) cc_final: 0.6674 (t80) REVERT: B 527 PHE cc_start: 0.8489 (p90) cc_final: 0.8255 (p90) REVERT: B 539 THR cc_start: 0.8435 (m) cc_final: 0.7909 (p) REVERT: B 745 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8068 (mt) REVERT: B 749 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8173 (pt) REVERT: B 961 ASP cc_start: 0.7490 (m-30) cc_final: 0.7173 (m-30) REVERT: B 1049 TYR cc_start: 0.8626 (t80) cc_final: 0.8364 (t80) REVERT: B 1054 GLU cc_start: 0.8120 (pm20) cc_final: 0.7751 (pm20) REVERT: B 1071 PHE cc_start: 0.7605 (m-80) cc_final: 0.7359 (m-10) REVERT: C 256 TYR cc_start: 0.7862 (m-80) cc_final: 0.7173 (m-80) REVERT: C 262 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8521 (t80) REVERT: C 306 ARG cc_start: 0.6529 (mmm-85) cc_final: 0.5906 (mmm160) REVERT: C 338 TYR cc_start: 0.7640 (p90) cc_final: 0.6961 (p90) REVERT: C 411 LYS cc_start: 0.7468 (tptm) cc_final: 0.6972 (tptp) REVERT: C 442 TYR cc_start: 0.6406 (p90) cc_final: 0.6116 (p90) REVERT: C 453 ARG cc_start: 0.5348 (OUTLIER) cc_final: 0.4285 (pmt100) REVERT: C 481 TYR cc_start: 0.5565 (t80) cc_final: 0.4640 (t80) REVERT: C 961 ASP cc_start: 0.7574 (m-30) cc_final: 0.7273 (m-30) REVERT: C 972 GLU cc_start: 0.7888 (pt0) cc_final: 0.7577 (tm-30) REVERT: C 1054 GLU cc_start: 0.8338 (pp20) cc_final: 0.7853 (pp20) outliers start: 126 outliers final: 98 residues processed: 435 average time/residue: 0.1422 time to fit residues: 101.6769 Evaluate side-chains 428 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 322 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 388 VAL Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 525 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 599 GLN Chi-restraints excluded: chain A residue 614 GLN 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 736 LEU 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 891 ILE 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 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1042 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 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 385 ASP Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG 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 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 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 969 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 51 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 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 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 603 CYS 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 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: 0.9980 chunk 35 optimal weight: 0.6980 chunk 296 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 626 ASN A 883 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.176377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.138694 restraints weight = 38922.734| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.48 r_work: 0.3529 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 25918 Z= 0.158 Angle : 0.690 14.019 35340 Z= 0.340 Chirality : 0.049 0.318 4088 Planarity : 0.004 0.061 4498 Dihedral : 5.872 35.510 3396 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 4.49 % Allowed : 14.90 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % Twisted General : 0.07 % 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: -1.91 (0.15), residues: 3135 helix: 1.01 (0.21), residues: 628 sheet: -1.12 (0.20), residues: 635 loop : -2.24 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 315 TYR 0.020 0.001 TYR C 689 PHE 0.016 0.001 PHE C 870 TRP 0.008 0.001 TRP C 476 HIS 0.004 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (25859) covalent geometry : angle 0.66823 / 0.33 (35190) SS BOND : bond 0.00339 / 0.22 ( 18) SS BOND : angle 1.61039 / 1.05 ( 36) hydrogen bonds : bond 0.03566 / 2.38 ( 793) hydrogen bonds : angle 5.34580 / 3.72 ( 2244) Misc. bond : bond 0.00031 / 0.02 ( 3) link_NAG-ASN : bond 0.00594 / 0.42 ( 38) link_NAG-ASN : angle 2.96379 / 2.04 ( 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 451 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 328 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.7519 (ttp80) REVERT: A 262 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8566 (t80) REVERT: A 294 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7807 (pt0) REVERT: A 306 ARG cc_start: 0.6909 (mmm-85) cc_final: 0.5944 (mmm160) REVERT: A 316 PHE cc_start: 0.6585 (t80) cc_final: 0.6110 (t80) REVERT: A 342 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7620 (ttm170) REVERT: A 411 LYS cc_start: 0.7352 (tptp) cc_final: 0.7016 (tppt) REVERT: A 442 TYR cc_start: 0.6155 (p90) cc_final: 0.5896 (p90) REVERT: A 451 PHE cc_start: 0.8264 (m-80) cc_final: 0.7970 (m-80) REVERT: A 453 ARG cc_start: 0.5610 (OUTLIER) cc_final: 0.4309 (pmt100) REVERT: A 539 THR cc_start: 0.8378 (m) cc_final: 0.7955 (p) REVERT: A 599 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7063 (mm-40) REVERT: A 961 ASP cc_start: 0.7897 (m-30) cc_final: 0.7529 (m-30) REVERT: A 1022 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8700 (p) REVERT: A 1054 GLU cc_start: 0.8317 (pm20) cc_final: 0.7955 (pm20) REVERT: B 32 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.7030 (mp10) REVERT: B 256 TYR cc_start: 0.8009 (m-80) cc_final: 0.7783 (m-80) REVERT: B 263 MET cc_start: 0.8223 (ttt) cc_final: 0.7965 (ttt) REVERT: B 294 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7719 (mt-10) REVERT: B 302 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6820 (m) REVERT: B 316 PHE cc_start: 0.6750 (t80) cc_final: 0.6280 (t80) REVERT: B 340 TRP cc_start: 0.7619 (p-90) cc_final: 0.7045 (p-90) REVERT: B 342 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7859 (ttm110) REVERT: B 410 TYR cc_start: 0.7236 (t80) cc_final: 0.6735 (t80) REVERT: B 527 PHE cc_start: 0.8508 (p90) cc_final: 0.8290 (p90) REVERT: B 745 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7857 (mt) REVERT: B 749 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8172 (pt) REVERT: B 840 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8776 (mm) REVERT: B 972 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7985 (tm-30) REVERT: B 1049 TYR cc_start: 0.8573 (t80) cc_final: 0.8335 (t80) REVERT: B 1054 GLU cc_start: 0.8190 (pm20) cc_final: 0.7853 (pm20) REVERT: C 256 TYR cc_start: 0.7770 (m-80) cc_final: 0.7166 (m-80) REVERT: C 262 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8568 (t80) REVERT: C 306 ARG cc_start: 0.6794 (mmm-85) cc_final: 0.5958 (mmm160) REVERT: C 411 LYS cc_start: 0.7558 (tptm) cc_final: 0.7035 (tptp) REVERT: C 442 TYR cc_start: 0.6430 (p90) cc_final: 0.6132 (p90) REVERT: C 453 ARG cc_start: 0.5391 (OUTLIER) cc_final: 0.4303 (pmt100) REVERT: C 481 TYR cc_start: 0.5541 (t80) cc_final: 0.4821 (t80) REVERT: C 551 PHE cc_start: 0.7742 (m-10) cc_final: 0.7467 (m-80) REVERT: C 961 ASP cc_start: 0.7665 (m-30) cc_final: 0.7379 (m-30) REVERT: C 1054 GLU cc_start: 0.8319 (pp20) cc_final: 0.7853 (pp20) outliers start: 123 outliers final: 98 residues processed: 418 average time/residue: 0.1434 time to fit residues: 98.7811 Evaluate side-chains 426 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 317 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 388 VAL Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 500 SER 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 599 GLN 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 652 ILE Chi-restraints excluded: chain A residue 707 GLU 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 832 ILE 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 922 THR 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 1042 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 211 SER 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 372 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL 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 840 LEU 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 969 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 172 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 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 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 601 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 736 LEU Chi-restraints excluded: chain C residue 846 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 199 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 186 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 310 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 228 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 883 GLN A 931 GLN B 201 GLN B 280 GLN B 492 GLN C 883 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.175470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138368 restraints weight = 38656.468| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.73 r_work: 0.3514 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25918 Z= 0.174 Angle : 0.703 14.246 35340 Z= 0.344 Chirality : 0.049 0.321 4088 Planarity : 0.004 0.061 4498 Dihedral : 5.897 39.309 3396 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 4.16 % Allowed : 15.77 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % 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: -1.88 (0.15), residues: 3135 helix: 0.95 (0.21), residues: 635 sheet: -0.96 (0.20), residues: 610 loop : -2.25 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 306 TYR 0.020 0.001 TYR C 689 PHE 0.020 0.001 PHE B1071 TRP 0.005 0.001 TRP B 340 HIS 0.004 0.001 HIS A1040 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (25859) covalent geometry : angle 0.68171 / 0.34 (35190) SS BOND : bond 0.00322 / 0.21 ( 18) SS BOND : angle 1.58151 / 1.00 ( 36) hydrogen bonds : bond 0.03606 / 2.40 ( 793) hydrogen bonds : angle 5.37436 / 3.74 ( 2244) Misc. bond : bond 0.00029 / 0.01 ( 3) link_NAG-ASN : bond 0.00623 / 0.43 ( 38) link_NAG-ASN : angle 2.95729 / 2.02 ( 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 442 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 328 time to evaluate : 0.900 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: A 232 ARG cc_start: 0.7754 (ttp-110) cc_final: 0.7529 (ttp80) REVERT: A 262 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8675 (t80) REVERT: A 294 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7809 (pt0) REVERT: A 306 ARG cc_start: 0.6976 (mmm-85) cc_final: 0.6055 (mmm160) REVERT: A 316 PHE cc_start: 0.6815 (t80) cc_final: 0.6285 (t80) REVERT: A 411 LYS cc_start: 0.7357 (tptp) cc_final: 0.7026 (tppt) REVERT: A 453 ARG cc_start: 0.5625 (OUTLIER) cc_final: 0.4348 (pmt100) REVERT: A 539 THR cc_start: 0.8368 (m) cc_final: 0.7929 (p) REVERT: A 599 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6495 (mp10) REVERT: A 770 MET cc_start: 0.7914 (mtm) cc_final: 0.7661 (mtp) REVERT: A 961 ASP cc_start: 0.7925 (m-30) cc_final: 0.7545 (m-30) REVERT: A 1054 GLU cc_start: 0.8335 (pm20) cc_final: 0.8053 (pm20) REVERT: B 32 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.7023 (mp10) REVERT: B 130 PHE cc_start: 0.7212 (m-80) cc_final: 0.6110 (m-80) REVERT: B 256 TYR cc_start: 0.8025 (m-80) cc_final: 0.7781 (m-80) REVERT: B 263 MET cc_start: 0.8257 (ttt) cc_final: 0.7996 (ttt) REVERT: B 294 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7716 (mt-10) REVERT: B 306 ARG cc_start: 0.5738 (mmm-85) cc_final: 0.5504 (tpt170) REVERT: B 316 PHE cc_start: 0.6741 (t80) cc_final: 0.6250 (t80) REVERT: B 340 TRP cc_start: 0.7635 (p-90) cc_final: 0.7001 (p-90) REVERT: B 342 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7814 (ttm110) REVERT: B 410 TYR cc_start: 0.7221 (t80) cc_final: 0.6653 (t80) REVERT: B 494 TYR cc_start: 0.7244 (m-10) cc_final: 0.7015 (m-80) REVERT: B 527 PHE cc_start: 0.8560 (p90) cc_final: 0.8314 (p90) REVERT: B 733 ASN cc_start: 0.8528 (m-40) cc_final: 0.8287 (m-40) REVERT: B 745 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7973 (mt) REVERT: B 749 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8201 (pt) REVERT: B 840 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8793 (mm) REVERT: B 1049 TYR cc_start: 0.8580 (t80) cc_final: 0.8340 (t80) REVERT: C 256 TYR cc_start: 0.7760 (m-80) cc_final: 0.7154 (m-80) REVERT: C 262 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8579 (t80) REVERT: C 306 ARG cc_start: 0.6700 (mmm-85) cc_final: 0.6114 (mmm160) REVERT: C 411 LYS cc_start: 0.7556 (tptm) cc_final: 0.7031 (tptp) REVERT: C 442 TYR cc_start: 0.6422 (p90) cc_final: 0.6126 (p90) REVERT: C 453 ARG cc_start: 0.5415 (OUTLIER) cc_final: 0.4316 (pmt100) REVERT: C 481 TYR cc_start: 0.5547 (t80) cc_final: 0.4929 (t80) REVERT: C 961 ASP cc_start: 0.7567 (m-30) cc_final: 0.7300 (m-30) REVERT: C 1054 GLU cc_start: 0.8333 (pp20) cc_final: 0.7903 (pp20) outliers start: 114 outliers final: 100 residues processed: 414 average time/residue: 0.1485 time to fit residues: 101.8617 Evaluate side-chains 429 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 320 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 388 VAL Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 500 SER 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 599 GLN 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 652 ILE Chi-restraints excluded: chain A residue 704 ILE 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 832 ILE 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 922 THR 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 1042 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 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 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 302 THR Chi-restraints excluded: chain B residue 372 THR 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 571 LEU Chi-restraints excluded: chain B residue 594 VAL 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 840 LEU 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 969 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 172 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 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 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 601 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 232 optimal weight: 30.0000 chunk 276 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 252 optimal weight: 20.0000 chunk 255 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 280 GLN B 492 GLN B 632 GLN B 661 HIS B 901 ASN B1101 ASN C 280 GLN C 883 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.177286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.143311 restraints weight = 38767.533| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.31 r_work: 0.3530 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 25918 Z= 0.259 Angle : 0.773 14.437 35340 Z= 0.381 Chirality : 0.052 0.339 4088 Planarity : 0.005 0.061 4498 Dihedral : 6.131 37.910 3396 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 4.16 % Allowed : 15.74 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % Twisted General : 0.07 % 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: -2.08 (0.15), residues: 3135 helix: 0.63 (0.21), residues: 633 sheet: -1.10 (0.20), residues: 635 loop : -2.32 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 315 TYR 0.029 0.002 TYR B 598 PHE 0.028 0.002 PHE B1071 TRP 0.011 0.002 TRP B 476 HIS 0.007 0.001 HIS A1040 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.26 (25859) covalent geometry : angle 0.75244 / 0.38 (35190) SS BOND : bond 0.00503 / 0.34 ( 18) SS BOND : angle 1.77300 / 1.21 ( 36) hydrogen bonds : bond 0.04025 / 2.68 ( 793) hydrogen bonds : angle 5.60338 / 3.91 ( 2244) Misc. bond : bond 0.00034 / 0.02 ( 3) link_NAG-ASN : bond 0.00589 / 0.41 ( 38) link_NAG-ASN : angle 3.11548 / 2.12 ( 114) =============================================================================== Job complete usr+sys time: 6045.05 seconds wall clock time: 104 minutes 39.96 seconds (6279.96 seconds total)