Starting phenix.real_space_refine on Tue Mar 3 22:28:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xra_22293/03_2026/6xra_22293_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xra_22293/03_2026/6xra_22293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xra_22293/03_2026/6xra_22293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xra_22293/03_2026/6xra_22293.map" model { file = "/net/cci-nas-00/data/ceres_data/6xra_22293/03_2026/6xra_22293_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xra_22293/03_2026/6xra_22293_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 36 5.16 5 C 5469 2.51 5 N 1416 2.21 5 O 1887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8808 Number of models: 1 Model: "" Number of chains: 21 Chain: "C" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2688 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 11, 'TRANS': 336} Chain breaks: 2 Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2688 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 11, 'TRANS': 336} Chain breaks: 2 Chain: "B" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2688 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 11, 'TRANS': 336} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.33, per 1000 atoms: 0.26 Number of scatterers: 8808 At special positions: 0 Unit cell: (73.425, 74.25, 229.35, 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 36 16.00 O 1887 8.00 N 1416 7.00 C 5469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.09 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.09 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.09 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN E 3 " - " MAN E 4 " " MAN F 3 " - " MAN F 4 " " MAN J 3 " - " MAN J 4 " " MAN K 3 " - " MAN K 4 " " MAN O 3 " - " MAN O 4 " " MAN P 3 " - " MAN P 4 " ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " " NAG G 2 " - " MAN G 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG L 2 " - " MAN L 3 " " NAG O 2 " - " MAN O 3 " " NAG P 2 " - " MAN P 3 " " NAG Q 2 " - " MAN Q 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1401 " - " ASN A 709 " " NAG A1402 " - " ASN A 717 " " NAG B1401 " - " ASN B 709 " " NAG B1402 " - " ASN B 717 " " NAG C1401 " - " ASN C 709 " " NAG C1402 " - " ASN C 717 " " NAG D 1 " - " ASN C1074 " " NAG F 1 " - " ASN C1134 " " NAG G 1 " - " ASN C1158 " " NAG H 1 " - " ASN C1194 " " NAG I 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN A1158 " " NAG M 1 " - " ASN A1194 " " NAG N 1 " - " ASN B1074 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B1158 " " NAG R 1 " - " ASN B1194 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 301.4 milliseconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 52.6% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.738A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 769 removed outlier: 3.638A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 1034 removed outlier: 3.524A pdb=" N ASN C 953 " --> pdb=" O GLN C 949 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1154 Processing helix chain 'C' and resid 1168 through 1172 Processing helix chain 'C' and resid 1181 through 1193 Processing helix chain 'C' and resid 1194 through 1197 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.738A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.638A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 1034 removed outlier: 3.524A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1154 Processing helix chain 'A' and resid 1168 through 1172 Processing helix chain 'A' and resid 1181 through 1193 Processing helix chain 'A' and resid 1194 through 1197 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.738A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 769 removed outlier: 3.638A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 1034 removed outlier: 3.524A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1154 Processing helix chain 'B' and resid 1168 through 1172 Processing helix chain 'B' and resid 1181 through 1193 Processing helix chain 'B' and resid 1194 through 1197 Processing sheet with id=AA1, first strand: chain 'C' and resid 1047 through 1056 removed outlier: 5.578A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 1047 through 1056 removed outlier: 5.578A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AA4, first strand: chain 'C' and resid 1129 through 1134 removed outlier: 6.202A pdb=" N VAL C1129 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR B 724 " --> pdb=" O VAL C1129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY C1131 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE B 726 " --> pdb=" O GLY C1131 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C1133 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1129 through 1134 removed outlier: 6.202A pdb=" N VAL C1129 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR B 724 " --> pdb=" O VAL C1129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY C1131 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE B 726 " --> pdb=" O GLY C1131 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C1133 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1047 through 1056 removed outlier: 5.578A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1047 through 1056 removed outlier: 5.578A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AA9, first strand: chain 'B' and resid 1081 through 1083 539 hydrogen bonds defined for protein. 1530 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: 1.37 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1909 1.33 - 1.45: 2080 1.45 - 1.58: 4891 1.58 - 1.70: 6 1.70 - 1.83: 48 Bond restraints: 8934 Sorted by residual: bond pdb=" CA CYS B1043 " pdb=" C CYS B1043 " ideal model delta sigma weight residual 1.530 1.584 -0.054 1.17e-02 7.31e+03 2.14e+01 bond pdb=" CA CYS C1043 " pdb=" C CYS C1043 " ideal model delta sigma weight residual 1.530 1.584 -0.054 1.17e-02 7.31e+03 2.12e+01 bond pdb=" CA CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sigma weight residual 1.532 1.600 -0.068 1.48e-02 4.57e+03 2.12e+01 bond pdb=" CA CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sigma weight residual 1.532 1.600 -0.068 1.48e-02 4.57e+03 2.10e+01 bond pdb=" CA CYS A1043 " pdb=" C CYS A1043 " ideal model delta sigma weight residual 1.530 1.584 -0.054 1.17e-02 7.31e+03 2.09e+01 ... (remaining 8929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 9716 2.38 - 4.76: 2184 4.76 - 7.13: 205 7.13 - 9.51: 18 9.51 - 11.89: 9 Bond angle restraints: 12132 Sorted by residual: angle pdb=" N PHE A1042 " pdb=" CA PHE A1042 " pdb=" C PHE A1042 " ideal model delta sigma weight residual 110.20 99.11 11.09 1.58e+00 4.01e-01 4.92e+01 angle pdb=" N PHE C1042 " pdb=" CA PHE C1042 " pdb=" C PHE C1042 " ideal model delta sigma weight residual 110.20 99.12 11.08 1.58e+00 4.01e-01 4.92e+01 angle pdb=" N PHE B1042 " pdb=" CA PHE B1042 " pdb=" C PHE B1042 " ideal model delta sigma weight residual 110.20 99.14 11.06 1.58e+00 4.01e-01 4.90e+01 angle pdb=" N CYS B1126 " pdb=" CA CYS B1126 " pdb=" C CYS B1126 " ideal model delta sigma weight residual 112.24 120.60 -8.36 1.28e+00 6.10e-01 4.27e+01 angle pdb=" N CYS C1126 " pdb=" CA CYS C1126 " pdb=" C CYS C1126 " ideal model delta sigma weight residual 112.24 120.59 -8.35 1.28e+00 6.10e-01 4.25e+01 ... (remaining 12127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 5718 24.83 - 49.66: 330 49.66 - 74.48: 36 74.48 - 99.31: 54 99.31 - 124.14: 9 Dihedral angle restraints: 6147 sinusoidal: 3102 harmonic: 3045 Sorted by residual: dihedral pdb=" N ASN B 709 " pdb=" C ASN B 709 " pdb=" CA ASN B 709 " pdb=" CB ASN B 709 " ideal model delta harmonic sigma weight residual 122.80 141.15 -18.35 0 2.50e+00 1.60e-01 5.39e+01 dihedral pdb=" N ASN C 709 " pdb=" C ASN C 709 " pdb=" CA ASN C 709 " pdb=" CB ASN C 709 " ideal model delta harmonic sigma weight residual 122.80 141.15 -18.35 0 2.50e+00 1.60e-01 5.38e+01 dihedral pdb=" N ASN A 709 " pdb=" C ASN A 709 " pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " ideal model delta harmonic sigma weight residual 122.80 141.12 -18.32 0 2.50e+00 1.60e-01 5.37e+01 ... (remaining 6144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 1459 0.170 - 0.339: 116 0.339 - 0.509: 12 0.509 - 0.678: 6 0.678 - 0.848: 3 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CA ASN B 709 " pdb=" N ASN B 709 " pdb=" C ASN B 709 " pdb=" CB ASN B 709 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" CA ASN C 709 " pdb=" N ASN C 709 " pdb=" C ASN C 709 " pdb=" CB ASN C 709 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.79e+01 chirality pdb=" CA ASN A 709 " pdb=" N ASN A 709 " pdb=" C ASN A 709 " pdb=" CB ASN A 709 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.79e+01 ... (remaining 1593 not shown) Planarity restraints: 1506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1194 " 0.179 2.00e-02 2.50e+03 1.86e-01 4.30e+02 pdb=" CG ASN A1194 " -0.105 2.00e-02 2.50e+03 pdb=" OD1 ASN A1194 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A1194 " -0.285 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1194 " 0.179 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" CG ASN C1194 " -0.105 2.00e-02 2.50e+03 pdb=" OD1 ASN C1194 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C1194 " -0.285 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1194 " 0.169 2.00e-02 2.50e+03 1.79e-01 4.02e+02 pdb=" CG ASN B1194 " -0.103 2.00e-02 2.50e+03 pdb=" OD1 ASN B1194 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B1194 " -0.277 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.212 2.00e-02 2.50e+03 ... (remaining 1503 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 300 2.73 - 3.27: 8900 3.27 - 3.82: 13861 3.82 - 4.36: 17872 4.36 - 4.90: 28530 Nonbonded interactions: 69463 Sorted by model distance: nonbonded pdb=" OD1 ASN C1173 " pdb=" C1 NAG C1417 " model vdw 2.189 3.470 nonbonded pdb=" OD1 ASN B1173 " pdb=" C1 NAG B1417 " model vdw 2.259 3.470 nonbonded pdb=" OD1 ASN A1173 " pdb=" C1 NAG A1417 " model vdw 2.291 3.470 nonbonded pdb=" ND2 ASN C1173 " pdb=" C1 NAG C1417 " model vdw 2.296 3.550 nonbonded pdb=" CB ASN B 709 " pdb=" O THR B1077 " model vdw 2.305 3.440 ... (remaining 69458 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'Q' } 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: 11.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.000 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.013 0.155 8994 Z= 0.782 Angle : 2.162 36.452 12300 Z= 1.309 Chirality : 0.112 0.848 1596 Planarity : 0.012 0.069 1488 Dihedral : 17.927 124.138 4131 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.61 % Allowed : 7.82 % Favored : 89.58 % Cbeta Deviations : 1.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.22), residues: 1026 helix: -1.86 (0.18), residues: 480 sheet: 0.69 (0.55), residues: 84 loop : -1.96 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 995 TYR 0.120 0.031 TYR A 707 PHE 0.045 0.010 PHE A1103 TRP 0.115 0.048 TRP A1102 HIS 0.015 0.003 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01240 ( 8934) covalent geometry : angle 1.95045 (12132) SS BOND : bond 0.03161 ( 12) SS BOND : angle 7.30360 ( 24) hydrogen bonds : bond 0.22175 ( 516) hydrogen bonds : angle 8.70157 ( 1530) link_ALPHA1-3 : bond 0.00669 ( 6) link_ALPHA1-3 : angle 1.85691 ( 18) link_ALPHA1-4 : bond 0.00493 ( 9) link_ALPHA1-4 : angle 2.49106 ( 27) link_BETA1-4 : bond 0.00791 ( 15) link_BETA1-4 : angle 1.54023 ( 45) link_NAG-ASN : bond 0.11063 ( 18) link_NAG-ASN : angle 13.41738 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.339 Fit side-chains outliers start: 24 outliers final: 6 residues processed: 164 average time/residue: 0.4376 time to fit residues: 77.9456 Evaluate side-chains 84 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1082 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 703 ASN C 751 ASN C 762 GLN C 925 ASN C1064 HIS C1098 ASN C1101 HIS C1173 ASN A 703 ASN A 751 ASN A 925 ASN A1011 GLN A1064 HIS A1098 ASN A1101 HIS A1106 GLN B 703 ASN B 751 ASN B 925 ASN B1064 HIS B1098 ASN B1101 HIS B1106 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.173367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137106 restraints weight = 12112.809| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.60 r_work: 0.3674 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8994 Z= 0.196 Angle : 0.911 11.719 12300 Z= 0.428 Chirality : 0.051 0.456 1596 Planarity : 0.005 0.044 1488 Dihedral : 14.639 110.009 2265 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.67 % Allowed : 14.44 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.24), residues: 1026 helix: 0.54 (0.21), residues: 495 sheet: 0.53 (0.49), residues: 111 loop : -1.45 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1019 TYR 0.012 0.002 TYR A 741 PHE 0.016 0.002 PHE A1095 TRP 0.014 0.003 TRP B1102 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8934) covalent geometry : angle 0.81008 (12132) SS BOND : bond 0.00922 ( 12) SS BOND : angle 2.66692 ( 24) hydrogen bonds : bond 0.05577 ( 516) hydrogen bonds : angle 5.29148 ( 1530) link_ALPHA1-3 : bond 0.00805 ( 6) link_ALPHA1-3 : angle 1.89764 ( 18) link_ALPHA1-4 : bond 0.01346 ( 9) link_ALPHA1-4 : angle 2.99329 ( 27) link_BETA1-4 : bond 0.00646 ( 15) link_BETA1-4 : angle 1.41605 ( 45) link_NAG-ASN : bond 0.01846 ( 18) link_NAG-ASN : angle 5.56104 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 80 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1081 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6331 (pp) REVERT: A 751 ASN cc_start: 0.7578 (m-40) cc_final: 0.7196 (m-40) REVERT: A 1029 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7422 (tpp) REVERT: A 1163 ASP cc_start: 0.7131 (t0) cc_final: 0.6651 (m-30) REVERT: B 751 ASN cc_start: 0.7485 (m-40) cc_final: 0.7164 (m110) REVERT: B 1029 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7386 (tpp) REVERT: B 1150 GLU cc_start: 0.7237 (tp30) cc_final: 0.7025 (tp30) outliers start: 43 outliers final: 19 residues processed: 111 average time/residue: 0.4153 time to fit residues: 50.4599 Evaluate side-chains 80 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 22 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1058 HIS C1135 ASN A1135 ASN B1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.171234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135024 restraints weight = 12067.864| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.56 r_work: 0.3645 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8994 Z= 0.192 Angle : 0.845 10.350 12300 Z= 0.393 Chirality : 0.047 0.384 1596 Planarity : 0.004 0.046 1488 Dihedral : 13.734 109.338 2262 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.65 % Allowed : 15.74 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1026 helix: 1.31 (0.22), residues: 492 sheet: -0.16 (0.45), residues: 126 loop : -1.10 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 995 TYR 0.012 0.002 TYR A1067 PHE 0.018 0.002 PHE A1095 TRP 0.012 0.003 TRP B1102 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8934) covalent geometry : angle 0.73479 (12132) SS BOND : bond 0.00874 ( 12) SS BOND : angle 3.03759 ( 24) hydrogen bonds : bond 0.04890 ( 516) hydrogen bonds : angle 4.67066 ( 1530) link_ALPHA1-3 : bond 0.00549 ( 6) link_ALPHA1-3 : angle 1.80082 ( 18) link_ALPHA1-4 : bond 0.01473 ( 9) link_ALPHA1-4 : angle 3.11801 ( 27) link_BETA1-4 : bond 0.00529 ( 15) link_BETA1-4 : angle 2.14647 ( 45) link_NAG-ASN : bond 0.00797 ( 18) link_NAG-ASN : angle 5.23834 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 68 time to evaluate : 0.361 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: C 1072 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6585 (pm20) REVERT: C 1180 GLN cc_start: 0.5561 (tp40) cc_final: 0.4006 (mp-120) REVERT: C 1182 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6128 (mp0) REVERT: A 751 ASN cc_start: 0.7498 (m-40) cc_final: 0.7096 (m-40) REVERT: A 1163 ASP cc_start: 0.7125 (t0) cc_final: 0.6677 (m-30) REVERT: B 751 ASN cc_start: 0.7582 (m-40) cc_final: 0.7203 (m110) REVERT: B 1029 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7445 (tmt) REVERT: B 1182 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.5915 (mp0) outliers start: 52 outliers final: 24 residues processed: 104 average time/residue: 0.4407 time to fit residues: 49.9787 Evaluate side-chains 89 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1182 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 0.0060 chunk 82 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.170482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.134540 restraints weight = 12302.034| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.58 r_work: 0.3655 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8994 Z= 0.173 Angle : 0.764 9.843 12300 Z= 0.357 Chirality : 0.045 0.374 1596 Planarity : 0.004 0.048 1488 Dihedral : 12.968 107.261 2262 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 6.30 % Allowed : 16.50 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1026 helix: 1.79 (0.22), residues: 492 sheet: -0.33 (0.44), residues: 132 loop : -0.97 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 995 TYR 0.011 0.002 TYR B1067 PHE 0.013 0.002 PHE C1095 TRP 0.009 0.002 TRP A1102 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8934) covalent geometry : angle 0.67374 (12132) SS BOND : bond 0.00770 ( 12) SS BOND : angle 2.17247 ( 24) hydrogen bonds : bond 0.04493 ( 516) hydrogen bonds : angle 4.42178 ( 1530) link_ALPHA1-3 : bond 0.00511 ( 6) link_ALPHA1-3 : angle 1.73912 ( 18) link_ALPHA1-4 : bond 0.01586 ( 9) link_ALPHA1-4 : angle 3.20413 ( 27) link_BETA1-4 : bond 0.00413 ( 15) link_BETA1-4 : angle 1.00137 ( 45) link_NAG-ASN : bond 0.00757 ( 18) link_NAG-ASN : angle 4.69664 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 69 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 708 SER cc_start: 0.7708 (p) cc_final: 0.7479 (m) REVERT: C 1072 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6576 (pm20) REVERT: C 1113 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.6892 (mp10) REVERT: C 1147 SER cc_start: 0.7845 (m) cc_final: 0.7523 (p) REVERT: C 1182 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: A 1029 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7246 (tmt) REVERT: A 1113 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.6525 (mp10) REVERT: A 1130 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8047 (pp) REVERT: A 1147 SER cc_start: 0.7816 (m) cc_final: 0.7509 (p) REVERT: A 1163 ASP cc_start: 0.7041 (t0) cc_final: 0.6572 (m-30) REVERT: B 708 SER cc_start: 0.8001 (p) cc_final: 0.7640 (m) REVERT: B 1029 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7447 (tmt) REVERT: B 1113 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6733 (mp10) REVERT: B 1130 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.6934 (pp) REVERT: B 1147 SER cc_start: 0.7815 (m) cc_final: 0.7515 (p) REVERT: B 1157 LYS cc_start: 0.7339 (mttt) cc_final: 0.7123 (pmmt) REVERT: B 1182 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6056 (mp0) outliers start: 58 outliers final: 27 residues processed: 111 average time/residue: 0.4315 time to fit residues: 52.3124 Evaluate side-chains 98 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 61 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1182 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.167666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.132088 restraints weight = 12230.831| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.53 r_work: 0.3613 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8994 Z= 0.212 Angle : 0.790 9.831 12300 Z= 0.370 Chirality : 0.046 0.377 1596 Planarity : 0.004 0.046 1488 Dihedral : 12.624 107.177 2262 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.84 % Allowed : 18.57 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.25), residues: 1026 helix: 1.61 (0.22), residues: 495 sheet: -0.29 (0.43), residues: 132 loop : -1.17 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1019 TYR 0.024 0.002 TYR B1110 PHE 0.015 0.002 PHE B1156 TRP 0.006 0.002 TRP B1102 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8934) covalent geometry : angle 0.70793 (12132) SS BOND : bond 0.01055 ( 12) SS BOND : angle 2.14770 ( 24) hydrogen bonds : bond 0.04587 ( 516) hydrogen bonds : angle 4.39689 ( 1530) link_ALPHA1-3 : bond 0.00569 ( 6) link_ALPHA1-3 : angle 1.76230 ( 18) link_ALPHA1-4 : bond 0.01593 ( 9) link_ALPHA1-4 : angle 3.28864 ( 27) link_BETA1-4 : bond 0.00418 ( 15) link_BETA1-4 : angle 1.04016 ( 45) link_NAG-ASN : bond 0.00768 ( 18) link_NAG-ASN : angle 4.50530 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 59 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 945 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6207 (tp) REVERT: C 1072 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6553 (pm20) REVERT: C 1113 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.6693 (mp10) REVERT: C 1147 SER cc_start: 0.7796 (m) cc_final: 0.7556 (p) REVERT: C 1182 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6265 (mp0) REVERT: A 995 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7294 (mtm-85) REVERT: A 1029 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7683 (tpp) REVERT: A 1113 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.6612 (mp10) REVERT: A 1130 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8086 (pp) REVERT: A 1163 ASP cc_start: 0.7184 (t0) cc_final: 0.6599 (m-30) REVERT: B 708 SER cc_start: 0.8147 (OUTLIER) cc_final: 0.7914 (m) REVERT: B 1113 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.6691 (mp10) REVERT: B 1130 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.6942 (pp) REVERT: B 1147 SER cc_start: 0.7841 (m) cc_final: 0.7536 (p) REVERT: B 1157 LYS cc_start: 0.7481 (mttt) cc_final: 0.7260 (ptpt) REVERT: B 1182 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6184 (mp0) outliers start: 63 outliers final: 29 residues processed: 112 average time/residue: 0.4092 time to fit residues: 50.2312 Evaluate side-chains 94 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 54 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1182 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 0.8980 chunk 23 optimal weight: 0.0470 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 87 optimal weight: 0.3980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.170487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.135255 restraints weight = 12153.672| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.54 r_work: 0.3643 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8994 Z= 0.163 Angle : 0.744 9.871 12300 Z= 0.344 Chirality : 0.044 0.355 1596 Planarity : 0.004 0.043 1488 Dihedral : 12.136 106.955 2262 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.19 % Allowed : 20.41 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1026 helix: 1.89 (0.22), residues: 498 sheet: -0.26 (0.42), residues: 132 loop : -1.24 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 995 TYR 0.021 0.002 TYR B1110 PHE 0.010 0.002 PHE C1095 TRP 0.008 0.002 TRP B1102 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8934) covalent geometry : angle 0.66204 (12132) SS BOND : bond 0.00769 ( 12) SS BOND : angle 2.05497 ( 24) hydrogen bonds : bond 0.04337 ( 516) hydrogen bonds : angle 4.27820 ( 1530) link_ALPHA1-3 : bond 0.00566 ( 6) link_ALPHA1-3 : angle 1.70310 ( 18) link_ALPHA1-4 : bond 0.01610 ( 9) link_ALPHA1-4 : angle 3.31188 ( 27) link_BETA1-4 : bond 0.00455 ( 15) link_BETA1-4 : angle 0.94428 ( 45) link_NAG-ASN : bond 0.00787 ( 18) link_NAG-ASN : angle 4.29585 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 68 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 751 ASN cc_start: 0.7579 (m-40) cc_final: 0.7000 (m-40) REVERT: C 938 LEU cc_start: 0.3357 (OUTLIER) cc_final: 0.3128 (tt) REVERT: C 945 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6239 (tp) REVERT: C 1029 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7291 (tmt) REVERT: C 1072 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6472 (pm20) REVERT: C 1113 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.6670 (mp10) REVERT: C 1147 SER cc_start: 0.7778 (m) cc_final: 0.7525 (p) REVERT: C 1182 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6018 (mp0) REVERT: A 751 ASN cc_start: 0.7560 (m-40) cc_final: 0.7092 (m110) REVERT: A 1072 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6377 (pm20) REVERT: A 1130 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8059 (pp) REVERT: A 1147 SER cc_start: 0.7854 (m) cc_final: 0.7577 (p) REVERT: A 1163 ASP cc_start: 0.7161 (t0) cc_final: 0.6594 (m-30) REVERT: A 1182 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6075 (mp0) REVERT: B 708 SER cc_start: 0.8205 (OUTLIER) cc_final: 0.7981 (m) REVERT: B 751 ASN cc_start: 0.7590 (m-40) cc_final: 0.7054 (m110) REVERT: B 1029 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7553 (tmt) REVERT: B 1130 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.6854 (pp) REVERT: B 1147 SER cc_start: 0.7868 (m) cc_final: 0.7529 (p) REVERT: B 1157 LYS cc_start: 0.7503 (mttt) cc_final: 0.7285 (ptpt) outliers start: 57 outliers final: 27 residues processed: 111 average time/residue: 0.3830 time to fit residues: 46.5790 Evaluate side-chains 98 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 59 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1182 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 3 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 755 GLN A 992 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.164835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.128206 restraints weight = 12309.656| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.58 r_work: 0.3548 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8994 Z= 0.321 Angle : 0.902 10.070 12300 Z= 0.431 Chirality : 0.050 0.396 1596 Planarity : 0.006 0.065 1488 Dihedral : 12.322 107.829 2262 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.62 % Allowed : 21.50 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.25), residues: 1026 helix: 1.00 (0.21), residues: 495 sheet: -0.69 (0.41), residues: 132 loop : -1.37 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 995 TYR 0.038 0.004 TYR A1110 PHE 0.022 0.003 PHE B1156 TRP 0.004 0.002 TRP A1102 HIS 0.007 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00719 ( 8934) covalent geometry : angle 0.82573 (12132) SS BOND : bond 0.01454 ( 12) SS BOND : angle 2.96977 ( 24) hydrogen bonds : bond 0.05103 ( 516) hydrogen bonds : angle 4.72140 ( 1530) link_ALPHA1-3 : bond 0.00598 ( 6) link_ALPHA1-3 : angle 1.84761 ( 18) link_ALPHA1-4 : bond 0.01627 ( 9) link_ALPHA1-4 : angle 3.36845 ( 27) link_BETA1-4 : bond 0.00466 ( 15) link_BETA1-4 : angle 1.09653 ( 45) link_NAG-ASN : bond 0.00786 ( 18) link_NAG-ASN : angle 4.50720 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 53 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1113 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.6759 (mp10) REVERT: C 1147 SER cc_start: 0.7931 (m) cc_final: 0.7604 (p) REVERT: C 1182 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6178 (mp0) REVERT: A 751 ASN cc_start: 0.7856 (m-40) cc_final: 0.7417 (m-40) REVERT: A 1029 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7746 (tpp) REVERT: A 1072 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6578 (pm20) REVERT: A 1113 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.6629 (mp10) REVERT: A 1130 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8195 (pp) REVERT: A 1182 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: B 1130 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7104 (pp) REVERT: B 1147 SER cc_start: 0.7870 (m) cc_final: 0.7570 (p) REVERT: B 1157 LYS cc_start: 0.7592 (mttt) cc_final: 0.7386 (ptpt) REVERT: B 1182 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6212 (mp0) outliers start: 61 outliers final: 32 residues processed: 104 average time/residue: 0.4274 time to fit residues: 48.4881 Evaluate side-chains 91 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 50 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1182 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 755 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.168705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132860 restraints weight = 12142.643| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.58 r_work: 0.3606 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8994 Z= 0.176 Angle : 0.766 9.899 12300 Z= 0.355 Chirality : 0.044 0.360 1596 Planarity : 0.004 0.045 1488 Dihedral : 11.763 108.455 2262 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.89 % Allowed : 23.45 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.25), residues: 1026 helix: 1.55 (0.22), residues: 498 sheet: -0.62 (0.39), residues: 132 loop : -1.43 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 995 TYR 0.025 0.002 TYR A1110 PHE 0.018 0.002 PHE C1075 TRP 0.010 0.002 TRP A1102 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8934) covalent geometry : angle 0.68987 (12132) SS BOND : bond 0.00893 ( 12) SS BOND : angle 2.13553 ( 24) hydrogen bonds : bond 0.04409 ( 516) hydrogen bonds : angle 4.38615 ( 1530) link_ALPHA1-3 : bond 0.00547 ( 6) link_ALPHA1-3 : angle 1.74742 ( 18) link_ALPHA1-4 : bond 0.01710 ( 9) link_ALPHA1-4 : angle 3.32481 ( 27) link_BETA1-4 : bond 0.00439 ( 15) link_BETA1-4 : angle 0.96347 ( 45) link_NAG-ASN : bond 0.00770 ( 18) link_NAG-ASN : angle 4.17299 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 63 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 751 ASN cc_start: 0.7706 (m-40) cc_final: 0.7128 (m-40) REVERT: C 1113 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.6668 (mp10) REVERT: C 1147 SER cc_start: 0.7847 (m) cc_final: 0.7576 (p) REVERT: C 1182 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: A 751 ASN cc_start: 0.7681 (m-40) cc_final: 0.7285 (m110) REVERT: A 1029 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7750 (tpp) REVERT: A 1072 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6435 (pm20) REVERT: A 1113 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: A 1130 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8072 (pp) REVERT: A 1147 SER cc_start: 0.7942 (m) cc_final: 0.7556 (p) REVERT: A 1182 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6038 (mp0) REVERT: B 751 ASN cc_start: 0.7779 (m-40) cc_final: 0.7306 (m110) REVERT: B 1029 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7528 (tmt) REVERT: B 1130 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.6918 (pp) REVERT: B 1147 SER cc_start: 0.7800 (m) cc_final: 0.7474 (p) outliers start: 45 outliers final: 29 residues processed: 100 average time/residue: 0.4262 time to fit residues: 46.5495 Evaluate side-chains 97 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1182 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.168446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.132793 restraints weight = 12074.478| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.56 r_work: 0.3609 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8994 Z= 0.180 Angle : 0.752 9.858 12300 Z= 0.350 Chirality : 0.044 0.350 1596 Planarity : 0.004 0.045 1488 Dihedral : 11.266 108.139 2262 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.21 % Allowed : 23.67 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.25), residues: 1026 helix: 1.77 (0.22), residues: 498 sheet: -0.36 (0.42), residues: 126 loop : -1.49 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 995 TYR 0.027 0.002 TYR B1110 PHE 0.019 0.002 PHE B1075 TRP 0.011 0.003 TRP A1102 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8934) covalent geometry : angle 0.67704 (12132) SS BOND : bond 0.00936 ( 12) SS BOND : angle 2.05477 ( 24) hydrogen bonds : bond 0.04355 ( 516) hydrogen bonds : angle 4.29589 ( 1530) link_ALPHA1-3 : bond 0.00546 ( 6) link_ALPHA1-3 : angle 1.68733 ( 18) link_ALPHA1-4 : bond 0.01745 ( 9) link_ALPHA1-4 : angle 3.45645 ( 27) link_BETA1-4 : bond 0.00441 ( 15) link_BETA1-4 : angle 0.97638 ( 45) link_NAG-ASN : bond 0.00747 ( 18) link_NAG-ASN : angle 4.01973 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 60 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 751 ASN cc_start: 0.7658 (m-40) cc_final: 0.7085 (m-40) REVERT: C 1113 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7243 (mm110) REVERT: C 1147 SER cc_start: 0.7817 (m) cc_final: 0.7551 (p) REVERT: C 1182 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6062 (mp0) REVERT: A 751 ASN cc_start: 0.7734 (m-40) cc_final: 0.7299 (m110) REVERT: A 995 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7267 (mtt-85) REVERT: A 1029 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7733 (tpp) REVERT: A 1072 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6436 (pm20) REVERT: A 1113 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7637 (mp10) REVERT: A 1147 SER cc_start: 0.7714 (m) cc_final: 0.7445 (p) REVERT: A 1182 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6024 (mp0) REVERT: B 751 ASN cc_start: 0.7740 (m-40) cc_final: 0.7276 (m110) REVERT: B 1113 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7498 (mm110) REVERT: B 1130 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6876 (pp) REVERT: B 1147 SER cc_start: 0.7773 (m) cc_final: 0.7477 (p) outliers start: 48 outliers final: 32 residues processed: 100 average time/residue: 0.3761 time to fit residues: 41.5456 Evaluate side-chains 98 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 58 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1182 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 755 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.168211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.132311 restraints weight = 12090.561| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.58 r_work: 0.3602 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8994 Z= 0.189 Angle : 0.754 9.735 12300 Z= 0.351 Chirality : 0.044 0.344 1596 Planarity : 0.004 0.045 1488 Dihedral : 11.132 108.183 2260 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.21 % Allowed : 24.10 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1026 helix: 1.75 (0.22), residues: 498 sheet: -0.36 (0.42), residues: 126 loop : -1.51 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 995 TYR 0.027 0.002 TYR A1110 PHE 0.019 0.002 PHE C1075 TRP 0.013 0.003 TRP B1102 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 8934) covalent geometry : angle 0.68372 (12132) SS BOND : bond 0.00944 ( 12) SS BOND : angle 2.07636 ( 24) hydrogen bonds : bond 0.04374 ( 516) hydrogen bonds : angle 4.31453 ( 1530) link_ALPHA1-3 : bond 0.00539 ( 6) link_ALPHA1-3 : angle 1.68554 ( 18) link_ALPHA1-4 : bond 0.01701 ( 9) link_ALPHA1-4 : angle 3.30945 ( 27) link_BETA1-4 : bond 0.00463 ( 15) link_BETA1-4 : angle 1.03810 ( 45) link_NAG-ASN : bond 0.00747 ( 18) link_NAG-ASN : angle 3.91061 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 57 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 751 ASN cc_start: 0.7714 (m-40) cc_final: 0.7128 (m-40) REVERT: C 1113 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7296 (mm110) REVERT: C 1147 SER cc_start: 0.7798 (m) cc_final: 0.7544 (p) REVERT: C 1182 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6175 (mp0) REVERT: A 751 ASN cc_start: 0.7723 (m-40) cc_final: 0.7331 (m110) REVERT: A 1029 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7741 (tpp) REVERT: A 1113 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: A 1147 SER cc_start: 0.7736 (m) cc_final: 0.7477 (p) REVERT: A 1182 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6097 (mp0) REVERT: B 751 ASN cc_start: 0.7753 (m-40) cc_final: 0.7288 (m110) REVERT: B 1029 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7550 (tmt) REVERT: B 1113 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7538 (mm110) REVERT: B 1130 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.6871 (pp) REVERT: B 1147 SER cc_start: 0.7739 (m) cc_final: 0.7463 (p) outliers start: 48 outliers final: 33 residues processed: 96 average time/residue: 0.3821 time to fit residues: 40.3590 Evaluate side-chains 97 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 56 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1182 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.0060 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.169703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.134004 restraints weight = 12026.758| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.57 r_work: 0.3623 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8994 Z= 0.161 Angle : 0.721 9.601 12300 Z= 0.334 Chirality : 0.043 0.327 1596 Planarity : 0.004 0.046 1488 Dihedral : 10.886 107.928 2260 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.56 % Allowed : 24.86 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1026 helix: 2.03 (0.22), residues: 486 sheet: -0.27 (0.39), residues: 147 loop : -1.52 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.023 0.002 TYR B1110 PHE 0.020 0.002 PHE B1075 TRP 0.015 0.003 TRP B1102 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8934) covalent geometry : angle 0.65071 (12132) SS BOND : bond 0.00789 ( 12) SS BOND : angle 1.86970 ( 24) hydrogen bonds : bond 0.04200 ( 516) hydrogen bonds : angle 4.19469 ( 1530) link_ALPHA1-3 : bond 0.00534 ( 6) link_ALPHA1-3 : angle 1.64907 ( 18) link_ALPHA1-4 : bond 0.01675 ( 9) link_ALPHA1-4 : angle 3.31205 ( 27) link_BETA1-4 : bond 0.00436 ( 15) link_BETA1-4 : angle 0.98457 ( 45) link_NAG-ASN : bond 0.00723 ( 18) link_NAG-ASN : angle 3.80613 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3270.98 seconds wall clock time: 56 minutes 41.95 seconds (3401.95 seconds total)