Starting phenix.real_space_refine on Sun Jul 27 03:16:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xra_22293/07_2025/6xra_22293_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xra_22293/07_2025/6xra_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_22293/07_2025/6xra_22293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xra_22293/07_2025/6xra_22293.map" model { file = "/net/cci-nas-00/data/ceres_data/6xra_22293/07_2025/6xra_22293_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xra_22293/07_2025/6xra_22293_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.23, per 1000 atoms: 0.82 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: 2.99 Conformation dependent library (CDL) restraints added in 943.3 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: 0.86 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: 2.29 Time building geometry restraints manager: 3.50 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: 0.00 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: 142.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.930 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.920 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (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 TRP 0.115 0.048 TRP A1102 HIS 0.015 0.003 HIS C1048 PHE 0.045 0.010 PHE A1103 TYR 0.120 0.031 TYR A 707 ARG 0.004 0.001 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.11063 ( 18) link_NAG-ASN : angle 13.41738 ( 54) 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_ALPHA1-3 : bond 0.00669 ( 6) link_ALPHA1-3 : angle 1.85691 ( 18) hydrogen bonds : bond 0.22175 ( 516) hydrogen bonds : angle 8.70157 ( 1530) SS BOND : bond 0.03161 ( 12) SS BOND : angle 7.30360 ( 24) covalent geometry : bond 0.01240 ( 8934) covalent geometry : angle 1.95045 (12132) *********************** 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 : 0.882 Fit side-chains outliers start: 24 outliers final: 6 residues processed: 164 average time/residue: 0.8459 time to fit residues: 151.7099 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 : 0.894 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.0970 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.1980 chunk 41 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 C1106 GLN A 703 ASN A 751 ASN A 762 GLN A 925 ASN A1011 GLN A1098 ASN A1101 HIS A1106 GLN B 703 ASN B 751 ASN B 762 GLN B 925 ASN B1064 HIS B1098 ASN B1106 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.174370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138478 restraints weight = 11880.214| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.54 r_work: 0.3685 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8994 Z= 0.184 Angle : 0.908 11.658 12300 Z= 0.424 Chirality : 0.051 0.446 1596 Planarity : 0.005 0.043 1488 Dihedral : 14.464 108.606 2265 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.10 % Allowed : 13.68 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1026 helix: 0.64 (0.21), residues: 495 sheet: 0.60 (0.49), residues: 111 loop : -1.42 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B1102 HIS 0.006 0.001 HIS A1064 PHE 0.013 0.002 PHE A1095 TYR 0.010 0.002 TYR A 741 ARG 0.003 0.000 ARG B1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 18) link_NAG-ASN : angle 5.64054 ( 54) link_ALPHA1-4 : bond 0.01358 ( 9) link_ALPHA1-4 : angle 3.11790 ( 27) link_BETA1-4 : bond 0.00475 ( 15) link_BETA1-4 : angle 1.47973 ( 45) link_ALPHA1-3 : bond 0.00628 ( 6) link_ALPHA1-3 : angle 1.94253 ( 18) hydrogen bonds : bond 0.05332 ( 516) hydrogen bonds : angle 5.19856 ( 1530) SS BOND : bond 0.00580 ( 12) SS BOND : angle 2.65025 ( 24) covalent geometry : bond 0.00380 ( 8934) covalent geometry : angle 0.80298 (12132) *********************** 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 129 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 82 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1029 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7411 (tpp) REVERT: A 751 ASN cc_start: 0.7511 (m-40) cc_final: 0.7077 (m-40) REVERT: A 1029 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7423 (tpp) REVERT: A 1163 ASP cc_start: 0.7085 (t0) cc_final: 0.6616 (m-30) REVERT: B 751 ASN cc_start: 0.7447 (m-40) cc_final: 0.7139 (m110) REVERT: B 1029 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7413 (tpp) outliers start: 47 outliers final: 16 residues processed: 115 average time/residue: 0.7456 time to fit residues: 95.1088 Evaluate side-chains 76 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1029 MET Chi-restraints excluded: chain C residue 1074 ASN 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 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 62 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1058 HIS C1101 HIS C1135 ASN A1064 HIS A1135 ASN B1101 HIS B1135 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.171021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.134994 restraints weight = 12175.341| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.56 r_work: 0.3647 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8994 Z= 0.192 Angle : 0.857 10.372 12300 Z= 0.396 Chirality : 0.048 0.375 1596 Planarity : 0.004 0.046 1488 Dihedral : 13.690 109.320 2262 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.32 % Allowed : 14.88 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1026 helix: 1.36 (0.22), residues: 495 sheet: 0.02 (0.46), residues: 126 loop : -1.05 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B1102 HIS 0.005 0.001 HIS B1064 PHE 0.019 0.002 PHE A1095 TYR 0.012 0.002 TYR A1067 ARG 0.004 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00855 ( 18) link_NAG-ASN : angle 5.45007 ( 54) link_ALPHA1-4 : bond 0.01506 ( 9) link_ALPHA1-4 : angle 3.12728 ( 27) link_BETA1-4 : bond 0.00408 ( 15) link_BETA1-4 : angle 2.51597 ( 45) link_ALPHA1-3 : bond 0.00646 ( 6) link_ALPHA1-3 : angle 1.78716 ( 18) hydrogen bonds : bond 0.04883 ( 516) hydrogen bonds : angle 4.62623 ( 1530) SS BOND : bond 0.00799 ( 12) SS BOND : angle 2.88201 ( 24) covalent geometry : bond 0.00413 ( 8934) covalent geometry : angle 0.73859 (12132) *********************** 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 117 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 68 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1072 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6598 (pm20) REVERT: C 1163 ASP cc_start: 0.6938 (t0) cc_final: 0.6515 (m-30) REVERT: C 1180 GLN cc_start: 0.5605 (tp40) cc_final: 0.3933 (mp-120) REVERT: C 1182 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: A 1130 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8114 (pp) REVERT: A 1163 ASP cc_start: 0.7176 (t0) cc_final: 0.6721 (m-30) REVERT: B 751 ASN cc_start: 0.7583 (m-40) cc_final: 0.7205 (m110) REVERT: B 1029 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7464 (tmt) REVERT: B 1130 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7099 (pp) REVERT: B 1163 ASP cc_start: 0.7202 (t0) cc_final: 0.6736 (m-30) REVERT: B 1180 GLN cc_start: 0.5850 (tp40) cc_final: 0.3911 (mp-120) REVERT: B 1182 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.5961 (mp0) outliers start: 49 outliers final: 25 residues processed: 102 average time/residue: 0.8495 time to fit residues: 95.6081 Evaluate side-chains 91 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 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 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 1077 THR Chi-restraints excluded: chain A residue 1129 VAL 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 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 1130 ILE 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 70 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.170372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134999 restraints weight = 12024.721| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.49 r_work: 0.3639 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8994 Z= 0.179 Angle : 0.770 9.758 12300 Z= 0.359 Chirality : 0.045 0.370 1596 Planarity : 0.004 0.048 1488 Dihedral : 12.932 106.855 2262 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 6.30 % Allowed : 16.94 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1026 helix: 1.77 (0.22), residues: 492 sheet: -0.25 (0.45), residues: 132 loop : -0.98 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B1102 HIS 0.005 0.001 HIS A1064 PHE 0.014 0.002 PHE A1095 TYR 0.012 0.002 TYR B1067 ARG 0.003 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00764 ( 18) link_NAG-ASN : angle 4.68038 ( 54) link_ALPHA1-4 : bond 0.01524 ( 9) link_ALPHA1-4 : angle 3.20917 ( 27) link_BETA1-4 : bond 0.00402 ( 15) link_BETA1-4 : angle 0.97941 ( 45) link_ALPHA1-3 : bond 0.00582 ( 6) link_ALPHA1-3 : angle 1.76608 ( 18) hydrogen bonds : bond 0.04463 ( 516) hydrogen bonds : angle 4.44586 ( 1530) SS BOND : bond 0.00821 ( 12) SS BOND : angle 2.15052 ( 24) covalent geometry : bond 0.00386 ( 8934) covalent geometry : angle 0.68115 (12132) *********************** 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 125 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 67 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 708 SER cc_start: 0.7904 (p) cc_final: 0.7554 (m) REVERT: C 1072 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6654 (pm20) REVERT: C 1113 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6868 (mp10) REVERT: C 1147 SER cc_start: 0.7819 (m) cc_final: 0.7584 (p) REVERT: C 1180 GLN cc_start: 0.5582 (tp40) cc_final: 0.3958 (mp-120) REVERT: C 1182 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6221 (mp0) REVERT: A 1113 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6537 (mp10) REVERT: A 1130 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8075 (pp) REVERT: A 1147 SER cc_start: 0.7802 (m) cc_final: 0.7506 (p) REVERT: A 1163 ASP cc_start: 0.7089 (t0) cc_final: 0.6582 (m-30) REVERT: B 708 SER cc_start: 0.7926 (p) cc_final: 0.7580 (m) REVERT: B 1029 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7444 (tmt) REVERT: B 1113 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.6729 (mp10) REVERT: B 1130 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.6892 (pp) REVERT: B 1147 SER cc_start: 0.7835 (m) cc_final: 0.7525 (p) REVERT: B 1157 LYS cc_start: 0.7392 (mttt) cc_final: 0.7184 (pttm) REVERT: B 1182 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6091 (mp0) outliers start: 58 outliers final: 26 residues processed: 115 average time/residue: 1.1062 time to fit residues: 142.4588 Evaluate side-chains 97 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 1029 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1074 ASN 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 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 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 1129 VAL 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 71 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.168793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.133105 restraints weight = 12127.897| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.54 r_work: 0.3606 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8994 Z= 0.209 Angle : 0.795 9.890 12300 Z= 0.373 Chirality : 0.046 0.372 1596 Planarity : 0.004 0.048 1488 Dihedral : 12.534 107.091 2262 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 7.06 % Allowed : 18.13 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1026 helix: 1.63 (0.22), residues: 495 sheet: -0.15 (0.45), residues: 126 loop : -1.19 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B1102 HIS 0.005 0.001 HIS C1064 PHE 0.015 0.002 PHE B1156 TYR 0.023 0.002 TYR A1110 ARG 0.004 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00780 ( 18) link_NAG-ASN : angle 4.48273 ( 54) link_ALPHA1-4 : bond 0.01620 ( 9) link_ALPHA1-4 : angle 3.32310 ( 27) link_BETA1-4 : bond 0.00447 ( 15) link_BETA1-4 : angle 1.06252 ( 45) link_ALPHA1-3 : bond 0.00594 ( 6) link_ALPHA1-3 : angle 1.75642 ( 18) hydrogen bonds : bond 0.04574 ( 516) hydrogen bonds : angle 4.38832 ( 1530) SS BOND : bond 0.00989 ( 12) SS BOND : angle 2.16123 ( 24) covalent geometry : bond 0.00458 ( 8934) covalent geometry : angle 0.71340 (12132) *********************** 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 124 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 59 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 708 SER cc_start: 0.8115 (p) cc_final: 0.7888 (m) REVERT: C 945 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6312 (tp) REVERT: C 1072 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6520 (pm20) REVERT: C 1113 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.6673 (mp10) REVERT: C 1147 SER cc_start: 0.7815 (m) cc_final: 0.7580 (p) REVERT: C 1182 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: A 708 SER cc_start: 0.8176 (OUTLIER) cc_final: 0.7949 (m) REVERT: A 1029 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7724 (tpp) REVERT: A 1072 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6451 (pm20) REVERT: A 1130 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8131 (pp) REVERT: A 1147 SER cc_start: 0.7914 (m) cc_final: 0.7596 (p) REVERT: A 1163 ASP cc_start: 0.7230 (t0) cc_final: 0.6603 (m-30) REVERT: B 708 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7960 (m) REVERT: B 751 ASN cc_start: 0.7761 (m-40) cc_final: 0.7221 (m110) REVERT: B 1029 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7471 (tmt) REVERT: B 1113 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.6674 (mp10) REVERT: B 1130 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.6868 (pp) REVERT: B 1147 SER cc_start: 0.7808 (m) cc_final: 0.7518 (p) REVERT: B 1182 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6143 (mp0) outliers start: 65 outliers final: 29 residues processed: 111 average time/residue: 0.8488 time to fit residues: 103.5379 Evaluate side-chains 94 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 52 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 708 SER 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 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 B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.168436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132927 restraints weight = 12058.795| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.53 r_work: 0.3607 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3709 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= 0.193 Angle : 0.768 9.887 12300 Z= 0.357 Chirality : 0.044 0.355 1596 Planarity : 0.004 0.043 1488 Dihedral : 12.141 107.042 2262 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 6.41 % Allowed : 20.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1026 helix: 1.70 (0.22), residues: 495 sheet: -0.21 (0.43), residues: 126 loop : -1.21 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B1102 HIS 0.005 0.001 HIS C1064 PHE 0.012 0.002 PHE B1156 TYR 0.023 0.002 TYR A1110 ARG 0.004 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00749 ( 18) link_NAG-ASN : angle 4.29680 ( 54) link_ALPHA1-4 : bond 0.01656 ( 9) link_ALPHA1-4 : angle 3.33676 ( 27) link_BETA1-4 : bond 0.00436 ( 15) link_BETA1-4 : angle 0.94285 ( 45) link_ALPHA1-3 : bond 0.00565 ( 6) link_ALPHA1-3 : angle 1.72692 ( 18) hydrogen bonds : bond 0.04441 ( 516) hydrogen bonds : angle 4.35219 ( 1530) SS BOND : bond 0.00916 ( 12) SS BOND : angle 2.18661 ( 24) covalent geometry : bond 0.00422 ( 8934) covalent geometry : angle 0.68871 (12132) *********************** 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 113 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 54 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 945 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6195 (tp) REVERT: C 1072 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6602 (pm20) REVERT: C 1113 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.6625 (mp10) REVERT: C 1147 SER cc_start: 0.7859 (m) cc_final: 0.7579 (p) REVERT: C 1182 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6136 (mp0) REVERT: A 1029 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7715 (tpp) REVERT: A 1072 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: A 1113 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.6522 (mp10) REVERT: A 1130 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8061 (pp) REVERT: A 1147 SER cc_start: 0.7891 (m) cc_final: 0.7606 (p) REVERT: A 1182 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6084 (mp0) REVERT: B 747 THR cc_start: 0.7742 (m) cc_final: 0.7220 (m) REVERT: B 751 ASN cc_start: 0.7728 (m-40) cc_final: 0.7220 (m110) REVERT: B 995 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7229 (mtt-85) REVERT: B 1029 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7454 (tmt) REVERT: B 1113 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.6707 (mp10) REVERT: B 1130 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.6857 (pp) REVERT: B 1147 SER cc_start: 0.7791 (m) cc_final: 0.7457 (p) REVERT: B 1182 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6124 (mp0) outliers start: 59 outliers final: 28 residues processed: 101 average time/residue: 0.8492 time to fit residues: 94.0403 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 : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 723 THR 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 1008 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 10.0000 chunk 21 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 93 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.170111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.135039 restraints weight = 12095.047| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.50 r_work: 0.3632 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8994 Z= 0.158 Angle : 0.730 9.750 12300 Z= 0.336 Chirality : 0.043 0.339 1596 Planarity : 0.004 0.045 1488 Dihedral : 11.489 106.912 2262 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.21 % Allowed : 22.04 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1026 helix: 2.00 (0.22), residues: 483 sheet: -0.14 (0.44), residues: 126 loop : -1.26 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1102 HIS 0.004 0.001 HIS C1064 PHE 0.010 0.002 PHE B1075 TYR 0.021 0.002 TYR B1110 ARG 0.004 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 18) link_NAG-ASN : angle 4.09944 ( 54) link_ALPHA1-4 : bond 0.01707 ( 9) link_ALPHA1-4 : angle 3.38309 ( 27) link_BETA1-4 : bond 0.00439 ( 15) link_BETA1-4 : angle 0.88230 ( 45) link_ALPHA1-3 : bond 0.00566 ( 6) link_ALPHA1-3 : angle 1.67364 ( 18) hydrogen bonds : bond 0.04238 ( 516) hydrogen bonds : angle 4.18116 ( 1530) SS BOND : bond 0.00719 ( 12) SS BOND : angle 1.83198 ( 24) covalent geometry : bond 0.00332 ( 8934) covalent geometry : angle 0.65319 (12132) *********************** 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 104 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 56 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 747 THR cc_start: 0.7863 (m) cc_final: 0.7303 (m) REVERT: C 751 ASN cc_start: 0.7586 (m-40) cc_final: 0.6993 (m-40) REVERT: C 945 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6234 (tp) REVERT: C 1029 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7238 (tmt) REVERT: C 1113 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7204 (mm110) REVERT: C 1147 SER cc_start: 0.7750 (m) cc_final: 0.7506 (p) REVERT: C 1182 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6038 (mp0) REVERT: A 751 ASN cc_start: 0.7597 (m-40) cc_final: 0.7192 (m110) REVERT: A 1029 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7455 (tmt) REVERT: A 1072 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6339 (pm20) REVERT: A 1130 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8014 (pp) REVERT: A 1147 SER cc_start: 0.7686 (m) cc_final: 0.7421 (p) REVERT: A 1182 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: B 747 THR cc_start: 0.7698 (m) cc_final: 0.7159 (m) REVERT: B 751 ASN cc_start: 0.7656 (m-40) cc_final: 0.7186 (m110) REVERT: B 995 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7293 (mtt-85) REVERT: B 1029 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7471 (tmt) REVERT: B 1074 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7397 (m110) REVERT: B 1130 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.6790 (pp) REVERT: B 1147 SER cc_start: 0.7773 (m) cc_final: 0.7451 (p) outliers start: 48 outliers final: 26 residues processed: 94 average time/residue: 0.8545 time to fit residues: 88.1913 Evaluate side-chains 90 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 53 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 1074 ASN 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.167245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.131739 restraints weight = 12214.119| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.54 r_work: 0.3596 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8994 Z= 0.212 Angle : 0.777 9.779 12300 Z= 0.363 Chirality : 0.045 0.349 1596 Planarity : 0.004 0.043 1488 Dihedral : 11.199 106.874 2262 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.86 % Allowed : 22.37 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1026 helix: 1.73 (0.21), residues: 498 sheet: -0.25 (0.43), residues: 126 loop : -1.41 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A1102 HIS 0.006 0.001 HIS C1064 PHE 0.014 0.002 PHE B1156 TYR 0.028 0.002 TYR B1110 ARG 0.005 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00747 ( 18) link_NAG-ASN : angle 4.10707 ( 54) link_ALPHA1-4 : bond 0.01711 ( 9) link_ALPHA1-4 : angle 3.46904 ( 27) link_BETA1-4 : bond 0.00438 ( 15) link_BETA1-4 : angle 0.96838 ( 45) link_ALPHA1-3 : bond 0.00560 ( 6) link_ALPHA1-3 : angle 1.71130 ( 18) hydrogen bonds : bond 0.04454 ( 516) hydrogen bonds : angle 4.32513 ( 1530) SS BOND : bond 0.01047 ( 12) SS BOND : angle 2.25422 ( 24) covalent geometry : bond 0.00464 ( 8934) covalent geometry : angle 0.70125 (12132) *********************** 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 107 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 53 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 945 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6195 (tp) REVERT: C 1113 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.6677 (mp10) REVERT: C 1147 SER cc_start: 0.7831 (m) cc_final: 0.7574 (p) REVERT: C 1182 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: A 751 ASN cc_start: 0.7737 (m-40) cc_final: 0.7322 (m110) REVERT: A 1029 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7737 (tpp) REVERT: A 1072 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6459 (pm20) REVERT: A 1113 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: A 1130 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8055 (pp) REVERT: A 1147 SER cc_start: 0.7737 (m) cc_final: 0.7470 (p) REVERT: A 1182 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: B 751 ASN cc_start: 0.7743 (m-40) cc_final: 0.7269 (m110) REVERT: B 995 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7359 (mtt-85) REVERT: B 1029 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7474 (tpp) REVERT: B 1113 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7626 (mp10) REVERT: B 1130 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.6904 (pp) REVERT: B 1147 SER cc_start: 0.7767 (m) cc_final: 0.7464 (p) outliers start: 54 outliers final: 32 residues processed: 98 average time/residue: 0.7769 time to fit residues: 84.1705 Evaluate side-chains 95 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 52 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 708 SER 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 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 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 708 SER 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 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 740 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.168216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132857 restraints weight = 12134.630| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.53 r_work: 0.3604 rms_B_bonded: 2.94 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: 0.7267 moved from start: 0.4048 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= 0.192 Angle : 0.752 9.705 12300 Z= 0.350 Chirality : 0.044 0.342 1596 Planarity : 0.004 0.044 1488 Dihedral : 11.069 107.471 2260 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.89 % Allowed : 23.89 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1026 helix: 1.83 (0.22), residues: 486 sheet: -0.28 (0.43), residues: 126 loop : -1.40 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A1102 HIS 0.005 0.001 HIS C1064 PHE 0.019 0.002 PHE C1075 TYR 0.027 0.002 TYR C1110 ARG 0.004 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00751 ( 18) link_NAG-ASN : angle 3.96492 ( 54) link_ALPHA1-4 : bond 0.01665 ( 9) link_ALPHA1-4 : angle 3.35065 ( 27) link_BETA1-4 : bond 0.00493 ( 15) link_BETA1-4 : angle 1.05071 ( 45) link_ALPHA1-3 : bond 0.00558 ( 6) link_ALPHA1-3 : angle 1.70353 ( 18) hydrogen bonds : bond 0.04343 ( 516) hydrogen bonds : angle 4.28986 ( 1530) SS BOND : bond 0.00950 ( 12) SS BOND : angle 2.07231 ( 24) covalent geometry : bond 0.00420 ( 8934) covalent geometry : angle 0.67953 (12132) *********************** 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 98 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 53 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 751 ASN cc_start: 0.7697 (m-40) cc_final: 0.7129 (m-40) REVERT: C 945 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6279 (tp) REVERT: C 1113 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7259 (mm110) REVERT: C 1147 SER cc_start: 0.7820 (m) cc_final: 0.7565 (p) REVERT: C 1182 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: A 751 ASN cc_start: 0.7705 (m-40) cc_final: 0.7310 (m110) REVERT: A 1029 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7733 (tpp) REVERT: A 1072 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6453 (pm20) REVERT: A 1130 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8044 (pp) REVERT: A 1147 SER cc_start: 0.7838 (m) cc_final: 0.7568 (p) REVERT: A 1182 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6237 (mp0) REVERT: B 751 ASN cc_start: 0.7749 (m-40) cc_final: 0.7287 (m110) REVERT: B 995 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7321 (mtt-85) REVERT: B 1029 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7487 (tpp) REVERT: B 1130 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6840 (pp) REVERT: B 1147 SER cc_start: 0.7746 (m) cc_final: 0.7459 (p) outliers start: 45 outliers final: 32 residues processed: 90 average time/residue: 0.9341 time to fit residues: 92.5144 Evaluate side-chains 92 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 51 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 708 SER 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 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 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 708 SER 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 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 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 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 1029 MET 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 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 0.0980 chunk 80 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.169333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.134185 restraints weight = 12129.819| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.52 r_work: 0.3622 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8994 Z= 0.164 Angle : 0.721 9.579 12300 Z= 0.335 Chirality : 0.043 0.327 1596 Planarity : 0.004 0.045 1488 Dihedral : 10.827 107.308 2260 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.67 % Allowed : 24.43 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1026 helix: 2.05 (0.22), residues: 486 sheet: -0.16 (0.43), residues: 126 loop : -1.43 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B1102 HIS 0.008 0.001 HIS B1101 PHE 0.014 0.002 PHE C1075 TYR 0.021 0.002 TYR A1110 ARG 0.004 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00732 ( 18) link_NAG-ASN : angle 3.83059 ( 54) link_ALPHA1-4 : bond 0.01677 ( 9) link_ALPHA1-4 : angle 3.33526 ( 27) link_BETA1-4 : bond 0.00429 ( 15) link_BETA1-4 : angle 0.97099 ( 45) link_ALPHA1-3 : bond 0.00539 ( 6) link_ALPHA1-3 : angle 1.64795 ( 18) hydrogen bonds : bond 0.04198 ( 516) hydrogen bonds : angle 4.17035 ( 1530) SS BOND : bond 0.00790 ( 12) SS BOND : angle 1.87776 ( 24) covalent geometry : bond 0.00354 ( 8934) covalent geometry : angle 0.65034 (12132) ********************** 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 96 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 53 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 751 ASN cc_start: 0.7662 (m-40) cc_final: 0.7097 (m-40) REVERT: C 945 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6235 (tp) REVERT: C 1113 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7257 (mm110) REVERT: C 1147 SER cc_start: 0.7816 (m) cc_final: 0.7567 (p) REVERT: C 1182 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6125 (mp0) REVERT: A 751 ASN cc_start: 0.7560 (m-40) cc_final: 0.7217 (m110) REVERT: A 1029 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7239 (tmt) REVERT: A 1130 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7974 (pp) REVERT: A 1147 SER cc_start: 0.7688 (m) cc_final: 0.7440 (p) REVERT: A 1182 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6190 (mp0) REVERT: B 751 ASN cc_start: 0.7710 (m-40) cc_final: 0.7241 (m110) REVERT: B 995 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7291 (mtt-85) REVERT: B 1029 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7467 (tmt) REVERT: B 1113 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7547 (mm110) REVERT: B 1130 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.6794 (pp) outliers start: 43 outliers final: 31 residues processed: 89 average time/residue: 0.7531 time to fit residues: 74.7495 Evaluate side-chains 91 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 51 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 708 SER 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 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 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 708 SER 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 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 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 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 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 39 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.167318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131732 restraints weight = 12188.448| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.55 r_work: 0.3591 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8994 Z= 0.217 Angle : 0.768 9.518 12300 Z= 0.361 Chirality : 0.045 0.339 1596 Planarity : 0.005 0.044 1488 Dihedral : 10.917 107.429 2260 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.10 % Allowed : 23.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1026 helix: 1.77 (0.22), residues: 486 sheet: -0.28 (0.44), residues: 126 loop : -1.47 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B1102 HIS 0.006 0.001 HIS B1064 PHE 0.014 0.002 PHE C1075 TYR 0.030 0.002 TYR C1110 ARG 0.005 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 18) link_NAG-ASN : angle 3.91085 ( 54) link_ALPHA1-4 : bond 0.01658 ( 9) link_ALPHA1-4 : angle 3.29662 ( 27) link_BETA1-4 : bond 0.00425 ( 15) link_BETA1-4 : angle 1.02656 ( 45) link_ALPHA1-3 : bond 0.00545 ( 6) link_ALPHA1-3 : angle 1.68595 ( 18) hydrogen bonds : bond 0.04434 ( 516) hydrogen bonds : angle 4.29998 ( 1530) SS BOND : bond 0.01067 ( 12) SS BOND : angle 2.18881 ( 24) covalent geometry : bond 0.00484 ( 8934) covalent geometry : angle 0.69881 (12132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7197.02 seconds wall clock time: 126 minutes 24.37 seconds (7584.37 seconds total)