Starting phenix.real_space_refine on Thu Feb 13 13:40:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xra_22293/02_2025/6xra_22293_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xra_22293/02_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_22293/02_2025/6xra_22293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xra_22293/02_2025/6xra_22293.map" model { file = "/net/cci-nas-00/data/ceres_data/6xra_22293/02_2025/6xra_22293_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xra_22293/02_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.45, per 1000 atoms: 0.85 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: 2.91 Conformation dependent library (CDL) restraints added in 969.3 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: 0.95 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: 2.48 Time building geometry restraints manager: 3.22 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: 9.200 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.160 Find NCS groups from input model: 0.360 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.310 ------------------------------------------------------------------------------- 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 : 0.012 0.068 8934 Z= 0.812 Angle : 1.950 11.891 12132 Z= 1.274 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 *********************** 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 : 0.925 Fit side-chains outliers start: 24 outliers final: 6 residues processed: 164 average time/residue: 0.9203 time to fit residues: 164.9767 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 : 0.962 ------------------------------------------------------------------------------- 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: 0.3980 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: 0.4980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.173733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137800 restraints weight = 11895.944| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.53 r_work: 0.3679 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8934 Z= 0.266 Angle : 0.809 9.537 12132 Z= 0.404 Chirality : 0.052 0.457 1596 Planarity : 0.005 0.044 1488 Dihedral : 14.513 108.948 2265 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.89 % Allowed : 14.22 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.36 (0.24), residues: 1026 helix: 0.58 (0.21), residues: 495 sheet: 0.59 (0.49), residues: 111 loop : -1.45 (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 0.014 0.002 PHE A1095 TYR 0.011 0.002 TYR A 741 ARG 0.003 0.000 ARG B1091 *********************** 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 126 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 81 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1029 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7504 (tpp) REVERT: C 1081 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6366 (pp) REVERT: A 751 ASN cc_start: 0.7551 (m-40) cc_final: 0.7138 (m-40) REVERT: A 1029 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7438 (tpp) REVERT: A 1163 ASP cc_start: 0.7104 (t0) cc_final: 0.6621 (m-30) REVERT: B 751 ASN cc_start: 0.7484 (m-40) cc_final: 0.7181 (m110) REVERT: B 1029 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7394 (tpp) REVERT: B 1150 GLU cc_start: 0.7175 (tp30) cc_final: 0.6971 (tp30) outliers start: 45 outliers final: 17 residues processed: 112 average time/residue: 0.8129 time to fit residues: 100.3251 Evaluate side-chains 78 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE 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: 1.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 69 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS A1135 ASN B1135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.169642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.133627 restraints weight = 12211.753| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.53 r_work: 0.3646 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 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 : 0.005 0.075 8934 Z= 0.321 Angle : 0.764 8.287 12132 Z= 0.382 Chirality : 0.048 0.390 1596 Planarity : 0.005 0.049 1488 Dihedral : 13.774 109.485 2262 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.43 % Allowed : 16.29 % Favored : 78.28 % 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: 0.11 (0.25), residues: 1026 helix: 1.15 (0.22), residues: 492 sheet: -0.17 (0.45), residues: 126 loop : -1.17 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B1102 HIS 0.006 0.001 HIS B1064 PHE 0.020 0.002 PHE A1095 TYR 0.013 0.002 TYR A1067 ARG 0.005 0.001 ARG B 995 *********************** 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 111 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 61 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1180 GLN cc_start: 0.5617 (tp40) cc_final: 0.3919 (mp-120) REVERT: C 1182 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6197 (mp0) REVERT: A 995 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7343 (mtm-85) REVERT: A 1163 ASP cc_start: 0.7197 (t0) cc_final: 0.6702 (m-30) REVERT: B 995 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7212 (mtt-85) REVERT: B 1029 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7443 (tmt) REVERT: B 1113 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.6804 (mp10) REVERT: B 1130 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7108 (pp) REVERT: B 1182 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.5947 (mp0) outliers start: 50 outliers final: 28 residues processed: 99 average time/residue: 0.8965 time to fit residues: 97.1362 Evaluate side-chains 89 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 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 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 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: 0.9980 chunk 63 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 58 optimal weight: 0.0050 chunk 101 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 0.0170 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.171562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136678 restraints weight = 11988.505| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.47 r_work: 0.3661 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8934 Z= 0.214 Angle : 0.655 6.908 12132 Z= 0.326 Chirality : 0.044 0.367 1596 Planarity : 0.004 0.048 1488 Dihedral : 12.988 107.353 2262 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.75 % Allowed : 17.70 % Favored : 76.55 % 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: 1.79 (0.22), residues: 495 sheet: -0.29 (0.45), residues: 132 loop : -1.00 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1102 HIS 0.004 0.001 HIS C1064 PHE 0.012 0.002 PHE A1095 TYR 0.010 0.002 TYR B1047 ARG 0.003 0.000 ARG B 995 *********************** 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 121 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 68 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1072 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6536 (pm20) REVERT: C 1113 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.6883 (mp10) REVERT: C 1147 SER cc_start: 0.7794 (m) cc_final: 0.7566 (p) REVERT: C 1163 ASP cc_start: 0.6853 (t0) cc_final: 0.6472 (m-30) REVERT: C 1180 GLN cc_start: 0.5568 (tp40) cc_final: 0.3866 (mp-120) REVERT: C 1182 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6055 (mp0) REVERT: A 1113 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.6567 (mp10) REVERT: A 1130 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8032 (pp) REVERT: A 1147 SER cc_start: 0.7932 (m) cc_final: 0.7621 (p) REVERT: A 1163 ASP cc_start: 0.7034 (t0) cc_final: 0.6585 (m-30) REVERT: A 1180 GLN cc_start: 0.5793 (tp40) cc_final: 0.3876 (mp-120) REVERT: B 1029 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7450 (tmt) REVERT: B 1130 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.6953 (pp) REVERT: B 1147 SER cc_start: 0.7779 (m) cc_final: 0.7505 (p) REVERT: B 1163 ASP cc_start: 0.7226 (t0) cc_final: 0.6896 (m-30) REVERT: B 1182 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6100 (mp0) outliers start: 53 outliers final: 19 residues processed: 108 average time/residue: 0.9448 time to fit residues: 111.1655 Evaluate side-chains 88 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 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 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 1182 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 0.0670 chunk 15 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.168223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.132864 restraints weight = 12141.552| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.51 r_work: 0.3622 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8934 Z= 0.281 Angle : 0.698 7.535 12132 Z= 0.346 Chirality : 0.045 0.370 1596 Planarity : 0.004 0.046 1488 Dihedral : 12.530 107.011 2262 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.97 % Allowed : 19.11 % Favored : 74.92 % 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: 0.56 (0.25), residues: 1026 helix: 1.72 (0.22), residues: 495 sheet: -0.09 (0.45), residues: 126 loop : -1.20 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B1102 HIS 0.005 0.001 HIS C1064 PHE 0.015 0.002 PHE B1156 TYR 0.024 0.002 TYR B1110 ARG 0.004 0.001 ARG B1019 *********************** 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 114 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 59 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 708 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7857 (m) REVERT: C 945 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6234 (tp) REVERT: C 1147 SER cc_start: 0.7824 (m) cc_final: 0.7564 (p) REVERT: C 1182 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6269 (mp0) REVERT: A 1029 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7263 (tmt) REVERT: A 1147 SER cc_start: 0.7905 (m) cc_final: 0.7634 (p) REVERT: A 1163 ASP cc_start: 0.7179 (t0) cc_final: 0.6604 (m-30) REVERT: B 708 SER cc_start: 0.8138 (OUTLIER) cc_final: 0.7894 (m) REVERT: B 751 ASN cc_start: 0.7672 (m-40) cc_final: 0.7130 (m110) REVERT: B 995 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7176 (mtt-85) REVERT: B 1113 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.6767 (mp10) REVERT: B 1130 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.6934 (pp) REVERT: B 1147 SER cc_start: 0.7847 (m) cc_final: 0.7534 (p) REVERT: B 1182 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6061 (mp0) outliers start: 55 outliers final: 30 residues processed: 107 average time/residue: 0.8948 time to fit residues: 105.1615 Evaluate side-chains 91 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 53 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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 1027 THR Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE 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 1074 ASN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 chunk 8 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.168631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.133225 restraints weight = 12076.081| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.53 r_work: 0.3611 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8934 Z= 0.279 Angle : 0.689 8.182 12132 Z= 0.339 Chirality : 0.045 0.357 1596 Planarity : 0.004 0.045 1488 Dihedral : 12.196 106.949 2262 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 7.27 % Allowed : 19.65 % Favored : 73.07 % 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: 0.54 (0.25), residues: 1026 helix: 1.75 (0.22), residues: 495 sheet: -0.13 (0.44), residues: 126 loop : -1.27 (0.29), 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 0.013 0.002 PHE B1156 TYR 0.025 0.002 TYR A1110 ARG 0.004 0.000 ARG B 995 *********************** 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 122 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 55 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 945 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6201 (tp) REVERT: C 1072 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6562 (pm20) REVERT: C 1113 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.6619 (mp10) REVERT: C 1147 SER cc_start: 0.7852 (m) cc_final: 0.7579 (p) REVERT: C 1182 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6072 (mp0) REVERT: A 751 ASN cc_start: 0.7486 (m-40) cc_final: 0.7079 (m-40) REVERT: A 1029 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7259 (tmt) REVERT: A 1113 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.6494 (mp10) REVERT: A 1130 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8018 (pp) REVERT: A 1147 SER cc_start: 0.7768 (m) cc_final: 0.7487 (p) REVERT: A 1182 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6079 (mp0) REVERT: B 708 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.8085 (m) REVERT: B 751 ASN cc_start: 0.7702 (m-40) cc_final: 0.7224 (m110) REVERT: B 995 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7362 (mtt-85) REVERT: B 1029 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7545 (tmt) REVERT: B 1113 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.6593 (mp10) REVERT: B 1130 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.6871 (pp) REVERT: B 1147 SER cc_start: 0.7783 (m) cc_final: 0.7456 (p) REVERT: B 1182 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6081 (mp0) outliers start: 67 outliers final: 30 residues processed: 108 average time/residue: 0.8367 time to fit residues: 99.3527 Evaluate side-chains 94 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 51 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 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 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 VAL 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: 0.6980 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 chunk 77 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 751 ASN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.170381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.135391 restraints weight = 12145.235| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.52 r_work: 0.3640 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8934 Z= 0.213 Angle : 0.650 8.486 12132 Z= 0.316 Chirality : 0.043 0.340 1596 Planarity : 0.004 0.045 1488 Dihedral : 11.531 106.763 2262 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.10 % Allowed : 22.58 % Favored : 72.31 % 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: 0.78 (0.26), residues: 1026 helix: 2.09 (0.22), residues: 486 sheet: -0.06 (0.44), residues: 126 loop : -1.26 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1102 HIS 0.004 0.001 HIS C1064 PHE 0.021 0.002 PHE A1075 TYR 0.020 0.002 TYR A1110 ARG 0.003 0.000 ARG B 995 *********************** 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 105 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 58 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 945 LEU cc_start: 0.6428 (OUTLIER) cc_final: 0.6196 (tp) REVERT: C 1029 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7266 (tmt) REVERT: C 1147 SER cc_start: 0.7755 (m) cc_final: 0.7511 (p) REVERT: C 1182 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6066 (mp0) REVERT: A 751 ASN cc_start: 0.7568 (m-40) cc_final: 0.7169 (m110) REVERT: A 1029 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7250 (tmt) REVERT: A 1147 SER cc_start: 0.7678 (m) cc_final: 0.7418 (p) REVERT: A 1182 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6050 (mp0) REVERT: B 751 ASN cc_start: 0.7595 (m-40) cc_final: 0.7077 (m110) REVERT: B 995 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7268 (mtt-85) REVERT: B 1029 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7600 (tmt) REVERT: B 1113 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7604 (mp10) REVERT: B 1130 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.6804 (pp) REVERT: B 1147 SER cc_start: 0.7753 (m) cc_final: 0.7430 (p) outliers start: 47 outliers final: 26 residues processed: 96 average time/residue: 0.8655 time to fit residues: 91.3503 Evaluate side-chains 87 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 53 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 1029 MET Chi-restraints excluded: chain C residue 1074 ASN 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 1029 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 60 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.169728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.134633 restraints weight = 12185.069| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.52 r_work: 0.3625 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8934 Z= 0.238 Angle : 0.663 7.102 12132 Z= 0.322 Chirality : 0.044 0.336 1596 Planarity : 0.004 0.043 1488 Dihedral : 11.031 106.435 2260 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.10 % Allowed : 23.02 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.25), residues: 1026 helix: 2.09 (0.22), residues: 486 sheet: -0.05 (0.44), residues: 126 loop : -1.30 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1102 HIS 0.005 0.001 HIS C1064 PHE 0.019 0.002 PHE A1075 TYR 0.027 0.002 TYR A1110 ARG 0.004 0.000 ARG B 995 *********************** 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 101 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 54 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 945 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.6179 (tp) REVERT: C 1113 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7242 (mm110) REVERT: C 1147 SER cc_start: 0.7763 (m) cc_final: 0.7523 (p) REVERT: C 1182 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6103 (mp0) REVERT: A 751 ASN cc_start: 0.7573 (m-40) cc_final: 0.7161 (m110) REVERT: A 1029 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7227 (tmt) REVERT: A 1113 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7596 (mp10) REVERT: A 1147 SER cc_start: 0.7680 (m) cc_final: 0.7432 (p) REVERT: A 1182 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: B 751 ASN cc_start: 0.7593 (m-40) cc_final: 0.7083 (m110) REVERT: B 1029 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7595 (tmt) REVERT: B 1113 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: B 1130 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.6841 (pp) REVERT: B 1147 SER cc_start: 0.7727 (m) cc_final: 0.7440 (p) outliers start: 47 outliers final: 30 residues processed: 94 average time/residue: 0.8600 time to fit residues: 89.0621 Evaluate side-chains 90 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 51 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 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 1113 GLN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 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: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.167812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.132407 restraints weight = 12148.139| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.55 r_work: 0.3600 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8934 Z= 0.298 Angle : 0.692 6.404 12132 Z= 0.341 Chirality : 0.045 0.341 1596 Planarity : 0.005 0.044 1488 Dihedral : 10.970 106.766 2260 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.32 % Allowed : 23.24 % Favored : 71.44 % 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: 1.84 (0.22), residues: 486 sheet: -0.20 (0.44), residues: 126 loop : -1.35 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1102 HIS 0.005 0.001 HIS C1064 PHE 0.014 0.002 PHE A1075 TYR 0.029 0.002 TYR A1110 ARG 0.004 0.001 ARG B 995 *********************** 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 101 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 52 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 945 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6256 (tp) REVERT: C 1113 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7303 (mm110) REVERT: C 1147 SER cc_start: 0.7818 (m) cc_final: 0.7571 (p) REVERT: C 1182 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6207 (mp0) REVERT: A 751 ASN cc_start: 0.7727 (m-40) cc_final: 0.7325 (m110) REVERT: A 1029 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7724 (tpp) REVERT: A 1072 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6512 (pm20) REVERT: A 1147 SER cc_start: 0.7810 (m) cc_final: 0.7544 (p) REVERT: A 1182 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: B 751 ASN cc_start: 0.7753 (m-40) cc_final: 0.7275 (m110) REVERT: B 995 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7331 (mtt-85) REVERT: B 1029 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7577 (tmt) REVERT: B 1113 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: B 1130 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.6912 (pp) REVERT: B 1147 SER cc_start: 0.7716 (m) cc_final: 0.7439 (p) outliers start: 49 outliers final: 31 residues processed: 95 average time/residue: 0.8486 time to fit residues: 88.7734 Evaluate side-chains 90 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 50 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 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 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 1137 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 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 1077 THR Chi-restraints excluded: chain B residue 1081 ILE 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 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.168545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.133341 restraints weight = 12158.426| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.53 r_work: 0.3613 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8934 Z= 0.263 Angle : 0.670 6.663 12132 Z= 0.328 Chirality : 0.044 0.333 1596 Planarity : 0.004 0.043 1488 Dihedral : 10.905 107.234 2260 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.67 % Allowed : 23.89 % Favored : 71.44 % 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: 0.57 (0.25), residues: 1026 helix: 1.95 (0.22), residues: 486 sheet: -0.18 (0.44), residues: 126 loop : -1.41 (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 ********************** 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 98 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 55 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 945 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6259 (tp) REVERT: C 1113 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7324 (mm110) REVERT: C 1147 SER cc_start: 0.7797 (m) cc_final: 0.7559 (p) REVERT: C 1182 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6135 (mp0) REVERT: A 751 ASN cc_start: 0.7740 (m-40) cc_final: 0.7344 (m110) REVERT: A 1029 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7237 (tmt) REVERT: A 1147 SER cc_start: 0.7706 (m) cc_final: 0.7457 (p) REVERT: A 1182 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6257 (mp0) REVERT: B 751 ASN cc_start: 0.7749 (m-40) cc_final: 0.7286 (m110) REVERT: B 995 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7298 (mtt-85) REVERT: B 1029 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7618 (tmt) REVERT: B 1113 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: B 1130 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.6883 (pp) REVERT: B 1147 SER cc_start: 0.7700 (m) cc_final: 0.7432 (p) outliers start: 43 outliers final: 31 residues processed: 91 average time/residue: 0.8238 time to fit residues: 83.0115 Evaluate side-chains 92 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 53 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 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 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 1137 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 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 1077 THR Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.167551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.132149 restraints weight = 12200.921| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.54 r_work: 0.3600 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8934 Z= 0.290 Angle : 0.690 7.903 12132 Z= 0.339 Chirality : 0.044 0.334 1596 Planarity : 0.004 0.043 1488 Dihedral : 10.881 107.385 2260 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.13 % Allowed : 24.65 % 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: 0.44 (0.25), residues: 1026 helix: 1.84 (0.22), residues: 486 sheet: -0.26 (0.44), residues: 126 loop : -1.47 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B1102 HIS 0.006 0.001 HIS C1064 PHE 0.013 0.002 PHE B1156 TYR 0.027 0.002 TYR B1110 ARG 0.004 0.001 ARG B 995 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6077.70 seconds wall clock time: 108 minutes 34.90 seconds (6514.90 seconds total)