Starting phenix.real_space_refine on Sat Aug 23 17:28:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cau_16534/08_2025/8cau_16534_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cau_16534/08_2025/8cau_16534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cau_16534/08_2025/8cau_16534_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cau_16534/08_2025/8cau_16534_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cau_16534/08_2025/8cau_16534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cau_16534/08_2025/8cau_16534.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8695 2.51 5 N 2240 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13545 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "B" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "C" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "D" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "E" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "F" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "G" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "I" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "J" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "P" 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: "Q" 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: "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: "S" 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: "T" 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: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.47, per 1000 atoms: 0.40 Number of scatterers: 13545 At special positions: 0 Unit cell: (92.02, 92.88, 118.68, 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 60 16.00 O 2550 8.00 N 2240 7.00 C 8695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 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 BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 501 " - " ASN A 23 " " NAG A 502 " - " ASN A 67 " " NAG B 501 " - " ASN B 23 " " NAG B 502 " - " ASN B 67 " " NAG C 501 " - " ASN C 23 " " NAG C 502 " - " ASN C 67 " " NAG D 501 " - " ASN D 23 " " NAG D 502 " - " ASN D 67 " " NAG E 501 " - " ASN E 23 " " NAG E 502 " - " ASN E 67 " " NAG P 1 " - " ASN A 110 " " NAG Q 1 " - " ASN B 110 " " NAG R 1 " - " ASN C 110 " " NAG S 1 " - " ASN D 110 " " NAG T 1 " - " ASN E 110 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 960.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 39 sheets defined 4.5% alpha, 48.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.796A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 7 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 10 removed outlier: 3.550A pdb=" N TYR B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 8 " --> pdb=" O ARG B 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 4.170A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.512A pdb=" N TYR D 7 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 8 " --> pdb=" O ARG D 4 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'F' and resid 29 through 33 removed outlier: 4.015A pdb=" N TYR F 33 " --> pdb=" O PHE F 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 33 removed outlier: 4.041A pdb=" N TYR G 33 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 33 removed outlier: 4.023A pdb=" N TYR H 33 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 33 removed outlier: 4.023A pdb=" N TYR I 33 " --> pdb=" O PHE I 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 removed outlier: 3.997A pdb=" N TYR J 33 " --> pdb=" O PHE J 30 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 117 removed outlier: 7.291A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 30 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.605A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.605A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 125 removed outlier: 3.534A pdb=" N LEU B 49 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 48 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 30 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 79 Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 114 through 117 removed outlier: 3.543A pdb=" N TRP C 59 " --> pdb=" O CYS C 115 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 49 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 114 through 117 removed outlier: 3.543A pdb=" N TRP C 59 " --> pdb=" O CYS C 115 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 48 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN C 52 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE C 39 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N TRP C 54 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU C 37 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN C 56 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N SER C 58 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N SER C 33 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N THR C 60 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 10.051A pdb=" N TYR C 31 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 79 Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.581A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.581A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 117 Processing sheet with id=AB7, first strand: chain 'D' and resid 114 through 117 removed outlier: 3.959A pdb=" N VAL D 48 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 30 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 76 through 79 Processing sheet with id=AB9, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 114 through 117 Processing sheet with id=AC3, first strand: chain 'E' and resid 114 through 117 removed outlier: 3.920A pdb=" N VAL E 48 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 30 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 76 through 79 Processing sheet with id=AC5, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.563A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.563A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.605A pdb=" N LEU F 21 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.387A pdb=" N GLY F 11 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 119 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.387A pdb=" N GLY F 11 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 119 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR F 112 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.610A pdb=" N LEU G 21 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.388A pdb=" N GLY G 11 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 119 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP G 37 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.388A pdb=" N GLY G 11 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 119 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR G 112 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.623A pdb=" N LEU H 21 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.383A pdb=" N GLY H 11 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL H 119 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP H 37 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.383A pdb=" N GLY H 11 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL H 119 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR H 112 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 4 through 8 removed outlier: 3.612A pdb=" N LEU I 21 " --> pdb=" O LEU I 82 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.357A pdb=" N GLY I 11 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 119 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP I 37 " --> pdb=" O VAL I 49 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.357A pdb=" N GLY I 11 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 119 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR I 112 " --> pdb=" O ALA I 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 8 removed outlier: 3.622A pdb=" N LEU J 21 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.357A pdb=" N GLY J 11 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 119 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP J 37 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.357A pdb=" N GLY J 11 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 119 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR J 112 " --> pdb=" O ALA J 99 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1083 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: 2.34 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4245 1.34 - 1.46: 3300 1.46 - 1.57: 6310 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 13945 Sorted by residual: bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.20e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.98e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.92e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.83e+00 ... (remaining 13940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 17870 0.98 - 1.97: 829 1.97 - 2.95: 203 2.95 - 3.93: 52 3.93 - 4.91: 6 Bond angle restraints: 18960 Sorted by residual: angle pdb=" N GLY C 166 " pdb=" CA GLY C 166 " pdb=" C GLY C 166 " ideal model delta sigma weight residual 115.80 110.89 4.91 1.74e+00 3.30e-01 7.98e+00 angle pdb=" CA GLY C 166 " pdb=" C GLY C 166 " pdb=" N TYR C 167 " ideal model delta sigma weight residual 118.95 115.96 2.99 1.06e+00 8.90e-01 7.96e+00 angle pdb=" N GLY B 166 " pdb=" CA GLY B 166 " pdb=" C GLY B 166 " ideal model delta sigma weight residual 115.80 110.91 4.89 1.74e+00 3.30e-01 7.88e+00 angle pdb=" CA GLY B 166 " pdb=" C GLY B 166 " pdb=" N TYR B 167 " ideal model delta sigma weight residual 118.95 116.00 2.95 1.06e+00 8.90e-01 7.74e+00 angle pdb=" CA GLY B 166 " pdb=" C GLY B 166 " pdb=" O GLY B 166 " ideal model delta sigma weight residual 119.04 121.02 -1.98 9.10e-01 1.21e+00 4.72e+00 ... (remaining 18955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7315 17.94 - 35.88: 794 35.88 - 53.82: 193 53.82 - 71.76: 56 71.76 - 89.70: 12 Dihedral angle restraints: 8370 sinusoidal: 3605 harmonic: 4765 Sorted by residual: dihedral pdb=" CA LYS E 45 " pdb=" C LYS E 45 " pdb=" N ASN E 46 " pdb=" CA ASN E 46 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual -86.00 -112.75 26.75 1 1.00e+01 1.00e-02 1.03e+01 dihedral pdb=" CB CYS B 127 " pdb=" SG CYS B 127 " pdb=" SG CYS B 141 " pdb=" CB CYS B 141 " ideal model delta sinusoidal sigma weight residual -86.00 -112.41 26.41 1 1.00e+01 1.00e-02 1.00e+01 ... (remaining 8367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1437 0.040 - 0.079: 379 0.079 - 0.119: 183 0.119 - 0.158: 16 0.158 - 0.198: 5 Chirality restraints: 2020 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.25e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN E 110 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 110 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 2017 not shown) Planarity restraints: 2415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 79 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO B 80 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 79 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 80 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 79 " 0.038 5.00e-02 4.00e+02 5.88e-02 5.52e+00 pdb=" N PRO C 80 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.032 5.00e-02 4.00e+02 ... (remaining 2412 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 177 2.61 - 3.18: 11191 3.18 - 3.75: 17651 3.75 - 4.33: 26285 4.33 - 4.90: 45695 Nonbonded interactions: 100999 Sorted by model distance: nonbonded pdb=" N GLU F 90 " pdb=" OE1 GLU F 90 " model vdw 2.033 3.120 nonbonded pdb=" OG SER D 183 " pdb=" OD1 ASP D 196 " model vdw 2.046 3.040 nonbonded pdb=" OG SER B 183 " pdb=" OD1 ASP B 196 " model vdw 2.062 3.040 nonbonded pdb=" OG SER A 183 " pdb=" OD1 ASP A 196 " model vdw 2.063 3.040 nonbonded pdb=" OG SER C 183 " pdb=" OD1 ASP C 196 " model vdw 2.076 3.040 ... (remaining 100994 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 503)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 503)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 503)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 503)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 503)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.45 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.750 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 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 : 0.003 0.041 13970 Z= 0.140 Angle : 0.535 7.646 19030 Z= 0.271 Chirality : 0.043 0.198 2020 Planarity : 0.005 0.062 2400 Dihedral : 16.187 89.698 5325 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.14 % Allowed : 20.07 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.17 (0.19), residues: 1620 helix: -3.56 (0.62), residues: 45 sheet: -1.10 (0.20), residues: 660 loop : -2.92 (0.17), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 4 TYR 0.011 0.001 TYR A 117 PHE 0.006 0.001 PHE I 69 TRP 0.024 0.001 TRP D 133 HIS 0.002 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00291 (13945) covalent geometry : angle 0.51718 (18960) SS BOND : bond 0.00093 ( 5) SS BOND : angle 0.36092 ( 10) hydrogen bonds : bond 0.12989 ( 349) hydrogen bonds : angle 5.95530 ( 1083) link_BETA1-4 : bond 0.01531 ( 5) link_BETA1-4 : angle 4.49599 ( 15) link_NAG-ASN : bond 0.00235 ( 15) link_NAG-ASN : angle 1.20670 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 TYR cc_start: 0.8597 (m-80) cc_final: 0.8329 (m-10) REVERT: F 74 ASP cc_start: 0.7938 (t0) cc_final: 0.7689 (t0) REVERT: F 91 ASP cc_start: 0.9111 (m-30) cc_final: 0.8721 (m-30) REVERT: G 7 GLU cc_start: 0.8264 (mp0) cc_final: 0.7929 (mp0) REVERT: G 74 ASP cc_start: 0.7984 (t0) cc_final: 0.7737 (t0) REVERT: H 74 ASP cc_start: 0.8049 (t0) cc_final: 0.7731 (t0) REVERT: H 91 ASP cc_start: 0.9003 (m-30) cc_final: 0.8601 (m-30) REVERT: I 74 ASP cc_start: 0.7846 (t0) cc_final: 0.7617 (t0) REVERT: J 74 ASP cc_start: 0.8032 (t0) cc_final: 0.7749 (t0) outliers start: 2 outliers final: 1 residues processed: 298 average time/residue: 0.1665 time to fit residues: 66.7292 Evaluate side-chains 269 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.061860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.044266 restraints weight = 63421.316| |-----------------------------------------------------------------------------| r_work (start): 0.2495 rms_B_bonded: 4.72 r_work: 0.2318 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2360 r_free = 0.2360 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2360 r_free = 0.2360 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13970 Z= 0.210 Angle : 0.738 9.227 19030 Z= 0.364 Chirality : 0.050 0.228 2020 Planarity : 0.005 0.059 2400 Dihedral : 10.642 71.603 2299 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 1.48 % Allowed : 18.59 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (0.19), residues: 1620 helix: -2.62 (0.70), residues: 45 sheet: -0.70 (0.20), residues: 665 loop : -2.97 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 68 TYR 0.023 0.001 TYR G 60 PHE 0.021 0.001 PHE D 134 TRP 0.027 0.001 TRP A 133 HIS 0.003 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00494 (13945) covalent geometry : angle 0.72005 (18960) SS BOND : bond 0.00352 ( 5) SS BOND : angle 0.61132 ( 10) hydrogen bonds : bond 0.03228 ( 349) hydrogen bonds : angle 5.02210 ( 1083) link_BETA1-4 : bond 0.01888 ( 5) link_BETA1-4 : angle 5.26744 ( 15) link_NAG-ASN : bond 0.00242 ( 15) link_NAG-ASN : angle 1.57499 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 276 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9237 (mp0) REVERT: A 205 ARG cc_start: 0.9046 (ttm110) cc_final: 0.8668 (ttm110) REVERT: B 170 ASN cc_start: 0.9091 (t0) cc_final: 0.8872 (t0) REVERT: C 205 ARG cc_start: 0.9072 (ttm110) cc_final: 0.8562 (ttm110) REVERT: D 205 ARG cc_start: 0.9067 (ttm110) cc_final: 0.8650 (ttm110) REVERT: E 70 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8952 (mt-10) REVERT: E 205 ARG cc_start: 0.9028 (ttm110) cc_final: 0.8652 (ttm110) REVERT: F 2 GLN cc_start: 0.8397 (mp10) cc_final: 0.8065 (pm20) REVERT: F 66 LYS cc_start: 0.9173 (tppt) cc_final: 0.8773 (tppp) REVERT: F 74 ASP cc_start: 0.7803 (t0) cc_final: 0.7283 (t0) REVERT: F 108 ASP cc_start: 0.8976 (m-30) cc_final: 0.8771 (m-30) REVERT: G 40 GLN cc_start: 0.9291 (tt0) cc_final: 0.8739 (tp-100) REVERT: G 44 LYS cc_start: 0.9140 (mppt) cc_final: 0.8746 (mppt) REVERT: G 74 ASP cc_start: 0.7666 (t0) cc_final: 0.7181 (t0) REVERT: H 74 ASP cc_start: 0.7837 (t0) cc_final: 0.7248 (t0) REVERT: H 83 GLN cc_start: 0.8897 (tp40) cc_final: 0.8471 (tp-100) REVERT: H 84 MET cc_start: 0.9103 (mtm) cc_final: 0.8586 (mtm) REVERT: I 74 ASP cc_start: 0.7602 (t0) cc_final: 0.7142 (t0) REVERT: J 66 LYS cc_start: 0.9181 (tppt) cc_final: 0.8771 (tppt) REVERT: J 74 ASP cc_start: 0.7856 (t0) cc_final: 0.7170 (t0) REVERT: J 83 GLN cc_start: 0.8845 (tp40) cc_final: 0.8540 (tp-100) outliers start: 21 outliers final: 11 residues processed: 286 average time/residue: 0.1624 time to fit residues: 62.6257 Evaluate side-chains 276 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 265 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 149 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.2993 r_free = 0.2993 target = 0.063100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.044637 restraints weight = 77017.033| |-----------------------------------------------------------------------------| r_work (start): 0.2540 rms_B_bonded: 5.25 r_work: 0.2353 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.2353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2366 r_free = 0.2366 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2366 r_free = 0.2366 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13970 Z= 0.127 Angle : 0.694 9.376 19030 Z= 0.338 Chirality : 0.047 0.235 2020 Planarity : 0.005 0.054 2400 Dihedral : 9.680 62.279 2295 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.41 % Allowed : 19.58 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.19), residues: 1620 helix: -1.95 (0.78), residues: 45 sheet: -0.50 (0.20), residues: 665 loop : -2.79 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 78 TYR 0.018 0.001 TYR G 60 PHE 0.009 0.001 PHE J 48 TRP 0.030 0.001 TRP A 133 HIS 0.003 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00288 (13945) covalent geometry : angle 0.67343 (18960) SS BOND : bond 0.00179 ( 5) SS BOND : angle 0.46150 ( 10) hydrogen bonds : bond 0.02708 ( 349) hydrogen bonds : angle 4.84981 ( 1083) link_BETA1-4 : bond 0.02012 ( 5) link_BETA1-4 : angle 5.21161 ( 15) link_NAG-ASN : bond 0.00126 ( 15) link_NAG-ASN : angle 1.80396 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 277 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9245 (mp0) REVERT: B 170 ASN cc_start: 0.9167 (t0) cc_final: 0.8579 (t0) REVERT: B 172 GLU cc_start: 0.9346 (mt-10) cc_final: 0.9118 (mp0) REVERT: C 192 GLU cc_start: 0.9148 (pt0) cc_final: 0.8916 (pt0) REVERT: C 205 ARG cc_start: 0.9073 (ttm110) cc_final: 0.8757 (ttm110) REVERT: D 138 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8707 (t) REVERT: D 205 ARG cc_start: 0.9080 (ttm110) cc_final: 0.8659 (ttm110) REVERT: E 70 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8995 (mt-10) REVERT: E 184 GLU cc_start: 0.9210 (tt0) cc_final: 0.8994 (tt0) REVERT: F 2 GLN cc_start: 0.8472 (mp10) cc_final: 0.8136 (mp10) REVERT: F 47 GLU cc_start: 0.8680 (pt0) cc_final: 0.8417 (pt0) REVERT: F 66 LYS cc_start: 0.9027 (tppt) cc_final: 0.8612 (tppp) REVERT: F 74 ASP cc_start: 0.7835 (t0) cc_final: 0.7291 (t0) REVERT: G 40 GLN cc_start: 0.9280 (tt0) cc_final: 0.8709 (tp40) REVERT: G 44 LYS cc_start: 0.9153 (mppt) cc_final: 0.8814 (mppt) REVERT: G 61 TYR cc_start: 0.9029 (m-80) cc_final: 0.8579 (m-80) REVERT: G 74 ASP cc_start: 0.7703 (t0) cc_final: 0.7199 (t0) REVERT: G 88 LYS cc_start: 0.9127 (mmtm) cc_final: 0.8844 (mmtm) REVERT: H 74 ASP cc_start: 0.7867 (t0) cc_final: 0.7249 (t0) REVERT: H 83 GLN cc_start: 0.8905 (tp40) cc_final: 0.8455 (tp-100) REVERT: I 74 ASP cc_start: 0.7670 (t0) cc_final: 0.7263 (t0) REVERT: J 66 LYS cc_start: 0.9075 (tppt) cc_final: 0.8706 (tppt) REVERT: J 74 ASP cc_start: 0.7842 (t0) cc_final: 0.7139 (t0) REVERT: J 83 GLN cc_start: 0.8889 (tp40) cc_final: 0.8583 (tp-100) REVERT: J 84 MET cc_start: 0.9321 (mtm) cc_final: 0.8651 (ttm) outliers start: 20 outliers final: 14 residues processed: 290 average time/residue: 0.1663 time to fit residues: 64.9883 Evaluate side-chains 279 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 264 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 97 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 110 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3005 r_free = 0.3005 target = 0.063394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.044465 restraints weight = 97475.563| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 5.76 r_work: 0.2337 rms_B_bonded: 5.44 restraints_weight: 2.0000 r_work (final): 0.2337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2352 r_free = 0.2352 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2352 r_free = 0.2352 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13970 Z= 0.124 Angle : 0.677 9.505 19030 Z= 0.326 Chirality : 0.047 0.241 2020 Planarity : 0.005 0.052 2400 Dihedral : 8.812 58.749 2295 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.76 % Allowed : 18.38 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.19), residues: 1620 helix: -1.47 (0.81), residues: 45 sheet: -0.35 (0.21), residues: 620 loop : -2.54 (0.17), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 68 TYR 0.013 0.001 TYR G 60 PHE 0.023 0.001 PHE D 134 TRP 0.032 0.001 TRP A 133 HIS 0.003 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00284 (13945) covalent geometry : angle 0.65512 (18960) SS BOND : bond 0.00161 ( 5) SS BOND : angle 0.44458 ( 10) hydrogen bonds : bond 0.02535 ( 349) hydrogen bonds : angle 4.74232 ( 1083) link_BETA1-4 : bond 0.01949 ( 5) link_BETA1-4 : angle 5.24650 ( 15) link_NAG-ASN : bond 0.00097 ( 15) link_NAG-ASN : angle 1.93085 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 267 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9400 (mt-10) cc_final: 0.8935 (mp0) REVERT: A 172 GLU cc_start: 0.9487 (mt-10) cc_final: 0.9234 (mp0) REVERT: A 205 ARG cc_start: 0.9075 (ttm110) cc_final: 0.8703 (ttm110) REVERT: B 70 GLU cc_start: 0.9468 (mt-10) cc_final: 0.9079 (mp0) REVERT: B 170 ASN cc_start: 0.9098 (t0) cc_final: 0.8780 (t0) REVERT: C 133 TRP cc_start: 0.8738 (m-90) cc_final: 0.8498 (m-90) REVERT: C 192 GLU cc_start: 0.9178 (pt0) cc_final: 0.8922 (pt0) REVERT: C 205 ARG cc_start: 0.9130 (ttm110) cc_final: 0.8740 (ttm110) REVERT: D 138 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8782 (t) REVERT: D 205 ARG cc_start: 0.9137 (ttm110) cc_final: 0.8718 (ttm110) REVERT: E 70 GLU cc_start: 0.9316 (mt-10) cc_final: 0.9111 (mt-10) REVERT: E 172 GLU cc_start: 0.9399 (mt-10) cc_final: 0.9128 (mp0) REVERT: E 205 ARG cc_start: 0.9125 (ttm110) cc_final: 0.8713 (ttm110) REVERT: F 2 GLN cc_start: 0.8597 (mp10) cc_final: 0.8145 (mp10) REVERT: F 66 LYS cc_start: 0.8963 (tppt) cc_final: 0.8576 (tppp) REVERT: F 74 ASP cc_start: 0.7890 (t0) cc_final: 0.7320 (t0) REVERT: G 40 GLN cc_start: 0.9243 (tt0) cc_final: 0.8679 (tp40) REVERT: G 44 LYS cc_start: 0.9213 (mppt) cc_final: 0.8892 (mppt) REVERT: G 46 ARG cc_start: 0.9275 (mtm110) cc_final: 0.9033 (mtm110) REVERT: G 61 TYR cc_start: 0.9077 (m-80) cc_final: 0.8705 (m-80) REVERT: G 74 ASP cc_start: 0.7878 (t0) cc_final: 0.7327 (t0) REVERT: H 74 ASP cc_start: 0.7948 (t0) cc_final: 0.7340 (t0) REVERT: H 83 GLN cc_start: 0.8911 (tp40) cc_final: 0.8445 (tp-100) REVERT: H 84 MET cc_start: 0.9114 (mtm) cc_final: 0.8755 (mtm) REVERT: I 74 ASP cc_start: 0.7812 (t0) cc_final: 0.7302 (t0) REVERT: J 74 ASP cc_start: 0.7934 (t0) cc_final: 0.7210 (t0) REVERT: J 83 GLN cc_start: 0.8924 (tp40) cc_final: 0.8574 (tp-100) REVERT: J 84 MET cc_start: 0.9118 (mtm) cc_final: 0.8707 (mtp) outliers start: 25 outliers final: 11 residues processed: 285 average time/residue: 0.1621 time to fit residues: 62.8302 Evaluate side-chains 278 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 266 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3007 r_free = 0.3007 target = 0.063453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.044749 restraints weight = 84794.477| |-----------------------------------------------------------------------------| r_work (start): 0.2525 rms_B_bonded: 5.44 r_work: 0.2330 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.2330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2371 r_free = 0.2371 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2371 r_free = 0.2371 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13970 Z= 0.125 Angle : 0.673 9.525 19030 Z= 0.324 Chirality : 0.047 0.241 2020 Planarity : 0.004 0.051 2400 Dihedral : 8.260 58.377 2295 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.41 % Allowed : 19.37 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.20), residues: 1620 helix: -1.06 (0.80), residues: 45 sheet: -0.25 (0.21), residues: 625 loop : -2.43 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 46 TYR 0.010 0.001 TYR I 60 PHE 0.010 0.001 PHE F 69 TRP 0.030 0.001 TRP A 133 HIS 0.003 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00287 (13945) covalent geometry : angle 0.65087 (18960) SS BOND : bond 0.00161 ( 5) SS BOND : angle 0.43867 ( 10) hydrogen bonds : bond 0.02455 ( 349) hydrogen bonds : angle 4.66653 ( 1083) link_BETA1-4 : bond 0.01979 ( 5) link_BETA1-4 : angle 5.24247 ( 15) link_NAG-ASN : bond 0.00087 ( 15) link_NAG-ASN : angle 1.94125 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9399 (mt-10) cc_final: 0.8940 (mp0) REVERT: A 172 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9211 (mp0) REVERT: A 205 ARG cc_start: 0.9091 (ttm110) cc_final: 0.8725 (ttm110) REVERT: B 170 ASN cc_start: 0.9076 (t0) cc_final: 0.8736 (t0) REVERT: C 70 GLU cc_start: 0.9401 (mt-10) cc_final: 0.8893 (mp0) REVERT: C 192 GLU cc_start: 0.9176 (pt0) cc_final: 0.8910 (pt0) REVERT: C 205 ARG cc_start: 0.9152 (ttm110) cc_final: 0.8604 (ttm110) REVERT: D 138 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8840 (t) REVERT: D 205 ARG cc_start: 0.9146 (ttm110) cc_final: 0.8736 (ttm110) REVERT: E 70 GLU cc_start: 0.9302 (mt-10) cc_final: 0.9084 (mt-10) REVERT: E 133 TRP cc_start: 0.8691 (m-90) cc_final: 0.8323 (m-90) REVERT: E 205 ARG cc_start: 0.9125 (ttm110) cc_final: 0.8703 (ttm110) REVERT: F 2 GLN cc_start: 0.8629 (mp10) cc_final: 0.8147 (mp10) REVERT: F 66 LYS cc_start: 0.8915 (tppt) cc_final: 0.8518 (tppp) REVERT: F 69 PHE cc_start: 0.8111 (m-10) cc_final: 0.7572 (m-10) REVERT: F 74 ASP cc_start: 0.7917 (t0) cc_final: 0.7364 (t0) REVERT: F 108 ASP cc_start: 0.9045 (m-30) cc_final: 0.8678 (m-30) REVERT: G 40 GLN cc_start: 0.9234 (tt0) cc_final: 0.8666 (tp40) REVERT: G 44 LYS cc_start: 0.9228 (mppt) cc_final: 0.8849 (mmtm) REVERT: G 61 TYR cc_start: 0.9078 (m-80) cc_final: 0.8731 (m-80) REVERT: G 74 ASP cc_start: 0.7950 (t0) cc_final: 0.7391 (t0) REVERT: H 74 ASP cc_start: 0.7973 (t0) cc_final: 0.7342 (t0) REVERT: H 83 GLN cc_start: 0.8911 (tp40) cc_final: 0.8445 (tp-100) REVERT: H 84 MET cc_start: 0.9139 (mtm) cc_final: 0.8693 (mtm) REVERT: I 74 ASP cc_start: 0.7852 (t0) cc_final: 0.7343 (t0) REVERT: J 74 ASP cc_start: 0.7965 (t0) cc_final: 0.7231 (t0) REVERT: J 83 GLN cc_start: 0.8918 (tp40) cc_final: 0.8573 (tp-100) REVERT: J 84 MET cc_start: 0.9164 (mtm) cc_final: 0.8817 (mtm) outliers start: 20 outliers final: 13 residues processed: 286 average time/residue: 0.1560 time to fit residues: 60.4998 Evaluate side-chains 277 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 263 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.2966 r_free = 0.2966 target = 0.061392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.042727 restraints weight = 94501.544| |-----------------------------------------------------------------------------| r_work (start): 0.2489 rms_B_bonded: 5.60 r_work: 0.2289 rms_B_bonded: 5.26 restraints_weight: 2.0000 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2303 r_free = 0.2303 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2303 r_free = 0.2303 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13970 Z= 0.242 Angle : 0.730 10.576 19030 Z= 0.352 Chirality : 0.048 0.242 2020 Planarity : 0.004 0.048 2400 Dihedral : 8.309 59.849 2295 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 1.62 % Allowed : 19.58 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.20), residues: 1620 helix: -0.77 (0.77), residues: 45 sheet: -0.25 (0.21), residues: 625 loop : -2.41 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 46 TYR 0.012 0.001 TYR I 60 PHE 0.023 0.001 PHE D 134 TRP 0.029 0.001 TRP C 133 HIS 0.002 0.001 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00572 (13945) covalent geometry : angle 0.70756 (18960) SS BOND : bond 0.00449 ( 5) SS BOND : angle 0.64770 ( 10) hydrogen bonds : bond 0.02866 ( 349) hydrogen bonds : angle 4.76201 ( 1083) link_BETA1-4 : bond 0.01771 ( 5) link_BETA1-4 : angle 5.46338 ( 15) link_NAG-ASN : bond 0.00205 ( 15) link_NAG-ASN : angle 2.04458 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 263 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9405 (mt-10) cc_final: 0.8960 (mp0) REVERT: A 172 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9191 (mp0) REVERT: A 205 ARG cc_start: 0.9098 (ttm110) cc_final: 0.8725 (ttm110) REVERT: B 70 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9101 (mp0) REVERT: B 170 ASN cc_start: 0.9150 (t0) cc_final: 0.8643 (t0) REVERT: C 70 GLU cc_start: 0.9412 (mt-10) cc_final: 0.8922 (mp0) REVERT: C 134 PHE cc_start: 0.8295 (t80) cc_final: 0.8056 (t80) REVERT: C 138 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.9027 (t) REVERT: C 205 ARG cc_start: 0.9181 (ttm110) cc_final: 0.8638 (ttm110) REVERT: D 138 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.8983 (t) REVERT: D 205 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8718 (ttm110) REVERT: E 133 TRP cc_start: 0.8725 (m-90) cc_final: 0.8304 (m-90) REVERT: E 138 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8865 (t) REVERT: E 205 ARG cc_start: 0.9152 (ttm110) cc_final: 0.8686 (ttm110) REVERT: F 66 LYS cc_start: 0.9142 (tppt) cc_final: 0.8750 (tppt) REVERT: F 74 ASP cc_start: 0.8111 (t0) cc_final: 0.7518 (t0) REVERT: F 108 ASP cc_start: 0.9073 (m-30) cc_final: 0.8708 (m-30) REVERT: G 40 GLN cc_start: 0.9220 (tt0) cc_final: 0.8567 (tp40) REVERT: G 44 LYS cc_start: 0.9272 (mppt) cc_final: 0.8833 (mmtm) REVERT: G 46 ARG cc_start: 0.9249 (mtm110) cc_final: 0.8991 (mtm110) REVERT: G 74 ASP cc_start: 0.8089 (t0) cc_final: 0.7461 (t0) REVERT: G 84 MET cc_start: 0.9186 (mtm) cc_final: 0.8809 (ttm) REVERT: H 74 ASP cc_start: 0.8131 (t0) cc_final: 0.7527 (t0) REVERT: H 83 GLN cc_start: 0.8928 (tp40) cc_final: 0.8526 (tp-100) REVERT: I 74 ASP cc_start: 0.8052 (t0) cc_final: 0.7475 (t0) REVERT: I 115 GLN cc_start: 0.8634 (tt0) cc_final: 0.7726 (tt0) REVERT: J 66 LYS cc_start: 0.9093 (ttmm) cc_final: 0.8879 (ttmm) REVERT: J 74 ASP cc_start: 0.8158 (t0) cc_final: 0.7443 (t0) REVERT: J 83 GLN cc_start: 0.8952 (tp40) cc_final: 0.8620 (tp-100) REVERT: J 84 MET cc_start: 0.9220 (mtm) cc_final: 0.8723 (mtm) outliers start: 23 outliers final: 14 residues processed: 280 average time/residue: 0.1679 time to fit residues: 63.4695 Evaluate side-chains 274 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 257 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 144 optimal weight: 0.0010 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 ASN D 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.061554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.042954 restraints weight = 83014.770| |-----------------------------------------------------------------------------| r_work (start): 0.2473 rms_B_bonded: 5.33 r_work: 0.2279 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.2279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2315 r_free = 0.2315 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2315 r_free = 0.2315 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13970 Z= 0.208 Angle : 0.717 10.182 19030 Z= 0.347 Chirality : 0.047 0.240 2020 Planarity : 0.004 0.047 2400 Dihedral : 8.201 59.993 2295 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.41 % Allowed : 20.21 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.19), residues: 1620 helix: -0.41 (0.78), residues: 45 sheet: -0.09 (0.20), residues: 665 loop : -2.51 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 46 TYR 0.010 0.001 TYR I 96 PHE 0.016 0.001 PHE C 134 TRP 0.030 0.001 TRP C 133 HIS 0.002 0.001 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00487 (13945) covalent geometry : angle 0.69409 (18960) SS BOND : bond 0.00345 ( 5) SS BOND : angle 0.60688 ( 10) hydrogen bonds : bond 0.02782 ( 349) hydrogen bonds : angle 4.75163 ( 1083) link_BETA1-4 : bond 0.01899 ( 5) link_BETA1-4 : angle 5.49790 ( 15) link_NAG-ASN : bond 0.00130 ( 15) link_NAG-ASN : angle 2.04922 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.9108 (ttm110) cc_final: 0.8746 (ttm110) REVERT: B 70 GLU cc_start: 0.9460 (mt-10) cc_final: 0.9095 (mp0) REVERT: B 170 ASN cc_start: 0.9117 (t0) cc_final: 0.8604 (t0) REVERT: B 205 ARG cc_start: 0.9107 (ttm110) cc_final: 0.8884 (ttm110) REVERT: C 134 PHE cc_start: 0.8293 (t80) cc_final: 0.8058 (t80) REVERT: C 138 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.9050 (t) REVERT: C 192 GLU cc_start: 0.9320 (pt0) cc_final: 0.9044 (pt0) REVERT: C 205 ARG cc_start: 0.9210 (ttm110) cc_final: 0.8685 (ttm110) REVERT: D 70 GLU cc_start: 0.9423 (mt-10) cc_final: 0.8935 (mp0) REVERT: D 138 VAL cc_start: 0.9261 (OUTLIER) cc_final: 0.9025 (t) REVERT: D 172 GLU cc_start: 0.9517 (mt-10) cc_final: 0.9314 (mp0) REVERT: D 205 ARG cc_start: 0.9181 (ttm110) cc_final: 0.8791 (ttm110) REVERT: E 133 TRP cc_start: 0.8658 (m-90) cc_final: 0.8329 (m-90) REVERT: E 138 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8903 (t) REVERT: E 205 ARG cc_start: 0.9164 (ttm110) cc_final: 0.8795 (ttm110) REVERT: F 66 LYS cc_start: 0.9227 (tppt) cc_final: 0.8824 (tppt) REVERT: F 69 PHE cc_start: 0.8112 (m-10) cc_final: 0.7506 (m-10) REVERT: F 74 ASP cc_start: 0.8114 (t0) cc_final: 0.7522 (t0) REVERT: F 108 ASP cc_start: 0.9047 (m-30) cc_final: 0.8689 (m-30) REVERT: G 40 GLN cc_start: 0.9179 (tt0) cc_final: 0.8475 (tp40) REVERT: G 44 LYS cc_start: 0.9276 (mppt) cc_final: 0.8862 (mmtm) REVERT: G 46 ARG cc_start: 0.9225 (mtm110) cc_final: 0.8955 (mtm110) REVERT: G 74 ASP cc_start: 0.8083 (t0) cc_final: 0.7456 (t0) REVERT: G 88 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8602 (mmtm) REVERT: H 46 ARG cc_start: 0.9183 (mtm110) cc_final: 0.8956 (mtm110) REVERT: H 74 ASP cc_start: 0.8080 (t0) cc_final: 0.7442 (t0) REVERT: H 83 GLN cc_start: 0.8938 (tp40) cc_final: 0.8528 (tp-100) REVERT: I 74 ASP cc_start: 0.8057 (t0) cc_final: 0.7500 (t0) REVERT: J 19 LEU cc_start: 0.9023 (mt) cc_final: 0.8168 (mt) REVERT: J 35 MET cc_start: 0.9415 (mmm) cc_final: 0.9182 (mmt) REVERT: J 66 LYS cc_start: 0.9126 (ttmm) cc_final: 0.8757 (ttmt) REVERT: J 74 ASP cc_start: 0.8153 (t0) cc_final: 0.7450 (t0) REVERT: J 83 GLN cc_start: 0.8933 (tp40) cc_final: 0.8608 (tp-100) REVERT: J 84 MET cc_start: 0.9231 (mtm) cc_final: 0.8727 (mtm) outliers start: 20 outliers final: 14 residues processed: 279 average time/residue: 0.1520 time to fit residues: 56.9061 Evaluate side-chains 274 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 257 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.2996 r_free = 0.2996 target = 0.062819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.044116 restraints weight = 82017.404| |-----------------------------------------------------------------------------| r_work (start): 0.2509 rms_B_bonded: 5.36 r_work: 0.2314 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2327 r_free = 0.2327 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2327 r_free = 0.2327 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13970 Z= 0.128 Angle : 0.702 11.074 19030 Z= 0.338 Chirality : 0.047 0.240 2020 Planarity : 0.004 0.047 2400 Dihedral : 7.829 59.649 2295 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 1.06 % Allowed : 20.28 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.19), residues: 1620 helix: 0.12 (0.79), residues: 45 sheet: 0.01 (0.20), residues: 670 loop : -2.43 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 46 TYR 0.009 0.001 TYR D 117 PHE 0.025 0.001 PHE D 134 TRP 0.035 0.001 TRP A 133 HIS 0.003 0.001 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00299 (13945) covalent geometry : angle 0.67973 (18960) SS BOND : bond 0.00160 ( 5) SS BOND : angle 0.45651 ( 10) hydrogen bonds : bond 0.02463 ( 349) hydrogen bonds : angle 4.64406 ( 1083) link_BETA1-4 : bond 0.02026 ( 5) link_BETA1-4 : angle 5.40471 ( 15) link_NAG-ASN : bond 0.00112 ( 15) link_NAG-ASN : angle 1.99073 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.9092 (ttm110) cc_final: 0.8719 (ttm110) REVERT: B 70 GLU cc_start: 0.9488 (mt-10) cc_final: 0.9063 (mp0) REVERT: B 205 ARG cc_start: 0.9111 (ttm110) cc_final: 0.8692 (ttm110) REVERT: C 134 PHE cc_start: 0.8260 (t80) cc_final: 0.7997 (t80) REVERT: C 138 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.9006 (t) REVERT: C 205 ARG cc_start: 0.9222 (ttm110) cc_final: 0.8666 (ttm-80) REVERT: D 70 GLU cc_start: 0.9435 (mt-10) cc_final: 0.8970 (mp0) REVERT: D 138 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.9006 (t) REVERT: D 172 GLU cc_start: 0.9514 (mt-10) cc_final: 0.9305 (mp0) REVERT: D 205 ARG cc_start: 0.9194 (ttm110) cc_final: 0.8801 (ttm110) REVERT: E 133 TRP cc_start: 0.8577 (m-90) cc_final: 0.8304 (m-90) REVERT: E 138 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8923 (t) REVERT: E 205 ARG cc_start: 0.9162 (ttm110) cc_final: 0.8712 (ttm110) REVERT: F 66 LYS cc_start: 0.9076 (tppt) cc_final: 0.8696 (tppt) REVERT: F 74 ASP cc_start: 0.8028 (t0) cc_final: 0.7460 (t0) REVERT: F 108 ASP cc_start: 0.9056 (m-30) cc_final: 0.8706 (m-30) REVERT: G 40 GLN cc_start: 0.9184 (tt0) cc_final: 0.8521 (tp40) REVERT: G 44 LYS cc_start: 0.9270 (mppt) cc_final: 0.8902 (mmtm) REVERT: G 74 ASP cc_start: 0.8050 (t0) cc_final: 0.7441 (t0) REVERT: H 35 MET cc_start: 0.9354 (mmp) cc_final: 0.9088 (mmp) REVERT: H 46 ARG cc_start: 0.9174 (mtm110) cc_final: 0.8933 (mtm110) REVERT: H 66 LYS cc_start: 0.9208 (tppt) cc_final: 0.8671 (tppt) REVERT: H 74 ASP cc_start: 0.8041 (t0) cc_final: 0.7418 (t0) REVERT: H 83 GLN cc_start: 0.8896 (tp40) cc_final: 0.8437 (tp-100) REVERT: I 69 PHE cc_start: 0.7404 (m-10) cc_final: 0.6803 (m-10) REVERT: I 74 ASP cc_start: 0.8019 (t0) cc_final: 0.7513 (t0) REVERT: J 19 LEU cc_start: 0.9045 (mt) cc_final: 0.8407 (mm) REVERT: J 66 LYS cc_start: 0.9013 (ttmm) cc_final: 0.8656 (ttmt) REVERT: J 74 ASP cc_start: 0.8103 (t0) cc_final: 0.7407 (t0) REVERT: J 83 GLN cc_start: 0.8935 (tp40) cc_final: 0.8608 (tp-100) REVERT: J 84 MET cc_start: 0.9220 (mtm) cc_final: 0.8716 (mtm) outliers start: 15 outliers final: 11 residues processed: 267 average time/residue: 0.1728 time to fit residues: 61.8290 Evaluate side-chains 267 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 253 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 120 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 81 optimal weight: 0.0670 chunk 110 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.7524 ------------------------------------------------------------------------------- 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 = 0.2998 r_free = 0.2998 target = 0.062771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.043747 restraints weight = 103114.914| |-----------------------------------------------------------------------------| r_work (start): 0.2497 rms_B_bonded: 5.84 r_work: 0.2292 rms_B_bonded: 5.44 restraints_weight: 2.0000 r_work (final): 0.2292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2328 r_free = 0.2328 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2328 r_free = 0.2328 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13970 Z= 0.154 Angle : 0.708 12.797 19030 Z= 0.339 Chirality : 0.047 0.242 2020 Planarity : 0.004 0.047 2400 Dihedral : 7.769 59.482 2295 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.06 % Allowed : 20.56 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.20), residues: 1620 helix: 0.54 (0.79), residues: 45 sheet: 0.05 (0.21), residues: 625 loop : -2.28 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 46 TYR 0.009 0.001 TYR D 117 PHE 0.015 0.001 PHE C 134 TRP 0.035 0.001 TRP A 133 HIS 0.003 0.001 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00363 (13945) covalent geometry : angle 0.68619 (18960) SS BOND : bond 0.00228 ( 5) SS BOND : angle 0.53328 ( 10) hydrogen bonds : bond 0.02532 ( 349) hydrogen bonds : angle 4.62034 ( 1083) link_BETA1-4 : bond 0.01937 ( 5) link_BETA1-4 : angle 5.40013 ( 15) link_NAG-ASN : bond 0.00061 ( 15) link_NAG-ASN : angle 1.97693 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 253 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.9442 (t0) cc_final: 0.9233 (t0) REVERT: A 205 ARG cc_start: 0.9096 (ttm110) cc_final: 0.8739 (ttm110) REVERT: B 70 GLU cc_start: 0.9501 (mt-10) cc_final: 0.9071 (mp0) REVERT: B 133 TRP cc_start: 0.8544 (m-90) cc_final: 0.8092 (m-90) REVERT: B 205 ARG cc_start: 0.9148 (ttm110) cc_final: 0.8740 (ttm110) REVERT: C 138 VAL cc_start: 0.9283 (OUTLIER) cc_final: 0.9060 (t) REVERT: C 192 GLU cc_start: 0.9315 (pt0) cc_final: 0.9042 (pt0) REVERT: C 205 ARG cc_start: 0.9236 (ttm110) cc_final: 0.8737 (ttm110) REVERT: D 70 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9024 (mp0) REVERT: D 138 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.9046 (t) REVERT: D 205 ARG cc_start: 0.9202 (ttm110) cc_final: 0.8836 (ttm110) REVERT: E 70 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9087 (mp0) REVERT: E 133 TRP cc_start: 0.8549 (m-90) cc_final: 0.8295 (m-90) REVERT: E 138 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8958 (t) REVERT: E 205 ARG cc_start: 0.9197 (ttm110) cc_final: 0.8772 (ttm110) REVERT: F 66 LYS cc_start: 0.9072 (tppt) cc_final: 0.8703 (tppt) REVERT: F 74 ASP cc_start: 0.8074 (t0) cc_final: 0.7515 (t0) REVERT: F 108 ASP cc_start: 0.9019 (m-30) cc_final: 0.8673 (m-30) REVERT: G 40 GLN cc_start: 0.9166 (tt0) cc_final: 0.8519 (tp40) REVERT: G 46 ARG cc_start: 0.9199 (mtm110) cc_final: 0.8996 (mtm110) REVERT: G 74 ASP cc_start: 0.8126 (t0) cc_final: 0.7503 (t0) REVERT: H 35 MET cc_start: 0.9386 (mmp) cc_final: 0.9122 (mmp) REVERT: H 46 ARG cc_start: 0.9188 (mtm110) cc_final: 0.8950 (mtm110) REVERT: H 66 LYS cc_start: 0.9212 (tppt) cc_final: 0.8678 (tppt) REVERT: H 74 ASP cc_start: 0.8131 (t0) cc_final: 0.7506 (t0) REVERT: H 83 GLN cc_start: 0.8869 (tp40) cc_final: 0.8396 (tp-100) REVERT: I 74 ASP cc_start: 0.8093 (t0) cc_final: 0.7559 (t0) REVERT: J 19 LEU cc_start: 0.9037 (mt) cc_final: 0.8397 (mm) REVERT: J 66 LYS cc_start: 0.9004 (ttmm) cc_final: 0.8660 (ttmt) REVERT: J 74 ASP cc_start: 0.8131 (t0) cc_final: 0.7457 (t0) REVERT: J 83 GLN cc_start: 0.8934 (tp40) cc_final: 0.8612 (tp-100) REVERT: J 84 MET cc_start: 0.9240 (mtm) cc_final: 0.8741 (mtm) outliers start: 15 outliers final: 10 residues processed: 265 average time/residue: 0.1603 time to fit residues: 56.9970 Evaluate side-chains 264 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 251 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 60 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 = 0.2974 r_free = 0.2974 target = 0.061615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.042754 restraints weight = 100661.487| |-----------------------------------------------------------------------------| r_work (start): 0.2470 rms_B_bonded: 5.75 r_work: 0.2268 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.2268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2282 r_free = 0.2282 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2282 r_free = 0.2282 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13970 Z= 0.224 Angle : 0.745 12.410 19030 Z= 0.358 Chirality : 0.047 0.243 2020 Planarity : 0.004 0.046 2400 Dihedral : 7.966 59.993 2295 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.13 % Allowed : 20.63 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.19), residues: 1620 helix: 0.68 (0.79), residues: 45 sheet: 0.07 (0.21), residues: 620 loop : -2.30 (0.17), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 68 TYR 0.010 0.001 TYR B 150 PHE 0.024 0.002 PHE D 134 TRP 0.032 0.001 TRP A 133 HIS 0.002 0.001 HIS J 32 Details of bonding type rmsd covalent geometry : bond 0.00528 (13945) covalent geometry : angle 0.72376 (18960) SS BOND : bond 0.00368 ( 5) SS BOND : angle 0.67101 ( 10) hydrogen bonds : bond 0.02829 ( 349) hydrogen bonds : angle 4.74432 ( 1083) link_BETA1-4 : bond 0.01820 ( 5) link_BETA1-4 : angle 5.49354 ( 15) link_NAG-ASN : bond 0.00156 ( 15) link_NAG-ASN : angle 2.03124 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.9441 (t0) cc_final: 0.9229 (t0) REVERT: A 205 ARG cc_start: 0.9117 (ttm110) cc_final: 0.8759 (ttm110) REVERT: B 70 GLU cc_start: 0.9501 (mt-10) cc_final: 0.9071 (mp0) REVERT: B 133 TRP cc_start: 0.8587 (m-90) cc_final: 0.8144 (m-90) REVERT: B 205 ARG cc_start: 0.9172 (ttm110) cc_final: 0.8751 (ttm110) REVERT: C 138 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9114 (t) REVERT: C 205 ARG cc_start: 0.9245 (ttm110) cc_final: 0.8803 (ttm-80) REVERT: D 70 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9023 (mp0) REVERT: D 134 PHE cc_start: 0.8264 (t80) cc_final: 0.7974 (t80) REVERT: D 138 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.9045 (t) REVERT: D 205 ARG cc_start: 0.9200 (ttm110) cc_final: 0.8584 (ttm110) REVERT: E 70 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9075 (mp0) REVERT: E 133 TRP cc_start: 0.8517 (m-90) cc_final: 0.8214 (m-90) REVERT: E 134 PHE cc_start: 0.8281 (t80) cc_final: 0.7793 (t80) REVERT: E 138 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8949 (t) REVERT: E 205 ARG cc_start: 0.9201 (ttm110) cc_final: 0.8332 (ttm110) REVERT: F 74 ASP cc_start: 0.8151 (t0) cc_final: 0.7552 (t0) REVERT: F 108 ASP cc_start: 0.9053 (m-30) cc_final: 0.8640 (m-30) REVERT: G 40 GLN cc_start: 0.9156 (tt0) cc_final: 0.8489 (tp40) REVERT: G 46 ARG cc_start: 0.9227 (mtm110) cc_final: 0.9018 (mtm110) REVERT: G 74 ASP cc_start: 0.8178 (t0) cc_final: 0.7550 (t0) REVERT: H 35 MET cc_start: 0.9421 (mmp) cc_final: 0.9161 (mmp) REVERT: H 66 LYS cc_start: 0.9301 (tppt) cc_final: 0.8738 (tppt) REVERT: H 74 ASP cc_start: 0.8198 (t0) cc_final: 0.7551 (t0) REVERT: H 83 GLN cc_start: 0.8878 (tp40) cc_final: 0.8413 (tp-100) REVERT: I 69 PHE cc_start: 0.7188 (m-80) cc_final: 0.6942 (m-10) REVERT: I 74 ASP cc_start: 0.8171 (t0) cc_final: 0.7593 (t0) REVERT: J 19 LEU cc_start: 0.9025 (mt) cc_final: 0.8176 (mt) REVERT: J 74 ASP cc_start: 0.8184 (t0) cc_final: 0.7497 (t0) REVERT: J 83 GLN cc_start: 0.8939 (tp40) cc_final: 0.8615 (tp-100) REVERT: J 84 MET cc_start: 0.9251 (mtm) cc_final: 0.8765 (mtp) outliers start: 16 outliers final: 11 residues processed: 258 average time/residue: 0.1652 time to fit residues: 57.1553 Evaluate side-chains 258 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 244 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 104 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3015 r_free = 0.3015 target = 0.063546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.045587 restraints weight = 74181.148| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 5.05 r_work: 0.2360 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2369 r_free = 0.2369 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2369 r_free = 0.2369 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13970 Z= 0.119 Angle : 0.718 13.241 19030 Z= 0.343 Chirality : 0.046 0.238 2020 Planarity : 0.004 0.047 2400 Dihedral : 7.448 59.069 2295 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.85 % Allowed : 21.27 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.20), residues: 1620 helix: 1.02 (0.80), residues: 45 sheet: 0.23 (0.21), residues: 620 loop : -2.25 (0.17), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 46 TYR 0.009 0.001 TYR D 117 PHE 0.025 0.001 PHE D 134 TRP 0.038 0.001 TRP A 133 HIS 0.004 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00280 (13945) covalent geometry : angle 0.69658 (18960) SS BOND : bond 0.00092 ( 5) SS BOND : angle 0.43100 ( 10) hydrogen bonds : bond 0.02425 ( 349) hydrogen bonds : angle 4.54471 ( 1083) link_BETA1-4 : bond 0.02156 ( 5) link_BETA1-4 : angle 5.45287 ( 15) link_NAG-ASN : bond 0.00168 ( 15) link_NAG-ASN : angle 1.88728 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3321.97 seconds wall clock time: 57 minutes 49.78 seconds (3469.78 seconds total)