Starting phenix.real_space_refine on Fri Jul 3 12:04:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fg4_50384/07_2026/9fg4_50384.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fg4_50384/07_2026/9fg4_50384.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fg4_50384/07_2026/9fg4_50384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fg4_50384/07_2026/9fg4_50384.map" model { file = "/net/cci-nas-00/data/ceres_data/9fg4_50384/07_2026/9fg4_50384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fg4_50384/07_2026/9fg4_50384.cif" } 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= -0.011 sd= 0.094 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 80 5.16 5 C 9193 2.51 5 N 2270 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14167 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2774 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 Chain: "B" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2712 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Chain: "C" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2712 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Chain: "D" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2774 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 Chain: "E" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2712 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.13, per 1000 atoms: 0.22 Number of scatterers: 14167 At special positions: 0 Unit cell: (99.1936, 101.673, 133.911, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 6 15.00 O 2618 8.00 N 2270 7.00 C 9193 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " 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 ALPHA1-3 " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG F 1 " - " ASN B 80 " " NAG G 1 " - " ASN C 80 " " NAG H 1 " - " ASN E 80 " " NAG a 1 " - " ASN A 111 " " NAG b 1 " - " ASN B 149 " " NAG c 1 " - " ASN C 149 " " NAG d 1 " - " ASN D 111 " " NAG e 1 " - " ASN E 149 " Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 583.1 milliseconds 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3182 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 41.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.593A pdb=" N LEU A 19 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 251 through 277 Processing helix chain 'A' and resid 284 through 309 removed outlier: 3.503A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 416 removed outlier: 3.964A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 246 through 272 removed outlier: 3.563A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 308 removed outlier: 3.562A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 472 removed outlier: 3.774A pdb=" N ASP B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Proline residue: B 457 - end of helix Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.687A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.593A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 246 through 272 removed outlier: 3.659A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 308 Processing helix chain 'C' and resid 445 through 472 removed outlier: 3.562A pdb=" N ASP C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 454 " --> pdb=" O ARG C 450 " (cutoff:3.500A) Proline residue: C 457 - end of helix Processing helix chain 'D' and resid 13 through 23 removed outlier: 3.554A pdb=" N LEU D 19 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.457A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.616A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 removed outlier: 3.656A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 310 removed outlier: 3.642A pdb=" N PHE D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 416 removed outlier: 3.925A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.625A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.526A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 246 through 267 removed outlier: 3.613A pdb=" N HIS E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 Processing helix chain 'E' and resid 279 through 308 removed outlier: 3.693A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 472 removed outlier: 3.668A pdb=" N ILE E 454 " --> pdb=" O ARG E 450 " (cutoff:3.500A) Proline residue: E 457 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 49 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 39 through 49 current: chain 'A' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 71 current: chain 'A' and resid 126 through 138 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.436A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 36 through 46 current: chain 'B' and resid 56 through 68 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 68 current: chain 'B' and resid 123 through 135 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.144A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 51 removed outlier: 6.246A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 68 current: chain 'C' and resid 123 through 135 Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.831A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 39 through 49 current: chain 'D' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 71 current: chain 'D' and resid 126 through 138 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.422A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 36 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 36 through 46 current: chain 'E' and resid 56 through 68 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 68 current: chain 'E' and resid 123 through 135 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.825A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1581 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: 2.21 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2313 1.32 - 1.45: 4196 1.45 - 1.57: 7868 1.57 - 1.69: 8 1.69 - 1.82: 140 Bond restraints: 14525 Sorted by residual: bond pdb=" O4 PIO A 501 " pdb=" P4 PIO A 501 " ideal model delta sigma weight residual 1.710 1.626 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O4 PIO D 501 " pdb=" P4 PIO D 501 " ideal model delta sigma weight residual 1.710 1.626 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O5 PIO D 501 " pdb=" P5 PIO D 501 " ideal model delta sigma weight residual 1.699 1.625 0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" O5 PIO A 501 " pdb=" P5 PIO A 501 " ideal model delta sigma weight residual 1.699 1.627 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C5 PIO D 501 " pdb=" O5 PIO D 501 " ideal model delta sigma weight residual 1.388 1.443 -0.055 2.00e-02 2.50e+03 7.67e+00 ... (remaining 14520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 18998 1.44 - 2.88: 598 2.88 - 4.32: 120 4.32 - 5.76: 26 5.76 - 7.20: 6 Bond angle restraints: 19748 Sorted by residual: angle pdb=" C LEU E 268 " pdb=" N ARG E 269 " pdb=" CA ARG E 269 " ideal model delta sigma weight residual 120.72 126.40 -5.68 1.67e+00 3.59e-01 1.16e+01 angle pdb=" N LYS C 274 " pdb=" CA LYS C 274 " pdb=" C LYS C 274 " ideal model delta sigma weight residual 110.80 117.59 -6.79 2.13e+00 2.20e-01 1.02e+01 angle pdb=" N LEU E 268 " pdb=" CA LEU E 268 " pdb=" C LEU E 268 " ideal model delta sigma weight residual 112.45 108.10 4.35 1.39e+00 5.18e-01 9.79e+00 angle pdb=" N LYS B 274 " pdb=" CA LYS B 274 " pdb=" C LYS B 274 " ideal model delta sigma weight residual 110.80 117.16 -6.36 2.13e+00 2.20e-01 8.91e+00 angle pdb=" C THR E 266 " pdb=" N HIS E 267 " pdb=" CA HIS E 267 " ideal model delta sigma weight residual 121.54 116.20 5.34 1.91e+00 2.74e-01 7.80e+00 ... (remaining 19743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 8561 21.23 - 42.45: 237 42.45 - 63.68: 35 63.68 - 84.91: 36 84.91 - 106.13: 21 Dihedral angle restraints: 8890 sinusoidal: 3944 harmonic: 4946 Sorted by residual: dihedral pdb=" CA PRO E 276 " pdb=" C PRO E 276 " pdb=" N TYR E 277 " pdb=" CA TYR E 277 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA VAL A 64 " pdb=" C VAL A 64 " pdb=" N PHE A 65 " pdb=" CA PHE A 65 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 8887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2053 0.066 - 0.132: 245 0.132 - 0.198: 19 0.198 - 0.264: 7 0.264 - 0.330: 1 Chirality restraints: 2325 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN C 80 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 80 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2322 not shown) Planarity restraints: 2393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 275 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO E 276 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 1 " -0.022 2.00e-02 2.50e+03 1.83e-02 4.17e+00 pdb=" C7 NAG b 1 " 0.002 2.00e-02 2.50e+03 pdb=" C8 NAG b 1 " -0.016 2.00e-02 2.50e+03 pdb=" N2 NAG b 1 " 0.030 2.00e-02 2.50e+03 pdb=" O7 NAG b 1 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " 0.020 2.00e-02 2.50e+03 1.68e-02 3.53e+00 pdb=" C7 NAG c 2 " -0.006 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " 0.016 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " -0.026 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " -0.003 2.00e-02 2.50e+03 ... (remaining 2390 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1941 2.76 - 3.29: 13427 3.29 - 3.83: 23771 3.83 - 4.36: 29692 4.36 - 4.90: 49991 Nonbonded interactions: 118822 Sorted by model distance: nonbonded pdb=" OH TYR D 60 " pdb=" O PRO D 154 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP B 43 " pdb=" OG SER D 206 " model vdw 2.277 3.040 nonbonded pdb=" O PHE C 221 " pdb=" OG1 THR C 225 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 60 " pdb=" O PRO A 154 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP E 146 " pdb=" NE2 GLN E 148 " model vdw 2.298 3.120 ... (remaining 118817 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.980 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.004 0.084 14561 Z= 0.194 Angle : 0.630 8.593 19851 Z= 0.310 Chirality : 0.046 0.330 2325 Planarity : 0.004 0.063 2385 Dihedral : 13.017 106.134 5693 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.00 % Allowed : 3.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1656 helix: 0.66 (0.21), residues: 579 sheet: 0.56 (0.25), residues: 434 loop : 0.43 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 255 TYR 0.017 0.001 TYR A 129 PHE 0.015 0.001 PHE B 98 TRP 0.014 0.001 TRP A 70 HIS 0.002 0.001 HIS E 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (14525) covalent geometry : angle 0.61817 / 0.31 (19748) SS BOND : bond 0.00249 / 0.13 ( 5) SS BOND : angle 1.59067 / 0.99 ( 10) hydrogen bonds : bond 0.21931 / 14.28 ( 564) hydrogen bonds : angle 7.34459 / 5.07 ( 1581) link_ALPHA1-3 : bond 0.00149 / 0.07 ( 5) link_ALPHA1-3 : angle 1.05706 / 0.62 ( 15) link_ALPHA1-6 : bond 0.00462 / 0.28 ( 5) link_ALPHA1-6 : angle 1.00483 / 0.55 ( 15) link_BETA1-4 : bond 0.00441 / 0.29 ( 13) link_BETA1-4 : angle 1.31048 / 0.84 ( 39) link_NAG-ASN : bond 0.00397 / 0.24 ( 8) link_NAG-ASN : angle 2.89947 / 1.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.8089 (mmm) cc_final: 0.7647 (mmm) outliers start: 15 outliers final: 5 residues processed: 111 average time/residue: 0.1075 time to fit residues: 18.6460 Evaluate side-chains 72 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN B 41 ASN B 64 GLN D 102 HIS ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.060510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051046 restraints weight = 65113.494| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.70 r_work: 0.3082 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14561 Z= 0.135 Angle : 0.551 7.395 19851 Z= 0.284 Chirality : 0.043 0.204 2325 Planarity : 0.004 0.060 2385 Dihedral : 10.979 82.439 2537 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.07 % Allowed : 6.00 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.21), residues: 1656 helix: 1.57 (0.21), residues: 588 sheet: 0.54 (0.24), residues: 452 loop : 0.94 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 269 TYR 0.022 0.002 TYR B 299 PHE 0.015 0.001 PHE A 304 TRP 0.010 0.001 TRP E 451 HIS 0.008 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (14525) covalent geometry : angle 0.53927 / 0.28 (19748) SS BOND : bond 0.00183 / 0.10 ( 5) SS BOND : angle 0.48078 / 0.27 ( 10) hydrogen bonds : bond 0.04207 / 2.75 ( 564) hydrogen bonds : angle 4.98072 / 3.44 ( 1581) link_ALPHA1-3 : bond 0.00688 / 0.37 ( 5) link_ALPHA1-3 : angle 2.18042 / 1.25 ( 15) link_ALPHA1-6 : bond 0.00443 / 0.27 ( 5) link_ALPHA1-6 : angle 1.87993 / 1.16 ( 15) link_BETA1-4 : bond 0.00344 / 0.21 ( 13) link_BETA1-4 : angle 1.54618 / 1.15 ( 39) link_NAG-ASN : bond 0.00223 / 0.14 ( 8) link_NAG-ASN : angle 1.73167 / 1.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7550 (p0) REVERT: A 114 MET cc_start: 0.9019 (mmm) cc_final: 0.8717 (mmm) REVERT: A 213 MET cc_start: 0.8331 (mmm) cc_final: 0.7559 (mmm) REVERT: A 228 ILE cc_start: 0.9372 (mt) cc_final: 0.9167 (tt) REVERT: C 40 MET cc_start: 0.8874 (mtt) cc_final: 0.8494 (mtp) REVERT: D 236 MET cc_start: 0.8872 (mtp) cc_final: 0.8587 (ttm) REVERT: E 61 MET cc_start: 0.9050 (ppp) cc_final: 0.8710 (ppp) outliers start: 16 outliers final: 7 residues processed: 86 average time/residue: 0.0949 time to fit residues: 13.6829 Evaluate side-chains 74 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 104 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.060080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050446 restraints weight = 67106.757| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.76 r_work: 0.3047 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14561 Z= 0.142 Angle : 0.518 6.781 19851 Z= 0.261 Chirality : 0.042 0.204 2325 Planarity : 0.004 0.072 2385 Dihedral : 9.882 74.049 2533 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.80 % Allowed : 6.66 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.21), residues: 1656 helix: 1.86 (0.21), residues: 588 sheet: 0.43 (0.24), residues: 452 loop : 1.00 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 269 TYR 0.027 0.001 TYR B 299 PHE 0.015 0.001 PHE A 304 TRP 0.009 0.001 TRP A 317 HIS 0.004 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (14525) covalent geometry : angle 0.50565 / 0.26 (19748) SS BOND : bond 0.00113 / 0.05 ( 5) SS BOND : angle 0.56497 / 0.37 ( 10) hydrogen bonds : bond 0.03504 / 2.29 ( 564) hydrogen bonds : angle 4.53175 / 3.16 ( 1581) link_ALPHA1-3 : bond 0.00964 / 0.51 ( 5) link_ALPHA1-3 : angle 2.04639 / 1.20 ( 15) link_ALPHA1-6 : bond 0.00633 / 0.37 ( 5) link_ALPHA1-6 : angle 1.95241 / 1.20 ( 15) link_BETA1-4 : bond 0.00353 / 0.21 ( 13) link_BETA1-4 : angle 1.43037 / 1.04 ( 39) link_NAG-ASN : bond 0.00327 / 0.20 ( 8) link_NAG-ASN : angle 1.73112 / 1.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9000 (mmm) cc_final: 0.8664 (mmm) REVERT: A 213 MET cc_start: 0.8416 (mmm) cc_final: 0.7971 (mmm) REVERT: C 40 MET cc_start: 0.8736 (mtt) cc_final: 0.8449 (mtm) REVERT: C 115 MET cc_start: 0.8573 (tmm) cc_final: 0.8372 (tmm) REVERT: D 112 MET cc_start: 0.8516 (tpp) cc_final: 0.8150 (ttm) REVERT: E 55 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8334 (tpt) REVERT: E 61 MET cc_start: 0.9082 (ppp) cc_final: 0.8575 (ppp) outliers start: 12 outliers final: 7 residues processed: 80 average time/residue: 0.0943 time to fit residues: 12.6477 Evaluate side-chains 72 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 128 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.058400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.048956 restraints weight = 66053.040| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.62 r_work: 0.3011 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14561 Z= 0.176 Angle : 0.535 8.206 19851 Z= 0.268 Chirality : 0.043 0.232 2325 Planarity : 0.004 0.070 2385 Dihedral : 8.795 65.601 2533 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.07 % Allowed : 7.20 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.21), residues: 1656 helix: 1.91 (0.21), residues: 595 sheet: 0.53 (0.25), residues: 413 loop : 0.83 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 269 TYR 0.028 0.002 TYR B 299 PHE 0.018 0.001 PHE A 304 TRP 0.009 0.001 TRP A 317 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (14525) covalent geometry : angle 0.52297 / 0.27 (19748) SS BOND : bond 0.00111 / 0.05 ( 5) SS BOND : angle 0.45344 / 0.25 ( 10) hydrogen bonds : bond 0.03185 / 2.08 ( 564) hydrogen bonds : angle 4.37329 / 3.06 ( 1581) link_ALPHA1-3 : bond 0.00955 / 0.51 ( 5) link_ALPHA1-3 : angle 2.30742 / 1.37 ( 15) link_ALPHA1-6 : bond 0.00756 / 0.43 ( 5) link_ALPHA1-6 : angle 2.02393 / 1.25 ( 15) link_BETA1-4 : bond 0.00347 / 0.20 ( 13) link_BETA1-4 : angle 1.39674 / 0.99 ( 39) link_NAG-ASN : bond 0.00287 / 0.17 ( 8) link_NAG-ASN : angle 1.50199 / 1.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9007 (mmm) cc_final: 0.8658 (mmm) REVERT: A 213 MET cc_start: 0.8483 (mmm) cc_final: 0.7871 (mmm) REVERT: C 40 MET cc_start: 0.8662 (mtt) cc_final: 0.8405 (mtm) REVERT: C 283 MET cc_start: 0.8521 (tpt) cc_final: 0.8300 (mmm) REVERT: D 112 MET cc_start: 0.8733 (tpp) cc_final: 0.8324 (ttm) REVERT: E 55 MET cc_start: 0.8723 (mmm) cc_final: 0.8393 (tpt) REVERT: E 61 MET cc_start: 0.9103 (ppp) cc_final: 0.8653 (ppp) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.0958 time to fit residues: 12.4241 Evaluate side-chains 73 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.056671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.047015 restraints weight = 66847.261| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.79 r_work: 0.2909 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14561 Z= 0.197 Angle : 0.540 6.178 19851 Z= 0.269 Chirality : 0.043 0.238 2325 Planarity : 0.004 0.065 2385 Dihedral : 8.157 60.896 2533 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.27 % Allowed : 7.59 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.21), residues: 1656 helix: 2.03 (0.21), residues: 593 sheet: 0.28 (0.24), residues: 446 loop : 0.91 (0.28), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 269 TYR 0.028 0.002 TYR B 299 PHE 0.020 0.001 PHE A 304 TRP 0.010 0.001 TRP A 70 HIS 0.003 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (14525) covalent geometry : angle 0.52860 / 0.27 (19748) SS BOND : bond 0.00078 / 0.04 ( 5) SS BOND : angle 0.41297 / 0.24 ( 10) hydrogen bonds : bond 0.03146 / 2.06 ( 564) hydrogen bonds : angle 4.28714 / 2.99 ( 1581) link_ALPHA1-3 : bond 0.00909 / 0.48 ( 5) link_ALPHA1-3 : angle 2.27495 / 1.36 ( 15) link_ALPHA1-6 : bond 0.00792 / 0.45 ( 5) link_ALPHA1-6 : angle 1.95424 / 1.20 ( 15) link_BETA1-4 : bond 0.00374 / 0.22 ( 13) link_BETA1-4 : angle 1.35559 / 0.95 ( 39) link_NAG-ASN : bond 0.00259 / 0.16 ( 8) link_NAG-ASN : angle 1.61751 / 1.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9156 (mmm) cc_final: 0.8744 (mmm) REVERT: A 213 MET cc_start: 0.8443 (mmm) cc_final: 0.7739 (mmm) REVERT: B 115 MET cc_start: 0.8729 (tmm) cc_final: 0.8329 (tmm) REVERT: B 176 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8609 (p) REVERT: C 40 MET cc_start: 0.8752 (mtt) cc_final: 0.8499 (mtm) REVERT: C 115 MET cc_start: 0.8580 (tmm) cc_final: 0.8167 (tmm) REVERT: D 112 MET cc_start: 0.8976 (tpp) cc_final: 0.8755 (tpp) REVERT: D 242 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7615 (mp10) REVERT: D 266 MET cc_start: 0.9402 (mmm) cc_final: 0.9077 (tpp) REVERT: E 55 MET cc_start: 0.8721 (mmm) cc_final: 0.8421 (tpt) outliers start: 19 outliers final: 12 residues processed: 79 average time/residue: 0.0917 time to fit residues: 12.1005 Evaluate side-chains 76 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 52 optimal weight: 9.9990 chunk 16 optimal weight: 0.1980 chunk 100 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 98 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 119 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.057510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.047897 restraints weight = 66521.998| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.81 r_work: 0.2941 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14561 Z= 0.107 Angle : 0.491 6.325 19851 Z= 0.243 Chirality : 0.042 0.236 2325 Planarity : 0.003 0.062 2385 Dihedral : 7.568 56.406 2533 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.13 % Allowed : 7.59 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.22), residues: 1656 helix: 2.13 (0.21), residues: 595 sheet: 0.48 (0.25), residues: 419 loop : 0.93 (0.28), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 269 TYR 0.023 0.001 TYR C 299 PHE 0.013 0.001 PHE A 304 TRP 0.006 0.001 TRP A 317 HIS 0.004 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (14525) covalent geometry : angle 0.47955 / 0.24 (19748) SS BOND : bond 0.00078 / 0.05 ( 5) SS BOND : angle 0.32449 / 0.18 ( 10) hydrogen bonds : bond 0.02885 / 1.89 ( 564) hydrogen bonds : angle 4.14279 / 2.89 ( 1581) link_ALPHA1-3 : bond 0.01016 / 0.53 ( 5) link_ALPHA1-3 : angle 2.16268 / 1.29 ( 15) link_ALPHA1-6 : bond 0.00869 / 0.49 ( 5) link_ALPHA1-6 : angle 1.89834 / 1.16 ( 15) link_BETA1-4 : bond 0.00370 / 0.21 ( 13) link_BETA1-4 : angle 1.30750 / 0.91 ( 39) link_NAG-ASN : bond 0.00172 / 0.10 ( 8) link_NAG-ASN : angle 1.43334 / 0.96 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.8402 (mmm) cc_final: 0.7706 (mmm) REVERT: B 176 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8610 (p) REVERT: C 40 MET cc_start: 0.8746 (mtt) cc_final: 0.8489 (mtt) REVERT: D 112 MET cc_start: 0.9004 (tpp) cc_final: 0.8774 (tpp) REVERT: D 242 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: D 266 MET cc_start: 0.9404 (mmm) cc_final: 0.9025 (tpp) REVERT: E 55 MET cc_start: 0.8759 (mmm) cc_final: 0.8452 (mmm) outliers start: 17 outliers final: 8 residues processed: 78 average time/residue: 0.0970 time to fit residues: 12.6520 Evaluate side-chains 73 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 62 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.056584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.046934 restraints weight = 66623.476| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.80 r_work: 0.2908 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14561 Z= 0.169 Angle : 0.517 6.263 19851 Z= 0.256 Chirality : 0.042 0.238 2325 Planarity : 0.003 0.062 2385 Dihedral : 7.296 53.117 2533 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.27 % Allowed : 7.66 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.22), residues: 1656 helix: 2.22 (0.21), residues: 590 sheet: 0.39 (0.25), residues: 419 loop : 0.87 (0.27), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 269 TYR 0.026 0.001 TYR B 299 PHE 0.018 0.001 PHE A 304 TRP 0.008 0.001 TRP A 70 HIS 0.005 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (14525) covalent geometry : angle 0.50626 / 0.25 (19748) SS BOND : bond 0.00073 / 0.04 ( 5) SS BOND : angle 0.36383 / 0.22 ( 10) hydrogen bonds : bond 0.02949 / 1.94 ( 564) hydrogen bonds : angle 4.15537 / 2.90 ( 1581) link_ALPHA1-3 : bond 0.00915 / 0.48 ( 5) link_ALPHA1-3 : angle 2.22407 / 1.34 ( 15) link_ALPHA1-6 : bond 0.00854 / 0.49 ( 5) link_ALPHA1-6 : angle 1.83487 / 1.12 ( 15) link_BETA1-4 : bond 0.00383 / 0.22 ( 13) link_BETA1-4 : angle 1.32925 / 0.93 ( 39) link_NAG-ASN : bond 0.00194 / 0.12 ( 8) link_NAG-ASN : angle 1.54281 / 1.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.8390 (mmm) cc_final: 0.7655 (mmm) REVERT: A 266 MET cc_start: 0.8996 (tpp) cc_final: 0.8648 (tpp) REVERT: B 176 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8598 (p) REVERT: C 40 MET cc_start: 0.8725 (mtt) cc_final: 0.8453 (mtt) REVERT: C 115 MET cc_start: 0.8577 (tmm) cc_final: 0.8363 (tmm) REVERT: D 112 MET cc_start: 0.9011 (tpp) cc_final: 0.8773 (tpp) REVERT: D 242 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: D 266 MET cc_start: 0.9425 (mmm) cc_final: 0.9027 (tpp) REVERT: E 55 MET cc_start: 0.8695 (mmm) cc_final: 0.8149 (tpp) REVERT: E 61 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8733 (ppp) REVERT: E 267 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.5514 (p90) outliers start: 19 outliers final: 11 residues processed: 79 average time/residue: 0.0990 time to fit residues: 13.0777 Evaluate side-chains 79 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 122 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 32 optimal weight: 0.0570 chunk 88 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 107 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.057566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.047920 restraints weight = 66106.617| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.80 r_work: 0.2945 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14561 Z= 0.093 Angle : 0.479 6.508 19851 Z= 0.236 Chirality : 0.041 0.238 2325 Planarity : 0.003 0.060 2385 Dihedral : 6.830 49.150 2533 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.00 % Allowed : 7.93 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.22), residues: 1656 helix: 2.34 (0.21), residues: 590 sheet: 0.46 (0.25), residues: 413 loop : 0.96 (0.27), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 269 TYR 0.021 0.001 TYR C 299 PHE 0.013 0.001 PHE A 298 TRP 0.005 0.001 TRP A 317 HIS 0.005 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (14525) covalent geometry : angle 0.46838 / 0.23 (19748) SS BOND : bond 0.00113 / 0.07 ( 5) SS BOND : angle 0.29496 / 0.19 ( 10) hydrogen bonds : bond 0.02749 / 1.80 ( 564) hydrogen bonds : angle 4.02272 / 2.81 ( 1581) link_ALPHA1-3 : bond 0.01004 / 0.53 ( 5) link_ALPHA1-3 : angle 2.04639 / 1.23 ( 15) link_ALPHA1-6 : bond 0.00919 / 0.52 ( 5) link_ALPHA1-6 : angle 1.74390 / 1.06 ( 15) link_BETA1-4 : bond 0.00405 / 0.23 ( 13) link_BETA1-4 : angle 1.27855 / 0.88 ( 39) link_NAG-ASN : bond 0.00184 / 0.10 ( 8) link_NAG-ASN : angle 1.44878 / 0.97 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9010 (ttm) cc_final: 0.8350 (ttm) REVERT: A 114 MET cc_start: 0.9140 (mmm) cc_final: 0.8691 (mmm) REVERT: A 213 MET cc_start: 0.8378 (mmm) cc_final: 0.7679 (mmm) REVERT: A 266 MET cc_start: 0.9055 (tpp) cc_final: 0.8614 (tpp) REVERT: B 176 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 40 MET cc_start: 0.8667 (mtt) cc_final: 0.8410 (mtt) REVERT: C 115 MET cc_start: 0.8555 (tmm) cc_final: 0.8328 (tmm) REVERT: D 112 MET cc_start: 0.8963 (tpp) cc_final: 0.8738 (tpp) REVERT: D 242 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: D 266 MET cc_start: 0.9410 (mmm) cc_final: 0.9031 (tpp) REVERT: E 55 MET cc_start: 0.8748 (mmm) cc_final: 0.8001 (tpp) REVERT: E 61 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8694 (ppp) REVERT: E 267 HIS cc_start: 0.5998 (OUTLIER) cc_final: 0.5420 (p90) outliers start: 15 outliers final: 10 residues processed: 81 average time/residue: 0.0948 time to fit residues: 12.8201 Evaluate side-chains 79 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 24 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 36 optimal weight: 0.0980 chunk 7 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.057067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.047400 restraints weight = 66550.425| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.79 r_work: 0.2928 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14561 Z= 0.128 Angle : 0.496 7.539 19851 Z= 0.242 Chirality : 0.041 0.235 2325 Planarity : 0.003 0.060 2385 Dihedral : 6.615 47.553 2533 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.07 % Allowed : 7.99 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.22), residues: 1656 helix: 2.35 (0.21), residues: 590 sheet: 0.47 (0.26), residues: 391 loop : 0.90 (0.27), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 394 TYR 0.024 0.001 TYR C 299 PHE 0.015 0.001 PHE A 304 TRP 0.006 0.001 TRP A 70 HIS 0.005 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (14525) covalent geometry : angle 0.48604 / 0.24 (19748) SS BOND : bond 0.00070 / 0.04 ( 5) SS BOND : angle 0.34275 / 0.22 ( 10) hydrogen bonds : bond 0.02769 / 1.82 ( 564) hydrogen bonds : angle 4.00940 / 2.80 ( 1581) link_ALPHA1-3 : bond 0.00921 / 0.49 ( 5) link_ALPHA1-3 : angle 2.05636 / 1.24 ( 15) link_ALPHA1-6 : bond 0.00906 / 0.51 ( 5) link_ALPHA1-6 : angle 1.66235 / 1.00 ( 15) link_BETA1-4 : bond 0.00417 / 0.24 ( 13) link_BETA1-4 : angle 1.28736 / 0.88 ( 39) link_NAG-ASN : bond 0.00152 / 0.10 ( 8) link_NAG-ASN : angle 1.51100 / 1.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9028 (ttm) cc_final: 0.8805 (ttm) REVERT: A 112 MET cc_start: 0.8752 (tpp) cc_final: 0.8542 (tpp) REVERT: A 213 MET cc_start: 0.8395 (mmm) cc_final: 0.7684 (mmm) REVERT: A 266 MET cc_start: 0.9112 (tpp) cc_final: 0.8632 (tpp) REVERT: B 176 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8583 (p) REVERT: B 243 ASN cc_start: 0.7915 (m-40) cc_final: 0.7212 (p0) REVERT: C 40 MET cc_start: 0.8701 (mtt) cc_final: 0.8439 (mtt) REVERT: C 115 MET cc_start: 0.8546 (tmm) cc_final: 0.8325 (tmm) REVERT: D 112 MET cc_start: 0.8998 (tpp) cc_final: 0.8761 (tpp) REVERT: D 266 MET cc_start: 0.9430 (mmm) cc_final: 0.9008 (tpp) REVERT: E 55 MET cc_start: 0.8796 (mmm) cc_final: 0.8150 (tpp) REVERT: E 61 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8711 (ppp) REVERT: E 267 HIS cc_start: 0.6041 (OUTLIER) cc_final: 0.5507 (p90) outliers start: 16 outliers final: 11 residues processed: 81 average time/residue: 0.0860 time to fit residues: 11.6507 Evaluate side-chains 82 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 5 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 162 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.057488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.047839 restraints weight = 66595.579| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.81 r_work: 0.2943 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14561 Z= 0.097 Angle : 0.484 8.801 19851 Z= 0.234 Chirality : 0.041 0.224 2325 Planarity : 0.003 0.060 2385 Dihedral : 6.270 50.831 2533 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.87 % Allowed : 8.19 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.22), residues: 1656 helix: 2.42 (0.21), residues: 590 sheet: 0.58 (0.26), residues: 419 loop : 0.97 (0.28), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 221 TYR 0.021 0.001 TYR B 299 PHE 0.013 0.001 PHE A 298 TRP 0.005 0.001 TRP B 237 HIS 0.005 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (14525) covalent geometry : angle 0.47435 / 0.23 (19748) SS BOND : bond 0.00081 / 0.04 ( 5) SS BOND : angle 0.30175 / 0.20 ( 10) hydrogen bonds : bond 0.02675 / 1.76 ( 564) hydrogen bonds : angle 3.93787 / 2.75 ( 1581) link_ALPHA1-3 : bond 0.00941 / 0.50 ( 5) link_ALPHA1-3 : angle 1.92319 / 1.16 ( 15) link_ALPHA1-6 : bond 0.00938 / 0.52 ( 5) link_ALPHA1-6 : angle 1.56240 / 0.92 ( 15) link_BETA1-4 : bond 0.00445 / 0.26 ( 13) link_BETA1-4 : angle 1.24583 / 0.84 ( 39) link_NAG-ASN : bond 0.00187 / 0.11 ( 8) link_NAG-ASN : angle 1.47432 / 0.98 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9015 (ttm) cc_final: 0.8347 (ttm) REVERT: A 112 MET cc_start: 0.8740 (tpp) cc_final: 0.8475 (tpp) REVERT: A 213 MET cc_start: 0.8383 (mmm) cc_final: 0.7714 (mmm) REVERT: A 266 MET cc_start: 0.9120 (tpp) cc_final: 0.8620 (tpp) REVERT: B 243 ASN cc_start: 0.7916 (m-40) cc_final: 0.7209 (p0) REVERT: C 40 MET cc_start: 0.8665 (mtt) cc_final: 0.8406 (mtt) REVERT: C 115 MET cc_start: 0.8546 (tmm) cc_final: 0.8303 (tmm) REVERT: D 112 MET cc_start: 0.8983 (tpp) cc_final: 0.8758 (tpp) REVERT: D 266 MET cc_start: 0.9409 (mmm) cc_final: 0.9025 (tpp) REVERT: E 55 MET cc_start: 0.8809 (mmm) cc_final: 0.8443 (mmm) REVERT: E 61 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8670 (ppp) REVERT: E 267 HIS cc_start: 0.5984 (OUTLIER) cc_final: 0.5377 (p90) outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 0.0937 time to fit residues: 12.7614 Evaluate side-chains 78 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 147 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 216 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.056321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.046654 restraints weight = 66717.708| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.79 r_work: 0.2905 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14561 Z= 0.198 Angle : 0.531 9.227 19851 Z= 0.259 Chirality : 0.042 0.221 2325 Planarity : 0.003 0.059 2385 Dihedral : 6.337 52.640 2532 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.93 % Allowed : 8.26 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.22), residues: 1656 helix: 2.31 (0.21), residues: 590 sheet: 0.48 (0.26), residues: 397 loop : 0.84 (0.27), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 269 TYR 0.027 0.002 TYR B 299 PHE 0.018 0.001 PHE A 304 TRP 0.007 0.001 TRP A 70 HIS 0.005 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (14525) covalent geometry : angle 0.52112 / 0.26 (19748) SS BOND : bond 0.00087 / 0.04 ( 5) SS BOND : angle 0.45057 / 0.28 ( 10) hydrogen bonds : bond 0.02861 / 1.88 ( 564) hydrogen bonds : angle 4.04435 / 2.82 ( 1581) link_ALPHA1-3 : bond 0.00794 / 0.43 ( 5) link_ALPHA1-3 : angle 2.04533 / 1.23 ( 15) link_ALPHA1-6 : bond 0.00875 / 0.49 ( 5) link_ALPHA1-6 : angle 1.55189 / 0.92 ( 15) link_BETA1-4 : bond 0.00434 / 0.26 ( 13) link_BETA1-4 : angle 1.30252 / 0.88 ( 39) link_NAG-ASN : bond 0.00224 / 0.14 ( 8) link_NAG-ASN : angle 1.62763 / 1.07 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2352.19 seconds wall clock time: 41 minutes 40.73 seconds (2500.73 seconds total)