Starting phenix.real_space_refine on Mon Aug 25 08:04:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eiz_28167/08_2025/8eiz_28167_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eiz_28167/08_2025/8eiz_28167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eiz_28167/08_2025/8eiz_28167_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eiz_28167/08_2025/8eiz_28167_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eiz_28167/08_2025/8eiz_28167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eiz_28167/08_2025/8eiz_28167.map" } resolution = 3.13 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= 0.006 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 S 75 5.16 5 C 8770 2.51 5 N 1985 2.21 5 O 2445 1.98 5 H 12825 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 26100 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5155 Classifications: {'peptide': 315} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 304} Chain breaks: 1 Chain: "B" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5155 Classifications: {'peptide': 315} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 304} Chain breaks: 1 Chain: "C" Number of atoms: 5154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5154 Classifications: {'peptide': 315} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 304} Chain breaks: 1 Chain: "D" Number of atoms: 5156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5156 Classifications: {'peptide': 315} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 304} Chain breaks: 1 Chain: "E" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5155 Classifications: {'peptide': 315} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 304} Chain breaks: 1 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WK3': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WK3': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WK3': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WK3': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WK3': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.40, per 1000 atoms: 0.17 Number of scatterers: 26100 At special positions: 0 Unit cell: (95.141, 94.072, 124.004, 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 75 16.00 O 2445 8.00 N 1985 7.00 C 8770 6.00 H 12825 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 181 " distance=2.02 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS D 129 " - pdb=" SG CYS D 143 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 181 " distance=2.02 Simple disulfide: pdb=" SG CYS E 129 " - pdb=" SG CYS E 143 " distance=2.03 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS E 181 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 114 " " NAG G 1 " - " ASN B 114 " " NAG H 1 " - " ASN C 114 " " NAG I 1 " - " ASN D 114 " " NAG J 1 " - " ASN E 114 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 879.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 5 sheets defined 34.1% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 209 through 225 removed outlier: 4.013A pdb=" N LEU A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 Processing helix chain 'A' and resid 263 through 289 Processing helix chain 'A' and resid 368 through 390 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.687A pdb=" N SER B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 222 removed outlier: 4.720A pdb=" N LEU B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 255 removed outlier: 3.710A pdb=" N ASP B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 289 removed outlier: 3.514A pdb=" N LEU B 267 " --> pdb=" O PRO B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 390 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 206 through 223 Proline residue: C 212 - end of helix Processing helix chain 'C' and resid 231 through 253 removed outlier: 3.858A pdb=" N THR C 235 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 289 Processing helix chain 'C' and resid 368 through 389 removed outlier: 3.586A pdb=" N LEU C 377 " --> pdb=" O PHE C 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 209 through 225 removed outlier: 4.523A pdb=" N LEU D 213 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 253 removed outlier: 3.707A pdb=" N THR D 235 " --> pdb=" O GLY D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 289 removed outlier: 3.567A pdb=" N LEU D 267 " --> pdb=" O PRO D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 390 Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 47 through 50 Processing helix chain 'E' and resid 97 through 101 removed outlier: 4.190A pdb=" N MET E 101 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 208 removed outlier: 3.753A pdb=" N SER E 208 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 222 removed outlier: 3.975A pdb=" N LEU E 213 " --> pdb=" O VAL E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 252 removed outlier: 4.210A pdb=" N THR E 235 " --> pdb=" O GLY E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 289 Processing helix chain 'E' and resid 368 through 390 removed outlier: 3.859A pdb=" N SER E 389 " --> pdb=" O LEU E 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 43 removed outlier: 6.882A pdb=" N SER A 33 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR A 64 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN A 56 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N MET A 43 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS A 54 " --> pdb=" O MET A 43 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 52 through 64 current: chain 'A' and resid 116 through 132 removed outlier: 13.474A pdb=" N TYR A 124 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 14.514A pdb=" N TYR A 148 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N ASN A 126 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N MET A 146 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU A 128 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 144 " --> pdb=" O LEU A 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 140 through 149 current: chain 'A' and resid 189 through 199 Processing sheet with id=AA2, first strand: chain 'B' and resid 32 through 43 removed outlier: 7.002A pdb=" N SER B 33 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR B 64 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN B 56 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET B 43 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS B 54 " --> pdb=" O MET B 43 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 52 through 64 current: chain 'B' and resid 116 through 132 removed outlier: 13.445A pdb=" N TYR B 124 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 14.299A pdb=" N TYR B 148 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N ASN B 126 " --> pdb=" O MET B 146 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N MET B 146 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU B 128 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 144 " --> pdb=" O LEU B 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 140 through 149 current: chain 'B' and resid 190 through 200 Processing sheet with id=AA3, first strand: chain 'C' and resid 32 through 43 removed outlier: 6.901A pdb=" N SER C 33 " --> pdb=" O TYR C 64 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR C 64 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN C 56 " --> pdb=" O ALA C 41 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET C 43 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS C 54 " --> pdb=" O MET C 43 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 52 through 64 current: chain 'C' and resid 116 through 132 removed outlier: 13.434A pdb=" N TYR C 124 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 14.164A pdb=" N TYR C 148 " --> pdb=" O TYR C 124 " (cutoff:3.500A) removed outlier: 10.661A pdb=" N ASN C 126 " --> pdb=" O MET C 146 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N MET C 146 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU C 128 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 144 " --> pdb=" O LEU C 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 140 through 149 current: chain 'C' and resid 190 through 199 Processing sheet with id=AA4, first strand: chain 'D' and resid 32 through 43 removed outlier: 6.891A pdb=" N SER D 33 " --> pdb=" O TYR D 64 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR D 64 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS D 37 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN D 56 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET D 43 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS D 54 " --> pdb=" O MET D 43 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 52 through 64 current: chain 'D' and resid 116 through 132 removed outlier: 13.491A pdb=" N TYR D 124 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 14.110A pdb=" N TYR D 148 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 10.984A pdb=" N ASN D 126 " --> pdb=" O MET D 146 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N MET D 146 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU D 128 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU D 144 " --> pdb=" O LEU D 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 140 through 149 current: chain 'D' and resid 190 through 199 Processing sheet with id=AA5, first strand: chain 'E' and resid 32 through 43 removed outlier: 6.827A pdb=" N SER E 33 " --> pdb=" O TYR E 64 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR E 64 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS E 37 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN E 56 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET E 43 " --> pdb=" O LYS E 54 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS E 54 " --> pdb=" O MET E 43 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 52 through 64 current: chain 'E' and resid 116 through 132 removed outlier: 13.549A pdb=" N TYR E 124 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 14.386A pdb=" N TYR E 148 " --> pdb=" O TYR E 124 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N ASN E 126 " --> pdb=" O MET E 146 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N MET E 146 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU E 128 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 144 " --> pdb=" O LEU E 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 140 through 149 current: chain 'E' and resid 189 through 199 438 hydrogen bonds defined for protein. 1287 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: 5.13 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 12805 1.02 - 1.21: 22 1.21 - 1.41: 5737 1.41 - 1.61: 7761 1.61 - 1.81: 110 Bond restraints: 26435 Sorted by residual: bond pdb=" ND2 ASN A 220 " pdb="HD21 ASN A 220 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN A 220 " pdb="HD22 ASN A 220 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" NE ARG C 172 " pdb=" HE ARG C 172 " ideal model delta sigma weight residual 0.860 0.969 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" NZ LYS C 173 " pdb=" HZ2 LYS C 173 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" NZ LYS C 173 " pdb=" HZ1 LYS C 173 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 26430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 46997 1.99 - 3.99: 498 3.99 - 5.98: 56 5.98 - 7.97: 11 7.97 - 9.96: 4 Bond angle restraints: 47566 Sorted by residual: angle pdb=" N SER A 384 " pdb=" CA SER A 384 " pdb=" C SER A 384 " ideal model delta sigma weight residual 111.07 104.78 6.29 1.07e+00 8.73e-01 3.45e+01 angle pdb=" N LYS C 173 " pdb=" CA LYS C 173 " pdb=" C LYS C 173 " ideal model delta sigma weight residual 109.39 118.52 -9.13 1.59e+00 3.96e-01 3.29e+01 angle pdb=" C PHE D 136 " pdb=" N PRO D 137 " pdb=" CD PRO D 137 " ideal model delta sigma weight residual 120.60 110.64 9.96 2.20e+00 2.07e-01 2.05e+01 angle pdb=" C PHE D 136 " pdb=" N PRO D 137 " pdb=" CA PRO D 137 " ideal model delta sigma weight residual 127.00 136.47 -9.47 2.40e+00 1.74e-01 1.56e+01 angle pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" C ARG C 172 " ideal model delta sigma weight residual 111.28 115.29 -4.01 1.09e+00 8.42e-01 1.35e+01 ... (remaining 47561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 11806 21.92 - 43.84: 752 43.84 - 65.76: 183 65.76 - 87.68: 44 87.68 - 109.60: 20 Dihedral angle restraints: 12805 sinusoidal: 6840 harmonic: 5965 Sorted by residual: dihedral pdb=" CB CYS B 164 " pdb=" SG CYS B 164 " pdb=" SG CYS B 181 " pdb=" CB CYS B 181 " ideal model delta sinusoidal sigma weight residual 93.00 136.70 -43.70 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" CB CYS D 164 " pdb=" SG CYS D 164 " pdb=" SG CYS D 181 " pdb=" CB CYS D 181 " ideal model delta sinusoidal sigma weight residual 93.00 135.91 -42.91 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CB CYS E 164 " pdb=" SG CYS E 164 " pdb=" SG CYS E 181 " pdb=" CB CYS E 181 " ideal model delta sinusoidal sigma weight residual 93.00 135.02 -42.02 1 1.00e+01 1.00e-02 2.47e+01 ... (remaining 12802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1659 0.055 - 0.109: 358 0.109 - 0.164: 63 0.164 - 0.218: 5 0.218 - 0.273: 5 Chirality restraints: 2090 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2087 not shown) Planarity restraints: 3746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 220 " -0.188 2.00e-02 2.50e+03 1.88e-01 5.33e+02 pdb=" CG ASN A 220 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 220 " 0.177 2.00e-02 2.50e+03 pdb=" ND2 ASN A 220 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 220 " 0.263 2.00e-02 2.50e+03 pdb="HD22 ASN A 220 " -0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 WK3 A 401 " 0.159 2.00e-02 2.50e+03 2.05e-01 5.24e+02 pdb=" C5 WK3 A 401 " -0.064 2.00e-02 2.50e+03 pdb=" C7 WK3 A 401 " 0.243 2.00e-02 2.50e+03 pdb=" N6 WK3 A 401 " -0.348 2.00e-02 2.50e+03 pdb=" O15 WK3 A 401 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 WK3 B 401 " 0.158 2.00e-02 2.50e+03 1.96e-01 4.79e+02 pdb=" C5 WK3 B 401 " -0.069 2.00e-02 2.50e+03 pdb=" C7 WK3 B 401 " 0.233 2.00e-02 2.50e+03 pdb=" N6 WK3 B 401 " -0.328 2.00e-02 2.50e+03 pdb=" O15 WK3 B 401 " 0.005 2.00e-02 2.50e+03 ... (remaining 3743 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 905 2.14 - 2.75: 48459 2.75 - 3.37: 71383 3.37 - 3.98: 94845 3.98 - 4.60: 147182 Nonbonded interactions: 362774 Sorted by model distance: nonbonded pdb=" O SER A 167 " pdb=" HG1 THR A 168 " model vdw 1.523 2.450 nonbonded pdb=" OD2 ASP C 45 " pdb=" HE1 TRP C 175 " model vdw 1.556 2.450 nonbonded pdb=" HG SER E 167 " pdb=" OD1 ASP E 169 " model vdw 1.581 2.450 nonbonded pdb="HD22 ASN D 47 " pdb=" OE1 GLU D 50 " model vdw 1.625 2.450 nonbonded pdb=" HD2 PHE C 217 " pdb="HD13 ILE C 218 " model vdw 1.642 2.270 ... (remaining 362769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 200 or (resid 201 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 202 through 390 or \ (resid 391 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG or name HD11 \ or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) or resid 392 \ through 401)) selection = (chain 'B' and (resid 1 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3)) or resid 72 through 390 or (resid 391 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name H \ A or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or n \ ame HD21 or name HD22 or name HD23)) or resid 392 through 401)) selection = (chain 'C' and (resid 1 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3)) or resid 72 through 401)) selection = (chain 'D' and (resid 1 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3)) or resid 72 through 200 or (resid 201 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name CE or name NZ \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 202 th \ rough 390 or (resid 391 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG o \ r name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) o \ r resid 392 through 401)) selection = (chain 'E' and (resid 1 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3)) or resid 72 through 390 or (resid 391 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name H \ A or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or n \ ame HD21 or name HD22 or name HD23)) or resid 392 through 401)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.550 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: 0.120 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.880 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.006 0.060 13635 Z= 0.276 Angle : 0.722 9.964 18500 Z= 0.385 Chirality : 0.048 0.273 2090 Planarity : 0.010 0.205 2230 Dihedral : 17.797 109.596 5160 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 14.08 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.51 (0.21), residues: 1555 helix: 1.11 (0.24), residues: 493 sheet: -0.48 (0.24), residues: 469 loop : -1.40 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 52 TYR 0.012 0.002 TYR C 247 PHE 0.030 0.002 PHE E 241 TRP 0.013 0.002 TRP B 2 HIS 0.003 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00597 (13610) covalent geometry : angle 0.71837 (18435) SS BOND : bond 0.00452 ( 10) SS BOND : angle 0.79811 ( 20) hydrogen bonds : bond 0.13213 ( 438) hydrogen bonds : angle 6.33816 ( 1287) link_BETA1-4 : bond 0.00211 ( 10) link_BETA1-4 : angle 1.50429 ( 30) link_NAG-ASN : bond 0.00504 ( 5) link_NAG-ASN : angle 1.68897 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7645 (t80) cc_final: 0.7136 (t80) REVERT: A 213 LEU cc_start: 0.9112 (tp) cc_final: 0.8911 (tt) REVERT: E 134 ARG cc_start: 0.8359 (ttt90) cc_final: 0.8085 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2320 time to fit residues: 72.3992 Evaluate side-chains 198 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 ASN D 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.137577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.096140 restraints weight = 53401.727| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.48 r_work: 0.3004 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13635 Z= 0.198 Angle : 0.595 7.244 18500 Z= 0.304 Chirality : 0.044 0.162 2090 Planarity : 0.005 0.056 2230 Dihedral : 10.500 66.747 2075 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.82 % Allowed : 15.44 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.35 (0.21), residues: 1555 helix: 1.69 (0.23), residues: 507 sheet: -0.64 (0.24), residues: 448 loop : -1.56 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 23 TYR 0.012 0.001 TYR D 247 PHE 0.016 0.001 PHE C 271 TRP 0.010 0.001 TRP B 2 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00451 (13610) covalent geometry : angle 0.58593 (18435) SS BOND : bond 0.00335 ( 10) SS BOND : angle 0.60979 ( 20) hydrogen bonds : bond 0.04977 ( 438) hydrogen bonds : angle 4.62257 ( 1287) link_BETA1-4 : bond 0.00402 ( 10) link_BETA1-4 : angle 2.43954 ( 30) link_NAG-ASN : bond 0.00550 ( 5) link_NAG-ASN : angle 1.54772 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7873 (t80) cc_final: 0.7567 (t80) REVERT: A 134 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7798 (tpt-90) REVERT: A 236 PHE cc_start: 0.8746 (t80) cc_final: 0.8542 (t80) REVERT: D 146 MET cc_start: 0.8936 (mtt) cc_final: 0.8552 (mtt) REVERT: D 257 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8277 (mmmt) REVERT: E 134 ARG cc_start: 0.8525 (ttt90) cc_final: 0.8273 (ttm-80) outliers start: 12 outliers final: 8 residues processed: 212 average time/residue: 0.2079 time to fit residues: 65.0039 Evaluate side-chains 208 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 200 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 112 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095653 restraints weight = 52222.042| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.33 r_work: 0.2962 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13635 Z= 0.129 Angle : 0.516 5.667 18500 Z= 0.266 Chirality : 0.043 0.152 2090 Planarity : 0.004 0.052 2230 Dihedral : 6.651 54.614 2075 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.75 % Allowed : 15.03 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.15 (0.22), residues: 1555 helix: 2.13 (0.23), residues: 509 sheet: -0.86 (0.23), residues: 454 loop : -1.43 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.013 0.001 TYR D 247 PHE 0.020 0.001 PHE C 271 TRP 0.006 0.001 TRP B 2 HIS 0.002 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00293 (13610) covalent geometry : angle 0.50841 (18435) SS BOND : bond 0.00238 ( 10) SS BOND : angle 0.45459 ( 20) hydrogen bonds : bond 0.04337 ( 438) hydrogen bonds : angle 4.18517 ( 1287) link_BETA1-4 : bond 0.00376 ( 10) link_BETA1-4 : angle 2.10521 ( 30) link_NAG-ASN : bond 0.00255 ( 5) link_NAG-ASN : angle 1.31650 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7999 (t80) cc_final: 0.7592 (t80) REVERT: A 134 ARG cc_start: 0.7986 (ttt180) cc_final: 0.7710 (tpt-90) REVERT: A 236 PHE cc_start: 0.8762 (t80) cc_final: 0.8513 (t80) REVERT: A 255 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8384 (mp) REVERT: E 134 ARG cc_start: 0.8565 (ttt90) cc_final: 0.8330 (ttt90) outliers start: 11 outliers final: 8 residues processed: 216 average time/residue: 0.2187 time to fit residues: 69.8917 Evaluate side-chains 207 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.094954 restraints weight = 52020.805| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.33 r_work: 0.2947 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13635 Z= 0.165 Angle : 0.506 5.514 18500 Z= 0.265 Chirality : 0.043 0.161 2090 Planarity : 0.004 0.055 2230 Dihedral : 5.457 44.094 2075 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.22 % Allowed : 14.90 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.04 (0.22), residues: 1555 helix: 2.40 (0.23), residues: 503 sheet: -0.83 (0.23), residues: 449 loop : -1.49 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 134 TYR 0.012 0.001 TYR D 247 PHE 0.019 0.001 PHE C 271 TRP 0.007 0.001 TRP A 2 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00379 (13610) covalent geometry : angle 0.49930 (18435) SS BOND : bond 0.00264 ( 10) SS BOND : angle 0.50651 ( 20) hydrogen bonds : bond 0.04105 ( 438) hydrogen bonds : angle 4.02023 ( 1287) link_BETA1-4 : bond 0.00303 ( 10) link_BETA1-4 : angle 1.96024 ( 30) link_NAG-ASN : bond 0.00412 ( 5) link_NAG-ASN : angle 1.25276 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8056 (t80) cc_final: 0.7642 (t80) REVERT: A 134 ARG cc_start: 0.8031 (ttt180) cc_final: 0.7743 (tpt-90) REVERT: A 236 PHE cc_start: 0.8790 (t80) cc_final: 0.8516 (t80) REVERT: A 255 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8403 (mp) REVERT: E 134 ARG cc_start: 0.8616 (ttt90) cc_final: 0.8409 (ttt90) outliers start: 18 outliers final: 11 residues processed: 214 average time/residue: 0.2269 time to fit residues: 70.9281 Evaluate side-chains 209 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 152 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN D 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.095003 restraints weight = 51977.619| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.31 r_work: 0.2957 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13635 Z= 0.156 Angle : 0.489 5.094 18500 Z= 0.258 Chirality : 0.042 0.185 2090 Planarity : 0.004 0.054 2230 Dihedral : 4.658 26.184 2075 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.22 % Allowed : 16.05 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.02 (0.22), residues: 1555 helix: 2.56 (0.23), residues: 503 sheet: -0.88 (0.23), residues: 457 loop : -1.48 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 134 TYR 0.012 0.001 TYR D 247 PHE 0.027 0.001 PHE A 214 TRP 0.007 0.001 TRP A 2 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00359 (13610) covalent geometry : angle 0.48402 (18435) SS BOND : bond 0.00264 ( 10) SS BOND : angle 0.48615 ( 20) hydrogen bonds : bond 0.03885 ( 438) hydrogen bonds : angle 3.89212 ( 1287) link_BETA1-4 : bond 0.00316 ( 10) link_BETA1-4 : angle 1.59986 ( 30) link_NAG-ASN : bond 0.00375 ( 5) link_NAG-ASN : angle 1.23210 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8077 (t80) cc_final: 0.7670 (t80) REVERT: A 134 ARG cc_start: 0.8059 (ttt180) cc_final: 0.7775 (tpt-90) REVERT: A 236 PHE cc_start: 0.8761 (t80) cc_final: 0.8475 (t80) REVERT: A 255 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8477 (mp) REVERT: E 134 ARG cc_start: 0.8607 (ttt90) cc_final: 0.8338 (ttt90) outliers start: 18 outliers final: 12 residues processed: 215 average time/residue: 0.2233 time to fit residues: 70.6248 Evaluate side-chains 207 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 97 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.093362 restraints weight = 52391.763| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.32 r_work: 0.2918 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13635 Z= 0.227 Angle : 0.523 5.463 18500 Z= 0.277 Chirality : 0.043 0.183 2090 Planarity : 0.004 0.055 2230 Dihedral : 4.568 22.607 2075 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.29 % Allowed : 15.65 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.05 (0.22), residues: 1555 helix: 2.54 (0.23), residues: 504 sheet: -0.73 (0.24), residues: 437 loop : -1.55 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 134 TYR 0.011 0.001 TYR A 8 PHE 0.021 0.001 PHE C 271 TRP 0.008 0.001 TRP A 2 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00525 (13610) covalent geometry : angle 0.51844 (18435) SS BOND : bond 0.00332 ( 10) SS BOND : angle 0.60403 ( 20) hydrogen bonds : bond 0.03890 ( 438) hydrogen bonds : angle 3.92152 ( 1287) link_BETA1-4 : bond 0.00310 ( 10) link_BETA1-4 : angle 1.55852 ( 30) link_NAG-ASN : bond 0.00559 ( 5) link_NAG-ASN : angle 1.36551 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8146 (t80) cc_final: 0.7503 (t80) REVERT: A 236 PHE cc_start: 0.8796 (t80) cc_final: 0.8551 (t80) REVERT: A 255 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8612 (mp) REVERT: E 134 ARG cc_start: 0.8621 (ttt90) cc_final: 0.8395 (ttt90) outliers start: 19 outliers final: 14 residues processed: 213 average time/residue: 0.2065 time to fit residues: 64.7686 Evaluate side-chains 210 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 8 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.133972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.094852 restraints weight = 51853.596| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.32 r_work: 0.2940 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13635 Z= 0.136 Angle : 0.483 4.562 18500 Z= 0.255 Chirality : 0.042 0.185 2090 Planarity : 0.004 0.056 2230 Dihedral : 4.336 20.513 2075 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.29 % Allowed : 16.05 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.12 (0.22), residues: 1555 helix: 2.66 (0.23), residues: 504 sheet: -0.78 (0.24), residues: 445 loop : -1.49 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 134 TYR 0.012 0.001 TYR D 247 PHE 0.021 0.001 PHE B 274 TRP 0.008 0.001 TRP A 2 HIS 0.001 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00314 (13610) covalent geometry : angle 0.47881 (18435) SS BOND : bond 0.00225 ( 10) SS BOND : angle 0.42632 ( 20) hydrogen bonds : bond 0.03726 ( 438) hydrogen bonds : angle 3.76650 ( 1287) link_BETA1-4 : bond 0.00289 ( 10) link_BETA1-4 : angle 1.44172 ( 30) link_NAG-ASN : bond 0.00277 ( 5) link_NAG-ASN : angle 1.06029 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8136 (t80) cc_final: 0.7790 (t80) REVERT: A 236 PHE cc_start: 0.8853 (t80) cc_final: 0.8562 (t80) REVERT: A 255 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8562 (mp) REVERT: B 52 ARG cc_start: 0.8480 (mtm180) cc_final: 0.8072 (ptp90) REVERT: E 134 ARG cc_start: 0.8618 (ttt90) cc_final: 0.8401 (ttt90) outliers start: 19 outliers final: 15 residues processed: 214 average time/residue: 0.2077 time to fit residues: 65.5850 Evaluate side-chains 213 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 81 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 0.0470 chunk 46 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.094955 restraints weight = 51988.215| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.34 r_work: 0.2947 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13635 Z= 0.127 Angle : 0.480 4.862 18500 Z= 0.253 Chirality : 0.042 0.184 2090 Planarity : 0.004 0.055 2230 Dihedral : 4.198 19.392 2075 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.16 % Allowed : 16.39 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.17 (0.22), residues: 1555 helix: 2.71 (0.23), residues: 504 sheet: -0.80 (0.24), residues: 446 loop : -1.42 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 134 TYR 0.012 0.001 TYR D 247 PHE 0.017 0.001 PHE A 214 TRP 0.007 0.001 TRP A 2 HIS 0.001 0.000 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00294 (13610) covalent geometry : angle 0.47626 (18435) SS BOND : bond 0.00216 ( 10) SS BOND : angle 0.42954 ( 20) hydrogen bonds : bond 0.03630 ( 438) hydrogen bonds : angle 3.69656 ( 1287) link_BETA1-4 : bond 0.00285 ( 10) link_BETA1-4 : angle 1.40692 ( 30) link_NAG-ASN : bond 0.00263 ( 5) link_NAG-ASN : angle 1.03985 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8156 (t80) cc_final: 0.7491 (t80) REVERT: A 236 PHE cc_start: 0.8879 (t80) cc_final: 0.8553 (t80) REVERT: A 255 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8548 (mp) REVERT: B 52 ARG cc_start: 0.8471 (mtm180) cc_final: 0.8046 (ptp90) REVERT: E 134 ARG cc_start: 0.8635 (ttt90) cc_final: 0.8426 (ttt90) outliers start: 17 outliers final: 15 residues processed: 215 average time/residue: 0.2253 time to fit residues: 70.6685 Evaluate side-chains 215 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 146 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.133813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.095024 restraints weight = 51941.100| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.26 r_work: 0.2947 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13635 Z= 0.151 Angle : 0.489 4.838 18500 Z= 0.259 Chirality : 0.042 0.184 2090 Planarity : 0.004 0.055 2230 Dihedral : 4.191 19.888 2075 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.22 % Allowed : 16.46 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.20 (0.22), residues: 1555 helix: 2.73 (0.23), residues: 504 sheet: -0.78 (0.24), residues: 440 loop : -1.41 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 134 TYR 0.013 0.001 TYR C 75 PHE 0.016 0.001 PHE C 214 TRP 0.006 0.001 TRP A 2 HIS 0.001 0.000 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00348 (13610) covalent geometry : angle 0.48515 (18435) SS BOND : bond 0.00250 ( 10) SS BOND : angle 0.47193 ( 20) hydrogen bonds : bond 0.03608 ( 438) hydrogen bonds : angle 3.67982 ( 1287) link_BETA1-4 : bond 0.00293 ( 10) link_BETA1-4 : angle 1.39133 ( 30) link_NAG-ASN : bond 0.00328 ( 5) link_NAG-ASN : angle 1.07093 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8142 (t80) cc_final: 0.7489 (t80) REVERT: A 255 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8620 (mp) REVERT: B 52 ARG cc_start: 0.8485 (mtm180) cc_final: 0.8119 (ptp90) outliers start: 18 outliers final: 15 residues processed: 212 average time/residue: 0.2270 time to fit residues: 70.0932 Evaluate side-chains 212 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 22 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.134232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.095290 restraints weight = 51760.934| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.31 r_work: 0.2948 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13635 Z= 0.134 Angle : 0.483 4.847 18500 Z= 0.256 Chirality : 0.042 0.165 2090 Planarity : 0.005 0.073 2230 Dihedral : 4.135 19.341 2075 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.09 % Allowed : 16.73 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.26 (0.22), residues: 1555 helix: 2.79 (0.23), residues: 504 sheet: -0.75 (0.24), residues: 440 loop : -1.38 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 134 TYR 0.026 0.001 TYR C 75 PHE 0.037 0.001 PHE A 236 TRP 0.007 0.001 TRP A 2 HIS 0.001 0.000 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00309 (13610) covalent geometry : angle 0.47931 (18435) SS BOND : bond 0.00221 ( 10) SS BOND : angle 0.42678 ( 20) hydrogen bonds : bond 0.03566 ( 438) hydrogen bonds : angle 3.62925 ( 1287) link_BETA1-4 : bond 0.00284 ( 10) link_BETA1-4 : angle 1.36575 ( 30) link_NAG-ASN : bond 0.00268 ( 5) link_NAG-ASN : angle 1.01708 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8178 (t80) cc_final: 0.7542 (t80) REVERT: A 255 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8601 (mp) REVERT: B 52 ARG cc_start: 0.8479 (mtm180) cc_final: 0.8059 (ptp90) REVERT: B 274 PHE cc_start: 0.8893 (t80) cc_final: 0.8630 (t80) REVERT: E 134 ARG cc_start: 0.8525 (ttt90) cc_final: 0.8262 (ttt90) outliers start: 16 outliers final: 14 residues processed: 212 average time/residue: 0.2320 time to fit residues: 72.0400 Evaluate side-chains 213 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 268 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 152 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.134706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.095497 restraints weight = 51720.481| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.33 r_work: 0.2959 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13635 Z= 0.114 Angle : 0.472 5.000 18500 Z= 0.250 Chirality : 0.042 0.188 2090 Planarity : 0.004 0.059 2230 Dihedral : 4.009 17.960 2075 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.16 % Allowed : 16.80 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.36 (0.22), residues: 1555 helix: 2.88 (0.23), residues: 504 sheet: -0.73 (0.25), residues: 439 loop : -1.30 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 134 TYR 0.020 0.001 TYR C 75 PHE 0.021 0.001 PHE B 214 TRP 0.007 0.001 TRP A 2 HIS 0.001 0.000 HIS E 269 Details of bonding type rmsd covalent geometry : bond 0.00263 (13610) covalent geometry : angle 0.46921 (18435) SS BOND : bond 0.00186 ( 10) SS BOND : angle 0.40870 ( 20) hydrogen bonds : bond 0.03461 ( 438) hydrogen bonds : angle 3.56243 ( 1287) link_BETA1-4 : bond 0.00297 ( 10) link_BETA1-4 : angle 1.34076 ( 30) link_NAG-ASN : bond 0.00187 ( 5) link_NAG-ASN : angle 0.95457 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5680.18 seconds wall clock time: 96 minutes 59.87 seconds (5819.87 seconds total)