Starting phenix.real_space_refine on Sun May 25 05:50:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eiz_28167/05_2025/8eiz_28167_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eiz_28167/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8eiz_28167/05_2025/8eiz_28167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eiz_28167/05_2025/8eiz_28167.map" model { file = "/net/cci-nas-00/data/ceres_data/8eiz_28167/05_2025/8eiz_28167_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eiz_28167/05_2025/8eiz_28167_trim.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.73, per 1000 atoms: 0.49 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: 6.69 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.63 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: 7.88 Time building geometry restraints manager: 7.85 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 \ or resid 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 or resid 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 392 or resid 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 or resid 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 or resid 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: 1.330 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: 0.420 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 50.190 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.100 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.310 ------------------------------------------------------------------------------- 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 : 8.74 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.21), 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 TRP 0.013 0.002 TRP B 2 HIS 0.003 0.001 HIS C 118 PHE 0.030 0.002 PHE E 241 TYR 0.012 0.002 TYR C 247 ARG 0.009 0.001 ARG C 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 5) link_NAG-ASN : angle 1.68897 ( 15) link_BETA1-4 : bond 0.00211 ( 10) link_BETA1-4 : angle 1.50429 ( 30) hydrogen bonds : bond 0.13213 ( 438) hydrogen bonds : angle 6.33816 ( 1287) SS BOND : bond 0.00452 ( 10) SS BOND : angle 0.79811 ( 20) covalent geometry : bond 0.00597 (13610) covalent geometry : angle 0.71837 (18435) *********************** 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 : 1.936 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: 0.8084 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.5535 time to fit residues: 171.8476 Evaluate side-chains 200 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.138246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.096836 restraints weight = 53151.311| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.48 r_work: 0.3013 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0867 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= 0.164 Angle : 0.582 7.132 18500 Z= 0.295 Chirality : 0.044 0.158 2090 Planarity : 0.004 0.057 2230 Dihedral : 10.286 65.054 2075 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.68 % Allowed : 15.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1555 helix: 1.73 (0.23), residues: 509 sheet: -0.69 (0.24), residues: 456 loop : -1.50 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 2 HIS 0.002 0.001 HIS C 118 PHE 0.015 0.001 PHE C 271 TYR 0.013 0.001 TYR D 247 ARG 0.005 0.001 ARG B 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 5) link_NAG-ASN : angle 1.45867 ( 15) link_BETA1-4 : bond 0.00433 ( 10) link_BETA1-4 : angle 2.49977 ( 30) hydrogen bonds : bond 0.04951 ( 438) hydrogen bonds : angle 4.55930 ( 1287) SS BOND : bond 0.00286 ( 10) SS BOND : angle 0.52554 ( 20) covalent geometry : bond 0.00372 (13610) covalent geometry : angle 0.57240 (18435) *********************** 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 220 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7841 (t80) cc_final: 0.7520 (t80) REVERT: A 134 ARG cc_start: 0.8028 (ttt180) cc_final: 0.7781 (tpt-90) REVERT: D 146 MET cc_start: 0.8928 (mtt) cc_final: 0.8545 (mtt) REVERT: D 257 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8346 (mmmt) REVERT: E 134 ARG cc_start: 0.8514 (ttt90) cc_final: 0.8264 (ttm-80) outliers start: 10 outliers final: 6 residues processed: 213 average time/residue: 0.5460 time to fit residues: 170.4553 Evaluate side-chains 210 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 204 time to evaluate : 1.982 ------------------------------------------------------------------------------- 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 E residue 215 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 86 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN D 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.094981 restraints weight = 52013.236| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.26 r_work: 0.2951 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13635 Z= 0.182 Angle : 0.539 6.029 18500 Z= 0.278 Chirality : 0.044 0.158 2090 Planarity : 0.004 0.053 2230 Dihedral : 7.211 55.746 2075 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.82 % Allowed : 15.65 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1555 helix: 2.02 (0.23), residues: 509 sheet: -0.80 (0.23), residues: 449 loop : -1.51 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 2 HIS 0.002 0.001 HIS C 118 PHE 0.019 0.001 PHE C 271 TYR 0.013 0.001 TYR B 247 ARG 0.005 0.000 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 5) link_NAG-ASN : angle 1.39734 ( 15) link_BETA1-4 : bond 0.00404 ( 10) link_BETA1-4 : angle 2.17154 ( 30) hydrogen bonds : bond 0.04457 ( 438) hydrogen bonds : angle 4.29841 ( 1287) SS BOND : bond 0.00307 ( 10) SS BOND : angle 0.57566 ( 20) covalent geometry : bond 0.00418 (13610) covalent geometry : angle 0.53094 (18435) *********************** 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 221 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8006 (t80) cc_final: 0.7605 (t80) REVERT: A 134 ARG cc_start: 0.8006 (ttt180) cc_final: 0.7731 (tpt-90) REVERT: A 255 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8444 (mp) REVERT: E 134 ARG cc_start: 0.8574 (ttt90) cc_final: 0.8342 (ttt90) outliers start: 12 outliers final: 9 residues processed: 217 average time/residue: 0.5343 time to fit residues: 169.5942 Evaluate side-chains 210 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 200 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 278 LEU 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 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 60 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.133142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.093885 restraints weight = 52514.848| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.32 r_work: 0.2927 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13635 Z= 0.204 Angle : 0.527 5.401 18500 Z= 0.278 Chirality : 0.043 0.163 2090 Planarity : 0.004 0.055 2230 Dihedral : 5.472 39.396 2075 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.22 % Allowed : 15.31 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1555 helix: 2.31 (0.23), residues: 503 sheet: -0.80 (0.23), residues: 447 loop : -1.58 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 2 HIS 0.002 0.001 HIS E 269 PHE 0.011 0.001 PHE C 271 TYR 0.012 0.001 TYR D 247 ARG 0.005 0.000 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 5) link_NAG-ASN : angle 1.40004 ( 15) link_BETA1-4 : bond 0.00333 ( 10) link_BETA1-4 : angle 1.96771 ( 30) hydrogen bonds : bond 0.04131 ( 438) hydrogen bonds : angle 4.08116 ( 1287) SS BOND : bond 0.00317 ( 10) SS BOND : angle 0.58954 ( 20) covalent geometry : bond 0.00468 (13610) covalent geometry : angle 0.51984 (18435) *********************** 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 227 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8076 (t80) cc_final: 0.7469 (t80) REVERT: A 255 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8535 (mp) REVERT: D 257 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8346 (mmmt) REVERT: E 134 ARG cc_start: 0.8618 (ttt90) cc_final: 0.8323 (ttm-80) outliers start: 18 outliers final: 12 residues processed: 220 average time/residue: 0.5356 time to fit residues: 172.1276 Evaluate side-chains 211 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP 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 218 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 33 optimal weight: 0.0770 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 77 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.135159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.096021 restraints weight = 52107.728| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.34 r_work: 0.2978 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13635 Z= 0.099 Angle : 0.476 5.290 18500 Z= 0.250 Chirality : 0.042 0.200 2090 Planarity : 0.004 0.056 2230 Dihedral : 4.598 25.612 2075 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.02 % Allowed : 15.99 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1555 helix: 2.54 (0.23), residues: 503 sheet: -0.81 (0.24), residues: 444 loop : -1.45 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 2 HIS 0.002 0.001 HIS E 118 PHE 0.014 0.001 PHE B 274 TYR 0.013 0.001 TYR D 247 ARG 0.006 0.000 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 5) link_NAG-ASN : angle 1.01853 ( 15) link_BETA1-4 : bond 0.00322 ( 10) link_BETA1-4 : angle 1.57463 ( 30) hydrogen bonds : bond 0.03808 ( 438) hydrogen bonds : angle 3.82777 ( 1287) SS BOND : bond 0.00159 ( 10) SS BOND : angle 0.36088 ( 20) covalent geometry : bond 0.00223 (13610) covalent geometry : angle 0.47115 (18435) *********************** 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 230 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8076 (t80) cc_final: 0.7669 (t80) REVERT: A 172 ARG cc_start: 0.8017 (ttp-110) cc_final: 0.7705 (ptm-80) REVERT: A 255 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8469 (mp) REVERT: B 52 ARG cc_start: 0.8442 (mtm180) cc_final: 0.8023 (ptp90) REVERT: C 222 MET cc_start: 0.8135 (mmt) cc_final: 0.7893 (mmt) REVERT: D 236 PHE cc_start: 0.9328 (t80) cc_final: 0.9002 (t80) REVERT: E 134 ARG cc_start: 0.8602 (ttt90) cc_final: 0.8334 (ttt90) outliers start: 15 outliers final: 9 residues processed: 224 average time/residue: 0.5484 time to fit residues: 178.8046 Evaluate side-chains 211 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 1.926 ------------------------------------------------------------------------------- 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 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 272 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 90 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** D 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.092865 restraints weight = 52330.523| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.27 r_work: 0.2911 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13635 Z= 0.266 Angle : 0.540 5.152 18500 Z= 0.287 Chirality : 0.044 0.183 2090 Planarity : 0.004 0.055 2230 Dihedral : 4.674 23.338 2075 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.29 % Allowed : 15.92 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1555 helix: 2.48 (0.23), residues: 502 sheet: -0.78 (0.24), residues: 447 loop : -1.56 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 2 HIS 0.002 0.001 HIS C 118 PHE 0.014 0.001 PHE C 271 TYR 0.012 0.001 TYR A 8 ARG 0.006 0.001 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 5) link_NAG-ASN : angle 1.43120 ( 15) link_BETA1-4 : bond 0.00347 ( 10) link_BETA1-4 : angle 1.64328 ( 30) hydrogen bonds : bond 0.03965 ( 438) hydrogen bonds : angle 3.97226 ( 1287) SS BOND : bond 0.00365 ( 10) SS BOND : angle 0.71983 ( 20) covalent geometry : bond 0.00615 (13610) covalent geometry : angle 0.53429 (18435) *********************** 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 222 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8171 (t80) cc_final: 0.7541 (t80) REVERT: A 255 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8621 (mp) REVERT: E 134 ARG cc_start: 0.8615 (ttt90) cc_final: 0.8383 (ttt90) outliers start: 19 outliers final: 15 residues processed: 215 average time/residue: 0.5432 time to fit residues: 170.6428 Evaluate side-chains 214 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 2.087 ------------------------------------------------------------------------------- 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 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 94 VAL 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 50 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 126 optimal weight: 0.0070 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.095009 restraints weight = 52047.198| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.34 r_work: 0.2944 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1902 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= 0.115 Angle : 0.487 6.275 18500 Z= 0.258 Chirality : 0.042 0.183 2090 Planarity : 0.004 0.056 2230 Dihedral : 4.344 20.288 2075 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.09 % Allowed : 16.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1555 helix: 2.59 (0.23), residues: 504 sheet: -0.74 (0.24), residues: 434 loop : -1.48 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 2 HIS 0.002 0.001 HIS E 118 PHE 0.022 0.001 PHE B 214 TYR 0.014 0.001 TYR E 9 ARG 0.008 0.000 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 5) link_NAG-ASN : angle 0.98439 ( 15) link_BETA1-4 : bond 0.00273 ( 10) link_BETA1-4 : angle 1.43341 ( 30) hydrogen bonds : bond 0.03728 ( 438) hydrogen bonds : angle 3.78281 ( 1287) SS BOND : bond 0.00194 ( 10) SS BOND : angle 0.39089 ( 20) covalent geometry : bond 0.00261 (13610) covalent geometry : angle 0.48382 (18435) *********************** 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: 16 poor density : 206 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8169 (t80) cc_final: 0.7808 (t80) REVERT: A 255 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8546 (mp) REVERT: B 52 ARG cc_start: 0.8473 (mtm180) cc_final: 0.8062 (ptp90) REVERT: E 134 ARG cc_start: 0.8610 (ttt90) cc_final: 0.8392 (ttt90) outliers start: 16 outliers final: 14 residues processed: 216 average time/residue: 0.6296 time to fit residues: 201.7741 Evaluate side-chains 215 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 220 ASN 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 94 VAL 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 92 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.133590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.094712 restraints weight = 52034.394| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.31 r_work: 0.2943 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13635 Z= 0.160 Angle : 0.499 5.342 18500 Z= 0.264 Chirality : 0.042 0.185 2090 Planarity : 0.004 0.055 2230 Dihedral : 4.304 20.471 2075 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.29 % Allowed : 16.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1555 helix: 2.57 (0.23), residues: 504 sheet: -0.81 (0.24), residues: 440 loop : -1.44 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 2 HIS 0.002 0.000 HIS C 118 PHE 0.016 0.001 PHE C 271 TYR 0.012 0.001 TYR D 247 ARG 0.008 0.000 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 5) link_NAG-ASN : angle 1.12408 ( 15) link_BETA1-4 : bond 0.00301 ( 10) link_BETA1-4 : angle 1.44995 ( 30) hydrogen bonds : bond 0.03752 ( 438) hydrogen bonds : angle 3.82001 ( 1287) SS BOND : bond 0.00255 ( 10) SS BOND : angle 0.48134 ( 20) covalent geometry : bond 0.00368 (13610) covalent geometry : angle 0.49564 (18435) *********************** 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: 19 poor density : 204 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8161 (t80) cc_final: 0.7510 (t80) REVERT: A 255 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8571 (mp) REVERT: B 52 ARG cc_start: 0.8476 (mtm180) cc_final: 0.8061 (ptp90) REVERT: E 134 ARG cc_start: 0.8606 (ttt90) cc_final: 0.8404 (ttt90) outliers start: 19 outliers final: 15 residues processed: 216 average time/residue: 0.5656 time to fit residues: 180.5850 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 : 2.108 ------------------------------------------------------------------------------- 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 45 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 151 ASP 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 94 VAL 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 86 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 154 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.095548 restraints weight = 51794.575| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.32 r_work: 0.2953 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13635 Z= 0.120 Angle : 0.480 5.210 18500 Z= 0.255 Chirality : 0.042 0.186 2090 Planarity : 0.004 0.057 2230 Dihedral : 4.136 18.825 2075 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.16 % Allowed : 16.46 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1555 helix: 2.67 (0.23), residues: 504 sheet: -0.78 (0.24), residues: 437 loop : -1.38 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 2 HIS 0.002 0.000 HIS B 269 PHE 0.032 0.001 PHE B 214 TYR 0.012 0.001 TYR E 9 ARG 0.009 0.001 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 5) link_NAG-ASN : angle 0.98835 ( 15) link_BETA1-4 : bond 0.00301 ( 10) link_BETA1-4 : angle 1.39194 ( 30) hydrogen bonds : bond 0.03588 ( 438) hydrogen bonds : angle 3.70519 ( 1287) SS BOND : bond 0.00200 ( 10) SS BOND : angle 0.42173 ( 20) covalent geometry : bond 0.00276 (13610) covalent geometry : angle 0.47672 (18435) *********************** 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 223 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8161 (t80) cc_final: 0.7811 (t80) REVERT: A 255 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8551 (mp) REVERT: B 52 ARG cc_start: 0.8472 (mtm180) cc_final: 0.8054 (ptp90) REVERT: B 274 PHE cc_start: 0.8838 (t80) cc_final: 0.8527 (t80) REVERT: E 134 ARG cc_start: 0.8609 (ttt90) cc_final: 0.8146 (ttt90) outliers start: 17 outliers final: 13 residues processed: 218 average time/residue: 0.5493 time to fit residues: 174.3834 Evaluate side-chains 214 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 151 ASP 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 94 VAL 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 1 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.133907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.095205 restraints weight = 51827.671| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.27 r_work: 0.2950 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13635 Z= 0.145 Angle : 0.489 5.031 18500 Z= 0.259 Chirality : 0.042 0.157 2090 Planarity : 0.004 0.057 2230 Dihedral : 4.139 19.428 2075 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.16 % Allowed : 16.73 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1555 helix: 2.73 (0.23), residues: 504 sheet: -0.74 (0.24), residues: 442 loop : -1.35 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 2 HIS 0.001 0.000 HIS C 118 PHE 0.022 0.001 PHE A 236 TYR 0.018 0.001 TYR C 75 ARG 0.008 0.000 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 5) link_NAG-ASN : angle 1.07742 ( 15) link_BETA1-4 : bond 0.00286 ( 10) link_BETA1-4 : angle 1.38533 ( 30) hydrogen bonds : bond 0.03593 ( 438) hydrogen bonds : angle 3.69023 ( 1287) SS BOND : bond 0.00248 ( 10) SS BOND : angle 0.47441 ( 20) covalent geometry : bond 0.00338 (13610) covalent geometry : angle 0.48564 (18435) ********************** 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 219 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8179 (t80) cc_final: 0.7533 (t80) REVERT: A 255 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8583 (mp) REVERT: B 52 ARG cc_start: 0.8467 (mtm180) cc_final: 0.8059 (ptp90) REVERT: B 220 ASN cc_start: 0.8650 (t0) cc_final: 0.8436 (t0) REVERT: B 274 PHE cc_start: 0.8837 (t80) cc_final: 0.8512 (t80) REVERT: E 134 ARG cc_start: 0.8613 (ttt90) cc_final: 0.8162 (ttt90) outliers start: 17 outliers final: 13 residues processed: 215 average time/residue: 0.5487 time to fit residues: 171.4470 Evaluate side-chains 213 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE 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 151 ASP 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 94 VAL 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 114 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 2 optimal weight: 0.0970 chunk 129 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.095970 restraints weight = 51792.209| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.26 r_work: 0.2963 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13635 Z= 0.117 Angle : 0.475 4.960 18500 Z= 0.252 Chirality : 0.042 0.182 2090 Planarity : 0.004 0.059 2230 Dihedral : 4.030 18.252 2075 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.16 % Allowed : 17.07 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1555 helix: 2.82 (0.23), residues: 504 sheet: -0.76 (0.24), residues: 439 loop : -1.30 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 2 HIS 0.001 0.000 HIS B 269 PHE 0.021 0.001 PHE A 236 TYR 0.023 0.001 TYR C 75 ARG 0.009 0.001 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 5) link_NAG-ASN : angle 0.96569 ( 15) link_BETA1-4 : bond 0.00292 ( 10) link_BETA1-4 : angle 1.34098 ( 30) hydrogen bonds : bond 0.03516 ( 438) hydrogen bonds : angle 3.63175 ( 1287) SS BOND : bond 0.00192 ( 10) SS BOND : angle 0.40671 ( 20) covalent geometry : bond 0.00270 (13610) covalent geometry : angle 0.47168 (18435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12936.18 seconds wall clock time: 222 minutes 9.13 seconds (13329.13 seconds total)