Starting phenix.real_space_refine on Sun Jun 22 22:41:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eiz_28167/06_2025/8eiz_28167_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eiz_28167/06_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_28167/06_2025/8eiz_28167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eiz_28167/06_2025/8eiz_28167.map" model { file = "/net/cci-nas-00/data/ceres_data/8eiz_28167/06_2025/8eiz_28167_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eiz_28167/06_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-5710/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: 13.40, per 1000 atoms: 0.51 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: 7.15 Conformation dependent library (CDL) restraints added in 1.9 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: 1.84 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: 8.77 Time building geometry restraints manager: 8.63 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: 0.820 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: 0.400 Extract box with map and model: 0.850 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 55.080 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.760 ------------------------------------------------------------------------------- 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 : 1.822 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: 0.5595 time to fit residues: 173.6010 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 : 2.253 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.096835 restraints weight = 53151.311| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.48 r_work: 0.3012 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.23 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 : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7845 (t80) cc_final: 0.7525 (t80) REVERT: A 134 ARG cc_start: 0.8028 (ttt180) cc_final: 0.7782 (tpt-90) REVERT: D 146 MET cc_start: 0.8928 (mtt) cc_final: 0.8545 (mtt) REVERT: D 257 LYS cc_start: 0.8665 (mmmt) cc_final: 0.8347 (mmmt) REVERT: E 134 ARG cc_start: 0.8521 (ttt90) cc_final: 0.8271 (ttm-80) outliers start: 10 outliers final: 6 residues processed: 213 average time/residue: 0.5430 time to fit residues: 168.5158 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 : 2.094 ------------------------------------------------------------------------------- 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: 2.9990 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: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.132742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.093689 restraints weight = 52108.685| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.26 r_work: 0.2926 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13635 Z= 0.229 Angle : 0.559 5.729 18500 Z= 0.290 Chirality : 0.044 0.176 2090 Planarity : 0.004 0.052 2230 Dihedral : 6.623 50.208 2075 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.88 % Allowed : 15.44 % Favored : 83.67 % 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: -0.25 (0.21), residues: 1555 helix: 2.03 (0.23), residues: 507 sheet: -0.80 (0.23), residues: 446 loop : -1.56 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 2 HIS 0.002 0.001 HIS C 118 PHE 0.022 0.001 PHE C 271 TYR 0.016 0.001 TYR B 247 ARG 0.006 0.001 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 5) link_NAG-ASN : angle 1.48848 ( 15) link_BETA1-4 : bond 0.00492 ( 10) link_BETA1-4 : angle 2.06859 ( 30) hydrogen bonds : bond 0.04492 ( 438) hydrogen bonds : angle 4.29712 ( 1287) SS BOND : bond 0.00357 ( 10) SS BOND : angle 0.71354 ( 20) covalent geometry : bond 0.00526 (13610) covalent geometry : angle 0.55127 (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 223 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8044 (t80) cc_final: 0.7651 (t80) REVERT: A 134 ARG cc_start: 0.8039 (ttt180) cc_final: 0.7770 (tpt-90) REVERT: A 255 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8522 (mp) REVERT: E 134 ARG cc_start: 0.8630 (ttt90) cc_final: 0.8341 (ttm-80) outliers start: 13 outliers final: 9 residues processed: 218 average time/residue: 0.5470 time to fit residues: 174.8105 Evaluate side-chains 209 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 1.991 ------------------------------------------------------------------------------- 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 94 VAL 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 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: 20.0000 chunk 92 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.133942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.094644 restraints weight = 52445.959| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.33 r_work: 0.2939 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1555 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 : 0.501 5.242 18500 Z= 0.264 Chirality : 0.043 0.169 2090 Planarity : 0.004 0.056 2230 Dihedral : 5.177 33.750 2075 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.22 % Allowed : 15.99 % 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: -0.06 (0.22), residues: 1555 helix: 2.40 (0.23), residues: 503 sheet: -0.81 (0.23), residues: 446 loop : -1.55 (0.24), residues: 606 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 0.013 0.001 TYR D 247 ARG 0.006 0.000 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 5) link_NAG-ASN : angle 1.27971 ( 15) link_BETA1-4 : bond 0.00347 ( 10) link_BETA1-4 : angle 1.85923 ( 30) hydrogen bonds : bond 0.04030 ( 438) hydrogen bonds : angle 3.98233 ( 1287) SS BOND : bond 0.00270 ( 10) SS BOND : angle 0.45464 ( 20) covalent geometry : bond 0.00356 (13610) covalent geometry : angle 0.49492 (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 223 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8092 (t80) cc_final: 0.7459 (t80) REVERT: A 255 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8551 (mp) REVERT: E 134 ARG cc_start: 0.8615 (ttt90) cc_final: 0.8339 (ttt90) outliers start: 18 outliers final: 12 residues processed: 216 average time/residue: 0.5595 time to fit residues: 177.8923 Evaluate side-chains 208 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 1.937 ------------------------------------------------------------------------------- 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 218 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 33 optimal weight: 0.0020 chunk 22 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.135032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.096070 restraints weight = 52167.175| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.35 r_work: 0.2967 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13635 Z= 0.102 Angle : 0.469 5.230 18500 Z= 0.247 Chirality : 0.042 0.180 2090 Planarity : 0.004 0.056 2230 Dihedral : 4.395 18.383 2075 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.22 % Allowed : 15.92 % Favored : 82.86 % 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: -0.82 (0.24), residues: 444 loop : -1.44 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 2 HIS 0.001 0.000 HIS B 269 PHE 0.016 0.001 PHE B 274 TYR 0.014 0.001 TYR D 247 ARG 0.006 0.000 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 5) link_NAG-ASN : angle 1.01550 ( 15) link_BETA1-4 : bond 0.00319 ( 10) link_BETA1-4 : angle 1.49682 ( 30) hydrogen bonds : bond 0.03739 ( 438) hydrogen bonds : angle 3.78774 ( 1287) SS BOND : bond 0.00180 ( 10) SS BOND : angle 0.40276 ( 20) covalent geometry : bond 0.00231 (13610) covalent geometry : angle 0.46492 (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 229 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8093 (t80) cc_final: 0.7699 (t80) REVERT: A 236 PHE cc_start: 0.8829 (t80) cc_final: 0.8563 (t80) REVERT: A 255 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8446 (mp) REVERT: B 52 ARG cc_start: 0.8456 (mtm180) cc_final: 0.8025 (ptp90) REVERT: D 236 PHE cc_start: 0.9336 (t80) cc_final: 0.9017 (t80) REVERT: E 134 ARG cc_start: 0.8606 (ttt90) cc_final: 0.8348 (ttt90) outliers start: 18 outliers final: 11 residues processed: 223 average time/residue: 0.5509 time to fit residues: 179.2502 Evaluate side-chains 210 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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 278 LEU 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 90 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.094189 restraints weight = 52122.381| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.27 r_work: 0.2930 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13635 Z= 0.202 Angle : 0.507 4.612 18500 Z= 0.268 Chirality : 0.042 0.180 2090 Planarity : 0.004 0.055 2230 Dihedral : 4.420 21.354 2075 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.43 % Allowed : 15.85 % 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 (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: 2.59 (0.23), residues: 504 sheet: -0.75 (0.24), residues: 447 loop : -1.53 (0.24), residues: 604 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 0.017 0.001 PHE B 214 TYR 0.012 0.001 TYR D 247 ARG 0.007 0.001 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 5) link_NAG-ASN : angle 1.30131 ( 15) link_BETA1-4 : bond 0.00329 ( 10) link_BETA1-4 : angle 1.54056 ( 30) hydrogen bonds : bond 0.03812 ( 438) hydrogen bonds : angle 3.82274 ( 1287) SS BOND : bond 0.00313 ( 10) SS BOND : angle 0.58366 ( 20) covalent geometry : bond 0.00466 (13610) covalent geometry : angle 0.50207 (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 226 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8150 (t80) cc_final: 0.7516 (t80) REVERT: A 236 PHE cc_start: 0.8812 (t80) cc_final: 0.8534 (t80) REVERT: A 255 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8520 (mp) REVERT: E 134 ARG cc_start: 0.8611 (ttt90) cc_final: 0.8381 (ttt90) outliers start: 21 outliers final: 17 residues processed: 218 average time/residue: 0.5648 time to fit residues: 179.6772 Evaluate side-chains 215 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 1.972 ------------------------------------------------------------------------------- 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 243 SER Chi-restraints excluded: chain B residue 285 ILE 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: 2.9990 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 193 GLN E 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.095692 restraints weight = 51976.837| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.27 r_work: 0.2953 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1993 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= 0.127 Angle : 0.478 4.341 18500 Z= 0.252 Chirality : 0.042 0.175 2090 Planarity : 0.004 0.056 2230 Dihedral : 4.237 19.725 2075 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.43 % Allowed : 16.12 % 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 (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: 0.17 (0.22), residues: 1555 helix: 2.69 (0.23), residues: 504 sheet: -0.75 (0.24), residues: 442 loop : -1.45 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 2 HIS 0.001 0.001 HIS C 118 PHE 0.018 0.001 PHE B 274 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 0.00234 ( 5) link_NAG-ASN : angle 1.01172 ( 15) link_BETA1-4 : bond 0.00297 ( 10) link_BETA1-4 : angle 1.41362 ( 30) hydrogen bonds : bond 0.03656 ( 438) hydrogen bonds : angle 3.70499 ( 1287) SS BOND : bond 0.00208 ( 10) SS BOND : angle 0.39723 ( 20) covalent geometry : bond 0.00293 (13610) covalent geometry : angle 0.47407 (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 227 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8130 (t80) cc_final: 0.7776 (t80) REVERT: A 236 PHE cc_start: 0.8831 (t80) cc_final: 0.8551 (t80) REVERT: A 255 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 52 ARG cc_start: 0.8462 (mtm180) cc_final: 0.8046 (ptp90) REVERT: E 134 ARG cc_start: 0.8615 (ttt90) cc_final: 0.8400 (ttt90) outliers start: 21 outliers final: 17 residues processed: 219 average time/residue: 0.5490 time to fit residues: 176.7309 Evaluate side-chains 216 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 151 ASP Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 279 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 92 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 126 optimal weight: 0.0980 chunk 143 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.133391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.094677 restraints weight = 52030.374| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.26 r_work: 0.2939 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13635 Z= 0.171 Angle : 0.495 4.704 18500 Z= 0.262 Chirality : 0.042 0.182 2090 Planarity : 0.004 0.055 2230 Dihedral : 4.266 20.636 2075 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.29 % Allowed : 16.46 % Favored : 82.24 % 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: -0.74 (0.24), residues: 444 loop : -1.43 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 2 HIS 0.001 0.000 HIS C 118 PHE 0.016 0.001 PHE C 271 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 0.00409 ( 5) link_NAG-ASN : angle 1.14671 ( 15) link_BETA1-4 : bond 0.00327 ( 10) link_BETA1-4 : angle 1.44598 ( 30) hydrogen bonds : bond 0.03660 ( 438) hydrogen bonds : angle 3.73446 ( 1287) SS BOND : bond 0.00270 ( 10) SS BOND : angle 0.49014 ( 20) covalent geometry : bond 0.00396 (13610) covalent geometry : angle 0.49149 (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 221 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 2.224 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: 0.7522 (t80) REVERT: A 255 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8576 (mp) REVERT: B 52 ARG cc_start: 0.8480 (mtm180) cc_final: 0.8064 (ptp90) outliers start: 19 outliers final: 16 residues processed: 215 average time/residue: 0.5934 time to fit residues: 187.3879 Evaluate side-chains 217 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 2.114 ------------------------------------------------------------------------------- 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 151 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 151 ASP 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: 0.9980 chunk 89 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 154 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 7 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.134828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.096286 restraints weight = 51764.092| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.44 r_work: 0.2968 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13635 Z= 0.107 Angle : 0.471 4.989 18500 Z= 0.249 Chirality : 0.042 0.181 2090 Planarity : 0.004 0.059 2230 Dihedral : 4.048 18.075 2075 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: 0.28 (0.22), residues: 1555 helix: 2.71 (0.23), residues: 510 sheet: -0.70 (0.24), residues: 441 loop : -1.36 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 2 HIS 0.002 0.001 HIS B 269 PHE 0.024 0.001 PHE B 274 TYR 0.012 0.001 TYR D 247 ARG 0.009 0.001 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 5) link_NAG-ASN : angle 0.94081 ( 15) link_BETA1-4 : bond 0.00284 ( 10) link_BETA1-4 : angle 1.34062 ( 30) hydrogen bonds : bond 0.03478 ( 438) hydrogen bonds : angle 3.61551 ( 1287) SS BOND : bond 0.00166 ( 10) SS BOND : angle 0.38147 ( 20) covalent geometry : bond 0.00247 (13610) covalent geometry : angle 0.46788 (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 222 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 2.672 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: 0.8166 (t80) cc_final: 0.7504 (t80) REVERT: A 255 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8548 (mp) REVERT: B 52 ARG cc_start: 0.8477 (mtm180) cc_final: 0.8069 (ptp90) REVERT: B 274 PHE cc_start: 0.8833 (t80) cc_final: 0.8525 (t80) outliers start: 17 outliers final: 12 residues processed: 217 average time/residue: 0.6350 time to fit residues: 203.5762 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 : 3.323 ------------------------------------------------------------------------------- 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 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 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 1 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.094918 restraints weight = 51979.569| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.37 r_work: 0.2928 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13635 Z= 0.191 Angle : 0.504 6.961 18500 Z= 0.267 Chirality : 0.042 0.140 2090 Planarity : 0.004 0.055 2230 Dihedral : 4.213 20.718 2075 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.43 % Allowed : 16.46 % 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: 0.26 (0.22), residues: 1555 helix: 2.78 (0.23), residues: 504 sheet: -0.72 (0.24), residues: 447 loop : -1.39 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 2 HIS 0.001 0.000 HIS C 37 PHE 0.020 0.001 PHE B 274 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 0.00445 ( 5) link_NAG-ASN : angle 1.17700 ( 15) link_BETA1-4 : bond 0.00313 ( 10) link_BETA1-4 : angle 1.41950 ( 30) hydrogen bonds : bond 0.03587 ( 438) hydrogen bonds : angle 3.68561 ( 1287) SS BOND : bond 0.00299 ( 10) SS BOND : angle 0.52889 ( 20) covalent geometry : bond 0.00446 (13610) covalent geometry : angle 0.49977 (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 221 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8181 (t80) cc_final: 0.7568 (t80) REVERT: A 255 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8661 (mp) REVERT: B 220 ASN cc_start: 0.8936 (t0) cc_final: 0.8634 (t0) REVERT: B 274 PHE cc_start: 0.8849 (t80) cc_final: 0.8499 (t80) outliers start: 21 outliers final: 17 residues processed: 214 average time/residue: 0.5573 time to fit residues: 173.7863 Evaluate side-chains 217 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 240 VAL 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 151 ASP Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 151 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 114 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.134253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.096016 restraints weight = 51843.555| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.41 r_work: 0.2947 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13635 Z= 0.122 Angle : 0.480 6.841 18500 Z= 0.254 Chirality : 0.042 0.205 2090 Planarity : 0.004 0.060 2230 Dihedral : 4.086 19.138 2075 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.22 % Allowed : 16.73 % 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 (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: 0.34 (0.22), residues: 1555 helix: 2.87 (0.23), residues: 504 sheet: -0.71 (0.24), residues: 447 loop : -1.34 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 2 HIS 0.001 0.001 HIS C 118 PHE 0.020 0.001 PHE B 274 TYR 0.011 0.001 TYR E 9 ARG 0.008 0.001 ARG C 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 5) link_NAG-ASN : angle 1.00067 ( 15) link_BETA1-4 : bond 0.00300 ( 10) link_BETA1-4 : angle 1.34295 ( 30) hydrogen bonds : bond 0.03485 ( 438) hydrogen bonds : angle 3.60024 ( 1287) SS BOND : bond 0.00204 ( 10) SS BOND : angle 0.40781 ( 20) covalent geometry : bond 0.00284 (13610) covalent geometry : angle 0.47633 (18435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13710.38 seconds wall clock time: 236 minutes 19.15 seconds (14179.15 seconds total)