Starting phenix.real_space_refine on Tue Jun 24 15:11:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s50_19717/06_2025/8s50_19717_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s50_19717/06_2025/8s50_19717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s50_19717/06_2025/8s50_19717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s50_19717/06_2025/8s50_19717.map" model { file = "/net/cci-nas-00/data/ceres_data/8s50_19717/06_2025/8s50_19717_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s50_19717/06_2025/8s50_19717_trim.cif" } resolution = 3.33 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= 0.002 sd= 0.102 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 80 5.16 5 C 9136 2.51 5 N 2520 2.21 5 O 2902 1.98 5 H 14016 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28654 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "A" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "C" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "D" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "F" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "G" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "J" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "K" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Time building chain proxies: 25.19, per 1000 atoms: 0.88 Number of scatterers: 28654 At special positions: 0 Unit cell: (98.6112, 98.6112, 139.162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 O 2902 8.00 N 2520 7.00 C 9136 6.00 H 14016 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS A 318 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS A 317 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS D 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS D 317 " distance=2.03 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 357 " distance=2.03 Simple disulfide: pdb=" SG CYS D 210 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 357 " distance=2.03 Simple disulfide: pdb=" SG CYS F 210 " - pdb=" SG CYS F 271 " distance=2.03 Simple disulfide: pdb=" SG CYS F 317 " - pdb=" SG CYS G 318 " distance=2.03 Simple disulfide: pdb=" SG CYS F 318 " - pdb=" SG CYS G 317 " distance=2.03 Simple disulfide: pdb=" SG CYS G 179 " - pdb=" SG CYS G 357 " distance=2.03 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 179 " - pdb=" SG CYS J 357 " distance=2.03 Simple disulfide: pdb=" SG CYS J 210 " - pdb=" SG CYS J 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 317 " - pdb=" SG CYS K 318 " distance=2.03 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS K 317 " distance=2.03 Simple disulfide: pdb=" SG CYS K 179 " - pdb=" SG CYS K 357 " distance=2.03 Simple disulfide: pdb=" SG CYS K 210 " - pdb=" SG CYS K 271 " distance=2.04 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 NAG-ASN " NAG A 401 " - " ASN A 220 " " NAG B 401 " - " ASN B 220 " " NAG C 401 " - " ASN C 220 " " NAG D 401 " - " ASN D 220 " " NAG F 401 " - " ASN F 220 " " NAG G 401 " - " ASN G 220 " " NAG J 401 " - " ASN J 220 " " NAG K 401 " - " ASN K 220 " Time building additional restraints: 7.13 Conformation dependent library (CDL) restraints added in 3.8 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 16 sheets defined 13.5% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'B' and resid 151 through 173 removed outlier: 3.924A pdb=" N GLN B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 173 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.723A pdb=" N GLY B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 173 removed outlier: 3.616A pdb=" N GLN A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 173 " --> pdb=" O TRP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.765A pdb=" N GLY A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 173 removed outlier: 3.618A pdb=" N GLN C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TRP C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER C 173 " --> pdb=" O TRP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.726A pdb=" N GLY C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 173 removed outlier: 3.560A pdb=" N GLN D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TRP D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.763A pdb=" N GLY D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 173 removed outlier: 3.619A pdb=" N GLN F 158 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA F 165 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY F 168 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TRP F 169 " --> pdb=" O ALA F 165 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER F 173 " --> pdb=" O TRP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 352 removed outlier: 3.731A pdb=" N GLY F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 173 removed outlier: 3.563A pdb=" N GLN G 158 " --> pdb=" O GLU G 154 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA G 165 " --> pdb=" O ALA G 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL G 166 " --> pdb=" O ASP G 162 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY G 168 " --> pdb=" O HIS G 164 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP G 169 " --> pdb=" O ALA G 165 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER G 173 " --> pdb=" O TRP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 352 removed outlier: 3.772A pdb=" N GLY G 352 " --> pdb=" O ILE G 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 173 removed outlier: 3.533A pdb=" N GLN J 158 " --> pdb=" O GLU J 154 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA J 165 " --> pdb=" O ALA J 161 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL J 166 " --> pdb=" O ASP J 162 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY J 168 " --> pdb=" O HIS J 164 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TRP J 169 " --> pdb=" O ALA J 165 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER J 173 " --> pdb=" O TRP J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 352 removed outlier: 3.731A pdb=" N GLY J 352 " --> pdb=" O ILE J 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 173 removed outlier: 3.718A pdb=" N GLN K 158 " --> pdb=" O GLU K 154 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA K 165 " --> pdb=" O ALA K 161 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL K 166 " --> pdb=" O ASP K 162 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY K 168 " --> pdb=" O HIS K 164 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TRP K 169 " --> pdb=" O ALA K 165 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER K 173 " --> pdb=" O TRP K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 344 through 352 removed outlier: 3.758A pdb=" N GLY K 352 " --> pdb=" O ILE K 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 288 through 293 removed outlier: 6.660A pdb=" N LEU B 283 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 292 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 281 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 280 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 275 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER B 208 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE B 338 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS B 210 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B 336 " --> pdb=" O CYS B 210 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N SER B 330 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 255 through 258 removed outlier: 6.633A pdb=" N LEU B 240 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE B 223 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 308 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU B 370 " --> pdb=" O HIS B 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 293 removed outlier: 6.495A pdb=" N LEU A 283 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR A 292 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A 281 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 280 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A 275 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER A 208 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE A 338 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N CYS A 210 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE A 336 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N SER A 330 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 255 through 258 removed outlier: 6.608A pdb=" N LEU A 240 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A 223 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU A 308 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU A 370 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 288 through 293 removed outlier: 6.661A pdb=" N LEU C 283 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR C 292 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR C 281 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 280 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN C 275 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER C 208 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE C 338 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS C 210 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C 336 " --> pdb=" O CYS C 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 255 through 258 removed outlier: 6.630A pdb=" N LEU C 240 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE C 223 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU C 308 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU C 370 " --> pdb=" O HIS C 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 288 through 293 removed outlier: 6.497A pdb=" N LEU D 283 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR D 292 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR D 281 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER D 208 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE D 338 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS D 210 " --> pdb=" O PHE D 336 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE D 336 " --> pdb=" O CYS D 210 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N SER D 330 " --> pdb=" O THR D 216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 255 through 258 removed outlier: 6.608A pdb=" N LEU D 240 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE D 223 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU D 308 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU D 370 " --> pdb=" O HIS D 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 288 through 293 removed outlier: 6.670A pdb=" N LEU F 283 " --> pdb=" O ALA F 290 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR F 292 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR F 281 " --> pdb=" O THR F 292 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 280 " --> pdb=" O ASN F 275 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN F 275 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER F 208 " --> pdb=" O ILE F 338 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE F 338 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS F 210 " --> pdb=" O PHE F 336 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE F 336 " --> pdb=" O CYS F 210 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N SER F 330 " --> pdb=" O THR F 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 255 through 258 removed outlier: 6.625A pdb=" N LEU F 240 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE F 223 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU F 308 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU F 370 " --> pdb=" O HIS F 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 288 through 293 removed outlier: 6.508A pdb=" N LEU G 283 " --> pdb=" O ALA G 290 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR G 292 " --> pdb=" O THR G 281 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR G 281 " --> pdb=" O THR G 292 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 280 " --> pdb=" O ASN G 275 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN G 275 " --> pdb=" O LEU G 280 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER G 208 " --> pdb=" O ILE G 338 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE G 338 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS G 210 " --> pdb=" O PHE G 336 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE G 336 " --> pdb=" O CYS G 210 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N SER G 330 " --> pdb=" O THR G 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 255 through 258 removed outlier: 6.597A pdb=" N LEU G 240 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE G 223 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU G 308 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU G 370 " --> pdb=" O HIS G 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 288 through 293 removed outlier: 6.657A pdb=" N LEU J 283 " --> pdb=" O ALA J 290 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR J 292 " --> pdb=" O THR J 281 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR J 281 " --> pdb=" O THR J 292 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU J 280 " --> pdb=" O ASN J 275 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN J 275 " --> pdb=" O LEU J 280 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER J 208 " --> pdb=" O ILE J 338 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE J 338 " --> pdb=" O SER J 208 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N CYS J 210 " --> pdb=" O PHE J 336 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE J 336 " --> pdb=" O CYS J 210 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N SER J 330 " --> pdb=" O THR J 216 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 255 through 258 removed outlier: 6.622A pdb=" N LEU J 240 " --> pdb=" O ILE J 223 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE J 223 " --> pdb=" O LEU J 240 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU J 308 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU J 370 " --> pdb=" O HIS J 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 288 through 293 removed outlier: 6.496A pdb=" N LEU K 283 " --> pdb=" O ALA K 290 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR K 292 " --> pdb=" O THR K 281 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR K 281 " --> pdb=" O THR K 292 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU K 280 " --> pdb=" O ASN K 275 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN K 275 " --> pdb=" O LEU K 280 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER K 208 " --> pdb=" O ILE K 338 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE K 338 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N CYS K 210 " --> pdb=" O PHE K 336 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE K 336 " --> pdb=" O CYS K 210 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N SER K 330 " --> pdb=" O THR K 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 255 through 258 removed outlier: 6.607A pdb=" N LEU K 240 " --> pdb=" O ILE K 223 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE K 223 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU K 308 " --> pdb=" O VAL K 196 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU K 370 " --> pdb=" O HIS K 197 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1399 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: 10.65 Time building geometry restraints manager: 8.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 14016 1.04 - 1.24: 1556 1.24 - 1.44: 4928 1.44 - 1.64: 8172 1.64 - 1.83: 112 Bond restraints: 28784 Sorted by residual: bond pdb=" C1 NAG J 401 " pdb=" O5 NAG J 401 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.06e+00 bond pdb=" C1 NAG G 401 " pdb=" O5 NAG G 401 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 NAG D 401 " pdb=" O5 NAG D 401 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 ... (remaining 28779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 50543 1.35 - 2.70: 1192 2.70 - 4.05: 102 4.05 - 5.40: 3 5.40 - 6.75: 8 Bond angle restraints: 51848 Sorted by residual: angle pdb=" N GLY A 320 " pdb=" CA GLY A 320 " pdb=" C GLY A 320 " ideal model delta sigma weight residual 115.08 111.24 3.84 1.64e+00 3.72e-01 5.48e+00 angle pdb=" N GLY K 320 " pdb=" CA GLY K 320 " pdb=" C GLY K 320 " ideal model delta sigma weight residual 115.08 111.25 3.83 1.64e+00 3.72e-01 5.46e+00 angle pdb=" N GLY G 320 " pdb=" CA GLY G 320 " pdb=" C GLY G 320 " ideal model delta sigma weight residual 115.08 111.35 3.73 1.64e+00 3.72e-01 5.18e+00 angle pdb=" N GLY D 320 " pdb=" CA GLY D 320 " pdb=" C GLY D 320 " ideal model delta sigma weight residual 115.08 111.38 3.70 1.64e+00 3.72e-01 5.10e+00 angle pdb=" CG ASN K 220 " pdb=" ND2 ASN K 220 " pdb="HD21 ASN K 220 " ideal model delta sigma weight residual 120.00 126.75 -6.75 3.00e+00 1.11e-01 5.06e+00 ... (remaining 51843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 12030 16.87 - 33.75: 1195 33.75 - 50.62: 289 50.62 - 67.50: 102 67.50 - 84.37: 32 Dihedral angle restraints: 13648 sinusoidal: 7432 harmonic: 6216 Sorted by residual: dihedral pdb=" CB CYS C 318 " pdb=" SG CYS C 318 " pdb=" SG CYS D 317 " pdb=" CB CYS D 317 " ideal model delta sinusoidal sigma weight residual -86.00 -170.37 84.37 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS F 318 " pdb=" SG CYS F 318 " pdb=" SG CYS G 317 " pdb=" CB CYS G 317 " ideal model delta sinusoidal sigma weight residual -86.00 -170.21 84.21 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" CB CYS B 318 " pdb=" SG CYS B 318 " pdb=" SG CYS A 317 " pdb=" CB CYS A 317 " ideal model delta sinusoidal sigma weight residual -86.00 -170.14 84.14 1 1.00e+01 1.00e-02 8.62e+01 ... (remaining 13645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1323 0.031 - 0.061: 596 0.061 - 0.092: 118 0.092 - 0.122: 143 0.122 - 0.153: 52 Chirality restraints: 2232 Sorted by residual: chirality pdb=" C1 NAG G 401 " pdb=" ND2 ASN G 220 " pdb=" C2 NAG G 401 " pdb=" O5 NAG G 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" C1 NAG D 401 " pdb=" ND2 ASN D 220 " pdb=" C2 NAG D 401 " pdb=" O5 NAG D 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 220 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 2229 not shown) Planarity restraints: 4376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 232 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO G 233 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 233 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 233 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN K 232 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO K 233 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO K 233 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 233 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 232 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO A 233 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " -0.021 5.00e-02 4.00e+02 ... (remaining 4373 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2080 2.20 - 2.80: 59625 2.80 - 3.40: 78529 3.40 - 4.00: 111282 4.00 - 4.60: 169309 Nonbonded interactions: 420825 Sorted by model distance: nonbonded pdb=" O ILE K 371 " pdb=" HH TYR K 379 " model vdw 1.599 2.450 nonbonded pdb=" OE1 GLU D 370 " pdb=" HG SER G 189 " model vdw 1.624 2.450 nonbonded pdb=" OE1 GLU G 370 " pdb=" HG SER K 189 " model vdw 1.624 2.450 nonbonded pdb=" O ILE D 371 " pdb=" HH TYR D 379 " model vdw 1.634 2.450 nonbonded pdb=" O ILE G 371 " pdb=" HH TYR G 379 " model vdw 1.635 2.450 ... (remaining 420820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'B' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'C' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'D' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'F' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'G' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'J' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'K' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 3.720 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: 0.520 Extract box with map and model: 1.010 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 73.680 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.130 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14800 Z= 0.148 Angle : 0.583 13.528 20144 Z= 0.298 Chirality : 0.046 0.153 2232 Planarity : 0.003 0.038 2568 Dihedral : 13.595 74.861 5376 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.25 (0.19), residues: 1848 helix: 0.57 (0.36), residues: 208 sheet: -0.14 (0.23), residues: 520 loop : -1.50 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 212 HIS 0.002 0.001 HIS G 374 PHE 0.008 0.001 PHE J 225 TYR 0.012 0.001 TYR K 239 ARG 0.002 0.000 ARG J 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00826 ( 8) link_NAG-ASN : angle 7.79180 ( 24) hydrogen bonds : bond 0.12145 ( 534) hydrogen bonds : angle 6.29245 ( 1399) SS BOND : bond 0.00144 ( 24) SS BOND : angle 1.38361 ( 48) covalent geometry : bond 0.00312 (14768) covalent geometry : angle 0.51396 (20072) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 2.038 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: C 162 ASP cc_start: 0.7272 (t0) cc_final: 0.7049 (t70) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.5288 time to fit residues: 136.2345 Evaluate side-chains 139 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN A 254 ASN C 237 GLN D 254 ASN F 237 GLN G 254 ASN K 254 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.146472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114472 restraints weight = 119262.730| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.83 r_work: 0.3179 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14800 Z= 0.149 Angle : 0.523 4.881 20144 Z= 0.278 Chirality : 0.045 0.142 2232 Planarity : 0.003 0.035 2568 Dihedral : 4.958 22.533 2192 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.53 % Allowed : 4.79 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.19), residues: 1848 helix: 0.81 (0.37), residues: 208 sheet: -0.58 (0.22), residues: 576 loop : -1.50 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 212 HIS 0.002 0.001 HIS B 358 PHE 0.014 0.001 PHE J 225 TYR 0.013 0.002 TYR J 239 ARG 0.002 0.000 ARG B 157 Details of bonding type rmsd link_NAG-ASN : bond 0.00012 ( 8) link_NAG-ASN : angle 2.52557 ( 24) hydrogen bonds : bond 0.03372 ( 534) hydrogen bonds : angle 5.44633 ( 1399) SS BOND : bond 0.00159 ( 24) SS BOND : angle 1.34622 ( 48) covalent geometry : bond 0.00345 (14768) covalent geometry : angle 0.51232 (20072) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8082 (t60) cc_final: 0.7661 (t60) REVERT: A 169 TRP cc_start: 0.8092 (t60) cc_final: 0.7674 (t60) REVERT: C 162 ASP cc_start: 0.7518 (t0) cc_final: 0.7253 (t70) REVERT: G 169 TRP cc_start: 0.8057 (t60) cc_final: 0.7752 (t60) REVERT: J 169 TRP cc_start: 0.8157 (t60) cc_final: 0.7742 (t60) REVERT: K 169 TRP cc_start: 0.8086 (t60) cc_final: 0.7657 (t60) outliers start: 8 outliers final: 1 residues processed: 145 average time/residue: 0.5542 time to fit residues: 123.4217 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 288 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 96 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 148 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115350 restraints weight = 112965.930| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.72 r_work: 0.3202 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14800 Z= 0.128 Angle : 0.497 4.237 20144 Z= 0.267 Chirality : 0.044 0.144 2232 Planarity : 0.003 0.035 2568 Dihedral : 4.766 20.180 2192 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.07 % Allowed : 6.85 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.55 (0.19), residues: 1848 helix: -0.05 (0.33), residues: 256 sheet: -0.60 (0.22), residues: 576 loop : -1.55 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.002 0.001 HIS G 374 PHE 0.014 0.001 PHE F 225 TYR 0.012 0.001 TYR A 227 ARG 0.001 0.000 ARG A 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 8) link_NAG-ASN : angle 2.10239 ( 24) hydrogen bonds : bond 0.03096 ( 534) hydrogen bonds : angle 5.27057 ( 1399) SS BOND : bond 0.00644 ( 24) SS BOND : angle 1.60899 ( 48) covalent geometry : bond 0.00291 (14768) covalent geometry : angle 0.48611 (20072) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8214 (t60) cc_final: 0.7788 (t60) REVERT: B 210 CYS cc_start: 0.7693 (m) cc_final: 0.7362 (m) REVERT: B 227 TYR cc_start: 0.8912 (t80) cc_final: 0.8706 (t80) REVERT: A 227 TYR cc_start: 0.8778 (t80) cc_final: 0.8543 (t80) REVERT: C 162 ASP cc_start: 0.7598 (t0) cc_final: 0.7312 (t70) REVERT: C 169 TRP cc_start: 0.8320 (t60) cc_final: 0.7811 (t60) REVERT: C 210 CYS cc_start: 0.7680 (m) cc_final: 0.7358 (m) REVERT: F 210 CYS cc_start: 0.7687 (m) cc_final: 0.7360 (m) REVERT: F 227 TYR cc_start: 0.8910 (t80) cc_final: 0.8709 (t80) REVERT: J 169 TRP cc_start: 0.8362 (t60) cc_final: 0.7918 (t60) REVERT: J 210 CYS cc_start: 0.7675 (m) cc_final: 0.7348 (m) REVERT: K 169 TRP cc_start: 0.8260 (t60) cc_final: 0.7900 (t60) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.5699 time to fit residues: 117.7759 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 164 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 142 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.146422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114759 restraints weight = 120262.811| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.78 r_work: 0.3123 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14800 Z= 0.131 Angle : 0.486 5.225 20144 Z= 0.261 Chirality : 0.044 0.141 2232 Planarity : 0.003 0.032 2568 Dihedral : 4.699 19.197 2192 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.13 % Allowed : 7.85 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.51 (0.19), residues: 1848 helix: 0.01 (0.33), residues: 256 sheet: -0.61 (0.22), residues: 576 loop : -1.51 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 169 HIS 0.003 0.001 HIS A 269 PHE 0.013 0.001 PHE B 225 TYR 0.014 0.002 TYR C 227 ARG 0.002 0.000 ARG D 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00010 ( 8) link_NAG-ASN : angle 1.97287 ( 24) hydrogen bonds : bond 0.02936 ( 534) hydrogen bonds : angle 5.13371 ( 1399) SS BOND : bond 0.00480 ( 24) SS BOND : angle 1.52636 ( 48) covalent geometry : bond 0.00301 (14768) covalent geometry : angle 0.47638 (20072) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8317 (t60) cc_final: 0.7815 (t60) REVERT: B 210 CYS cc_start: 0.7806 (m) cc_final: 0.7448 (m) REVERT: C 162 ASP cc_start: 0.7612 (t0) cc_final: 0.7367 (t70) REVERT: C 169 TRP cc_start: 0.8320 (t60) cc_final: 0.7830 (t60) REVERT: C 210 CYS cc_start: 0.7793 (m) cc_final: 0.7436 (m) REVERT: F 169 TRP cc_start: 0.8319 (t60) cc_final: 0.7734 (t60) REVERT: F 210 CYS cc_start: 0.7794 (m) cc_final: 0.7434 (m) REVERT: G 169 TRP cc_start: 0.8380 (t60) cc_final: 0.7853 (t60) REVERT: J 169 TRP cc_start: 0.8375 (t60) cc_final: 0.7933 (t60) REVERT: J 210 CYS cc_start: 0.7808 (m) cc_final: 0.7453 (m) REVERT: K 169 TRP cc_start: 0.8234 (t60) cc_final: 0.7935 (t60) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 0.6595 time to fit residues: 139.2378 Evaluate side-chains 124 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 164 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.144870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112657 restraints weight = 118692.181| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.90 r_work: 0.3199 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14800 Z= 0.155 Angle : 0.497 4.268 20144 Z= 0.267 Chirality : 0.044 0.144 2232 Planarity : 0.003 0.033 2568 Dihedral : 4.763 19.493 2192 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 0.13 % Allowed : 8.31 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.55 (0.19), residues: 1848 helix: 0.00 (0.33), residues: 256 sheet: -0.66 (0.22), residues: 576 loop : -1.53 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 169 HIS 0.003 0.001 HIS D 269 PHE 0.013 0.001 PHE F 225 TYR 0.016 0.002 TYR F 227 ARG 0.001 0.000 ARG A 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00009 ( 8) link_NAG-ASN : angle 1.96664 ( 24) hydrogen bonds : bond 0.02970 ( 534) hydrogen bonds : angle 5.13394 ( 1399) SS BOND : bond 0.00378 ( 24) SS BOND : angle 1.47769 ( 48) covalent geometry : bond 0.00355 (14768) covalent geometry : angle 0.48798 (20072) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8225 (t60) cc_final: 0.7920 (t60) REVERT: B 210 CYS cc_start: 0.7242 (m) cc_final: 0.6854 (m) REVERT: C 210 CYS cc_start: 0.7234 (m) cc_final: 0.6847 (m) REVERT: F 169 TRP cc_start: 0.8229 (t60) cc_final: 0.7738 (t60) REVERT: F 210 CYS cc_start: 0.7257 (m) cc_final: 0.6866 (m) REVERT: G 169 TRP cc_start: 0.8179 (t60) cc_final: 0.7816 (t60) REVERT: J 169 TRP cc_start: 0.8298 (t60) cc_final: 0.7940 (t60) REVERT: J 210 CYS cc_start: 0.7257 (m) cc_final: 0.6869 (m) REVERT: K 169 TRP cc_start: 0.8234 (t60) cc_final: 0.7919 (t60) outliers start: 2 outliers final: 2 residues processed: 131 average time/residue: 0.7159 time to fit residues: 144.2607 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain D residue 288 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 2 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN C 315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112798 restraints weight = 113066.131| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.70 r_work: 0.3185 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14800 Z= 0.156 Angle : 0.496 4.256 20144 Z= 0.267 Chirality : 0.044 0.143 2232 Planarity : 0.003 0.034 2568 Dihedral : 4.781 19.927 2192 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.66 % Allowed : 7.78 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.58 (0.19), residues: 1848 helix: 0.00 (0.33), residues: 256 sheet: -0.67 (0.21), residues: 576 loop : -1.57 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 169 HIS 0.003 0.001 HIS A 269 PHE 0.013 0.001 PHE B 225 TYR 0.013 0.002 TYR J 239 ARG 0.001 0.000 ARG D 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00009 ( 8) link_NAG-ASN : angle 1.90626 ( 24) hydrogen bonds : bond 0.02945 ( 534) hydrogen bonds : angle 5.10980 ( 1399) SS BOND : bond 0.00351 ( 24) SS BOND : angle 1.43660 ( 48) covalent geometry : bond 0.00359 (14768) covalent geometry : angle 0.48780 (20072) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8347 (t60) cc_final: 0.8002 (t60) REVERT: J 169 TRP cc_start: 0.8424 (t60) cc_final: 0.8031 (t60) REVERT: K 169 TRP cc_start: 0.8324 (t60) cc_final: 0.8103 (t60) outliers start: 10 outliers final: 9 residues processed: 132 average time/residue: 0.5506 time to fit residues: 110.5721 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain J residue 288 GLU Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114796 restraints weight = 105419.255| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.59 r_work: 0.3201 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14800 Z= 0.120 Angle : 0.484 4.220 20144 Z= 0.259 Chirality : 0.044 0.141 2232 Planarity : 0.003 0.033 2568 Dihedral : 4.683 19.070 2192 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.27 % Allowed : 8.05 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.51 (0.19), residues: 1848 helix: 0.07 (0.33), residues: 256 sheet: -0.70 (0.20), residues: 648 loop : -1.49 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 169 HIS 0.002 0.001 HIS A 269 PHE 0.013 0.001 PHE B 225 TYR 0.011 0.002 TYR B 239 ARG 0.001 0.000 ARG D 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 8) link_NAG-ASN : angle 1.75348 ( 24) hydrogen bonds : bond 0.02811 ( 534) hydrogen bonds : angle 5.01900 ( 1399) SS BOND : bond 0.00299 ( 24) SS BOND : angle 1.29885 ( 48) covalent geometry : bond 0.00274 (14768) covalent geometry : angle 0.47651 (20072) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8325 (t60) cc_final: 0.7915 (t60) REVERT: A 169 TRP cc_start: 0.8335 (t60) cc_final: 0.7885 (t60) REVERT: J 169 TRP cc_start: 0.8403 (t60) cc_final: 0.8033 (t60) REVERT: K 169 TRP cc_start: 0.8314 (t60) cc_final: 0.8059 (t60) outliers start: 4 outliers final: 3 residues processed: 129 average time/residue: 0.5605 time to fit residues: 113.3212 Evaluate side-chains 123 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 152 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 125 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113798 restraints weight = 115714.384| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.76 r_work: 0.3231 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14800 Z= 0.134 Angle : 0.485 4.750 20144 Z= 0.260 Chirality : 0.044 0.140 2232 Planarity : 0.003 0.036 2568 Dihedral : 4.687 19.077 2192 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.60 % Allowed : 7.71 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.51 (0.19), residues: 1848 helix: 0.12 (0.33), residues: 256 sheet: -0.72 (0.20), residues: 648 loop : -1.49 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.002 0.001 HIS C 358 PHE 0.013 0.001 PHE B 225 TYR 0.012 0.002 TYR B 239 ARG 0.001 0.000 ARG K 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 8) link_NAG-ASN : angle 1.77360 ( 24) hydrogen bonds : bond 0.02814 ( 534) hydrogen bonds : angle 4.99762 ( 1399) SS BOND : bond 0.00293 ( 24) SS BOND : angle 1.31475 ( 48) covalent geometry : bond 0.00309 (14768) covalent geometry : angle 0.47765 (20072) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8105 (t60) cc_final: 0.7839 (t60) REVERT: A 169 TRP cc_start: 0.8188 (t60) cc_final: 0.7806 (t60) REVERT: F 169 TRP cc_start: 0.8142 (t60) cc_final: 0.7842 (t60) REVERT: J 169 TRP cc_start: 0.8256 (t60) cc_final: 0.7933 (t60) REVERT: K 169 TRP cc_start: 0.8164 (t60) cc_final: 0.7929 (t60) outliers start: 9 outliers final: 9 residues processed: 132 average time/residue: 0.5416 time to fit residues: 111.2547 Evaluate side-chains 128 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain J residue 288 GLU Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 101 optimal weight: 0.0970 chunk 84 optimal weight: 0.3980 chunk 92 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113321 restraints weight = 108387.141| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.81 r_work: 0.3140 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14800 Z= 0.103 Angle : 0.473 4.371 20144 Z= 0.253 Chirality : 0.044 0.136 2232 Planarity : 0.003 0.033 2568 Dihedral : 4.585 18.097 2192 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.27 % Allowed : 8.11 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.19), residues: 1848 helix: 0.14 (0.33), residues: 256 sheet: -0.68 (0.20), residues: 648 loop : -1.41 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.002 0.001 HIS A 269 PHE 0.012 0.001 PHE F 225 TYR 0.010 0.002 TYR B 239 ARG 0.001 0.000 ARG D 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 8) link_NAG-ASN : angle 1.63976 ( 24) hydrogen bonds : bond 0.02686 ( 534) hydrogen bonds : angle 4.91643 ( 1399) SS BOND : bond 0.00258 ( 24) SS BOND : angle 1.19802 ( 48) covalent geometry : bond 0.00234 (14768) covalent geometry : angle 0.46676 (20072) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8239 (t60) cc_final: 0.7911 (t60) REVERT: B 315 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7597 (t0) REVERT: A 169 TRP cc_start: 0.8348 (t60) cc_final: 0.7851 (t60) REVERT: F 169 TRP cc_start: 0.8290 (t60) cc_final: 0.7898 (t60) REVERT: G 169 TRP cc_start: 0.8324 (t60) cc_final: 0.7900 (t60) REVERT: J 169 TRP cc_start: 0.8391 (t60) cc_final: 0.7982 (t60) REVERT: K 169 TRP cc_start: 0.8324 (t60) cc_final: 0.7940 (t60) outliers start: 4 outliers final: 3 residues processed: 127 average time/residue: 0.5352 time to fit residues: 106.3765 Evaluate side-chains 124 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain G residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 57 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.145676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112486 restraints weight = 121936.345| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.98 r_work: 0.3194 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 14800 Z= 0.163 Angle : 0.707 59.194 20144 Z= 0.421 Chirality : 0.044 0.218 2232 Planarity : 0.003 0.033 2568 Dihedral : 4.579 18.077 2192 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.20 % Allowed : 8.44 % Favored : 91.36 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.19), residues: 1848 helix: 0.14 (0.33), residues: 256 sheet: -0.68 (0.20), residues: 648 loop : -1.41 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.002 0.001 HIS G 374 PHE 0.012 0.001 PHE F 225 TYR 0.011 0.002 TYR B 239 ARG 0.001 0.000 ARG B 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 8) link_NAG-ASN : angle 1.62117 ( 24) hydrogen bonds : bond 0.02704 ( 534) hydrogen bonds : angle 4.91520 ( 1399) SS BOND : bond 0.00255 ( 24) SS BOND : angle 1.21474 ( 48) covalent geometry : bond 0.00353 (14768) covalent geometry : angle 0.70334 (20072) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8105 (t60) cc_final: 0.7813 (t60) REVERT: A 169 TRP cc_start: 0.8206 (t60) cc_final: 0.7766 (t60) REVERT: F 169 TRP cc_start: 0.8161 (t60) cc_final: 0.7821 (t60) REVERT: G 169 TRP cc_start: 0.8187 (t60) cc_final: 0.7811 (t60) REVERT: J 169 TRP cc_start: 0.8263 (t60) cc_final: 0.7898 (t60) REVERT: K 169 TRP cc_start: 0.8186 (t60) cc_final: 0.7865 (t60) outliers start: 3 outliers final: 3 residues processed: 127 average time/residue: 0.5717 time to fit residues: 112.9611 Evaluate side-chains 125 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain G residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 134 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 34 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.145674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113109 restraints weight = 112668.962| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.86 r_work: 0.3144 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 14800 Z= 0.163 Angle : 0.707 59.200 20144 Z= 0.421 Chirality : 0.044 0.217 2232 Planarity : 0.003 0.033 2568 Dihedral : 4.579 18.077 2192 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.20 % Allowed : 8.44 % Favored : 91.36 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.19), residues: 1848 helix: 0.14 (0.33), residues: 256 sheet: -0.68 (0.20), residues: 648 loop : -1.41 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.002 0.001 HIS G 374 PHE 0.012 0.001 PHE F 225 TYR 0.011 0.002 TYR B 239 ARG 0.001 0.000 ARG B 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 8) link_NAG-ASN : angle 1.62118 ( 24) hydrogen bonds : bond 0.02704 ( 534) hydrogen bonds : angle 4.91520 ( 1399) SS BOND : bond 0.00255 ( 24) SS BOND : angle 1.21474 ( 48) covalent geometry : bond 0.00353 (14768) covalent geometry : angle 0.70334 (20072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14451.78 seconds wall clock time: 248 minutes 30.96 seconds (14910.96 seconds total)