Starting phenix.real_space_refine on Mon Aug 25 14:02:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s50_19717/08_2025/8s50_19717_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s50_19717/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8s50_19717/08_2025/8s50_19717_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s50_19717/08_2025/8s50_19717_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s50_19717/08_2025/8s50_19717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s50_19717/08_2025/8s50_19717.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.44, per 1000 atoms: 0.26 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: 2.24 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.52 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: 6.21 Time building geometry restraints manager: 3.23 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 401)) selection = (chain 'B' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 401)) selection = (chain 'C' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 401)) selection = (chain 'D' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 401)) selection = (chain 'F' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 401)) selection = (chain 'G' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 401)) selection = (chain 'J' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 401)) selection = (chain 'K' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 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: 3.930 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: 0.150 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 27.810 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- 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 : 10.33 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.000 ARG J 203 TYR 0.012 0.001 TYR K 239 PHE 0.008 0.001 PHE J 225 TRP 0.008 0.001 TRP G 212 HIS 0.002 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00312 (14768) covalent geometry : angle 0.51396 (20072) SS BOND : bond 0.00144 ( 24) SS BOND : angle 1.38361 ( 48) hydrogen bonds : bond 0.12145 ( 534) hydrogen bonds : angle 6.29245 ( 1399) link_NAG-ASN : bond 0.00826 ( 8) link_NAG-ASN : angle 7.79180 ( 24) *********************** 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 : 0.758 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: 0.2188 time to fit residues: 56.5313 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 : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 J 237 GLN K 254 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.146457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115016 restraints weight = 106605.242| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.68 r_work: 0.3235 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14800 Z= 0.153 Angle : 0.524 4.855 20144 Z= 0.279 Chirality : 0.045 0.144 2232 Planarity : 0.003 0.035 2568 Dihedral : 4.964 22.900 2192 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.53 % Allowed : 4.59 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.19), residues: 1848 helix: 0.79 (0.37), residues: 208 sheet: -0.57 (0.22), residues: 576 loop : -1.51 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 157 TYR 0.013 0.002 TYR J 239 PHE 0.014 0.001 PHE J 225 TRP 0.007 0.001 TRP B 212 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00352 (14768) covalent geometry : angle 0.51339 (20072) SS BOND : bond 0.00157 ( 24) SS BOND : angle 1.34665 ( 48) hydrogen bonds : bond 0.03489 ( 534) hydrogen bonds : angle 5.47927 ( 1399) link_NAG-ASN : bond 0.00064 ( 8) link_NAG-ASN : angle 2.58986 ( 24) *********************** 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 144 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8231 (t60) cc_final: 0.7767 (t60) REVERT: C 162 ASP cc_start: 0.7594 (t0) cc_final: 0.7297 (t70) REVERT: G 158 GLN cc_start: 0.8200 (mp10) cc_final: 0.7999 (mp10) REVERT: G 169 TRP cc_start: 0.8223 (t60) cc_final: 0.7895 (t60) REVERT: K 169 TRP cc_start: 0.8231 (t60) cc_final: 0.7751 (t60) outliers start: 8 outliers final: 0 residues processed: 144 average time/residue: 0.2233 time to fit residues: 49.3259 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 : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.146416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114371 restraints weight = 118262.792| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.84 r_work: 0.3138 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14800 Z= 0.141 Angle : 0.503 4.299 20144 Z= 0.270 Chirality : 0.044 0.145 2232 Planarity : 0.003 0.034 2568 Dihedral : 4.815 20.599 2192 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.19), residues: 1848 helix: -0.06 (0.33), residues: 256 sheet: -0.62 (0.22), residues: 576 loop : -1.59 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 332 TYR 0.012 0.001 TYR F 239 PHE 0.014 0.001 PHE F 225 TRP 0.012 0.001 TRP C 169 HIS 0.002 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00320 (14768) covalent geometry : angle 0.49162 (20072) SS BOND : bond 0.00675 ( 24) SS BOND : angle 1.67595 ( 48) hydrogen bonds : bond 0.03135 ( 534) hydrogen bonds : angle 5.31713 ( 1399) link_NAG-ASN : bond 0.00053 ( 8) link_NAG-ASN : angle 2.17059 ( 24) *********************** 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 137 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.709 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: B 169 TRP cc_start: 0.8114 (t60) cc_final: 0.7700 (t60) REVERT: B 210 CYS cc_start: 0.7172 (m) cc_final: 0.6853 (m) REVERT: B 227 TYR cc_start: 0.8833 (t80) cc_final: 0.8618 (t80) REVERT: A 169 TRP cc_start: 0.8151 (t60) cc_final: 0.7694 (t60) REVERT: C 162 ASP cc_start: 0.7574 (t0) cc_final: 0.7318 (t70) REVERT: C 169 TRP cc_start: 0.8200 (t60) cc_final: 0.7696 (t60) REVERT: C 210 CYS cc_start: 0.7161 (m) cc_final: 0.6849 (m) REVERT: C 227 TYR cc_start: 0.8820 (t80) cc_final: 0.8612 (t80) REVERT: D 169 TRP cc_start: 0.8130 (t60) cc_final: 0.7666 (t60) REVERT: F 210 CYS cc_start: 0.7192 (m) cc_final: 0.6873 (m) REVERT: F 227 TYR cc_start: 0.8826 (t80) cc_final: 0.8616 (t80) REVERT: G 169 TRP cc_start: 0.8108 (t60) cc_final: 0.7670 (t60) REVERT: J 210 CYS cc_start: 0.7183 (m) cc_final: 0.6866 (m) REVERT: J 227 TYR cc_start: 0.8818 (t80) cc_final: 0.8607 (t80) REVERT: K 169 TRP cc_start: 0.8150 (t60) cc_final: 0.7710 (t60) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.2289 time to fit residues: 48.2773 Evaluate side-chains 129 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 151 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114078 restraints weight = 108183.359| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.58 r_work: 0.3165 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14800 Z= 0.163 Angle : 0.505 5.548 20144 Z= 0.272 Chirality : 0.044 0.144 2232 Planarity : 0.003 0.036 2568 Dihedral : 4.858 20.457 2192 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.13 % Allowed : 7.45 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.19), residues: 1848 helix: -0.05 (0.33), residues: 256 sheet: -0.69 (0.22), residues: 576 loop : -1.62 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 332 TYR 0.016 0.002 TYR K 227 PHE 0.014 0.002 PHE J 225 TRP 0.012 0.001 TRP F 169 HIS 0.003 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00376 (14768) covalent geometry : angle 0.49402 (20072) SS BOND : bond 0.00505 ( 24) SS BOND : angle 1.63760 ( 48) hydrogen bonds : bond 0.03074 ( 534) hydrogen bonds : angle 5.25766 ( 1399) link_NAG-ASN : bond 0.00051 ( 8) link_NAG-ASN : angle 2.10705 ( 24) *********************** 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 133 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.538 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: B 169 TRP cc_start: 0.8344 (t60) cc_final: 0.7881 (t60) REVERT: B 210 CYS cc_start: 0.7773 (m) cc_final: 0.7392 (m) REVERT: A 169 TRP cc_start: 0.8318 (t60) cc_final: 0.7900 (t60) REVERT: C 162 ASP cc_start: 0.7562 (t0) cc_final: 0.7349 (t70) REVERT: C 169 TRP cc_start: 0.8308 (t60) cc_final: 0.7853 (t60) REVERT: C 210 CYS cc_start: 0.7787 (m) cc_final: 0.7412 (m) REVERT: D 169 TRP cc_start: 0.8290 (t60) cc_final: 0.7809 (t60) REVERT: F 169 TRP cc_start: 0.8323 (t60) cc_final: 0.7795 (t60) REVERT: F 210 CYS cc_start: 0.7804 (m) cc_final: 0.7425 (m) REVERT: G 169 TRP cc_start: 0.8296 (t60) cc_final: 0.7838 (t60) REVERT: J 169 TRP cc_start: 0.8383 (t60) cc_final: 0.7969 (t60) REVERT: J 210 CYS cc_start: 0.7799 (m) cc_final: 0.7420 (m) REVERT: K 169 TRP cc_start: 0.8317 (t60) cc_final: 0.7866 (t60) outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.2224 time to fit residues: 45.4769 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 : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 183 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 115 optimal weight: 0.0050 chunk 111 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 140 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.146500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114350 restraints weight = 118187.496| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.86 r_work: 0.3241 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14800 Z= 0.114 Angle : 0.475 4.226 20144 Z= 0.254 Chirality : 0.044 0.138 2232 Planarity : 0.003 0.033 2568 Dihedral : 4.618 18.512 2192 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.07 % Allowed : 8.05 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.19), residues: 1848 helix: 0.06 (0.33), residues: 256 sheet: -0.65 (0.21), residues: 576 loop : -1.51 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 332 TYR 0.011 0.002 TYR G 227 PHE 0.013 0.001 PHE B 225 TRP 0.009 0.001 TRP C 169 HIS 0.002 0.001 HIS K 374 Details of bonding type rmsd covalent geometry : bond 0.00258 (14768) covalent geometry : angle 0.46725 (20072) SS BOND : bond 0.00335 ( 24) SS BOND : angle 1.31275 ( 48) hydrogen bonds : bond 0.02800 ( 534) hydrogen bonds : angle 5.03515 ( 1399) link_NAG-ASN : bond 0.00113 ( 8) link_NAG-ASN : angle 1.74071 ( 24) *********************** 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 134 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.739 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: B 169 TRP cc_start: 0.8152 (t60) cc_final: 0.7843 (t60) REVERT: B 210 CYS cc_start: 0.7217 (m) cc_final: 0.6850 (m) REVERT: B 227 TYR cc_start: 0.8793 (t80) cc_final: 0.8560 (t80) REVERT: A 169 TRP cc_start: 0.8184 (t60) cc_final: 0.7821 (t60) REVERT: C 210 CYS cc_start: 0.7224 (m) cc_final: 0.6858 (m) REVERT: C 227 TYR cc_start: 0.8786 (t80) cc_final: 0.8561 (t80) REVERT: D 169 TRP cc_start: 0.8162 (t60) cc_final: 0.7810 (t60) REVERT: F 210 CYS cc_start: 0.7253 (m) cc_final: 0.6880 (m) REVERT: F 227 TYR cc_start: 0.8793 (t80) cc_final: 0.8566 (t80) REVERT: G 169 TRP cc_start: 0.8162 (t60) cc_final: 0.7830 (t60) REVERT: J 169 TRP cc_start: 0.8258 (t60) cc_final: 0.7928 (t60) REVERT: J 210 CYS cc_start: 0.7211 (m) cc_final: 0.6841 (m) REVERT: J 227 TYR cc_start: 0.8786 (t80) cc_final: 0.8556 (t80) REVERT: K 169 TRP cc_start: 0.8173 (t60) cc_final: 0.7842 (t60) outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.2269 time to fit residues: 47.1410 Evaluate side-chains 128 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 21 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 chunk 101 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 182 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.145400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113254 restraints weight = 112086.884| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.81 r_work: 0.3160 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1240 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= 0.121 Angle : 0.475 4.230 20144 Z= 0.255 Chirality : 0.044 0.141 2232 Planarity : 0.003 0.035 2568 Dihedral : 4.586 18.469 2192 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.19), residues: 1848 helix: 0.10 (0.32), residues: 256 sheet: -0.71 (0.20), residues: 648 loop : -1.47 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 332 TYR 0.011 0.002 TYR J 239 PHE 0.012 0.001 PHE B 225 TRP 0.009 0.001 TRP J 212 HIS 0.002 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00277 (14768) covalent geometry : angle 0.46761 (20072) SS BOND : bond 0.00311 ( 24) SS BOND : angle 1.32341 ( 48) hydrogen bonds : bond 0.02787 ( 534) hydrogen bonds : angle 4.98065 ( 1399) link_NAG-ASN : bond 0.00044 ( 8) link_NAG-ASN : angle 1.74977 ( 24) *********************** 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 134 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.658 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: B 169 TRP cc_start: 0.8213 (t60) cc_final: 0.7779 (t60) REVERT: B 210 CYS cc_start: 0.7261 (m) cc_final: 0.6887 (m) REVERT: B 227 TYR cc_start: 0.8827 (t80) cc_final: 0.8594 (t80) REVERT: A 169 TRP cc_start: 0.8216 (t60) cc_final: 0.7879 (t60) REVERT: C 169 TRP cc_start: 0.8182 (t60) cc_final: 0.7816 (t60) REVERT: C 210 CYS cc_start: 0.7258 (m) cc_final: 0.6885 (m) REVERT: C 227 TYR cc_start: 0.8821 (t80) cc_final: 0.8596 (t80) REVERT: D 169 TRP cc_start: 0.8214 (t60) cc_final: 0.7815 (t60) REVERT: F 210 CYS cc_start: 0.7267 (m) cc_final: 0.6888 (m) REVERT: F 227 TYR cc_start: 0.8825 (t80) cc_final: 0.8595 (t80) REVERT: G 169 TRP cc_start: 0.8199 (t60) cc_final: 0.7820 (t60) REVERT: J 169 TRP cc_start: 0.8269 (t60) cc_final: 0.7905 (t60) REVERT: J 210 CYS cc_start: 0.7025 (m) cc_final: 0.6732 (m) REVERT: J 227 TYR cc_start: 0.8814 (t80) cc_final: 0.8591 (t80) REVERT: K 169 TRP cc_start: 0.8217 (t60) cc_final: 0.7839 (t60) outliers start: 4 outliers final: 2 residues processed: 134 average time/residue: 0.2335 time to fit residues: 48.0819 Evaluate side-chains 130 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain D residue 288 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 139 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.144123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111106 restraints weight = 113750.401| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.88 r_work: 0.3156 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14800 Z= 0.161 Angle : 0.498 4.256 20144 Z= 0.267 Chirality : 0.044 0.143 2232 Planarity : 0.003 0.036 2568 Dihedral : 4.769 19.529 2192 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.60 % Allowed : 7.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.19), residues: 1848 helix: 0.12 (0.33), residues: 256 sheet: -0.78 (0.20), residues: 648 loop : -1.53 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 332 TYR 0.013 0.002 TYR J 239 PHE 0.013 0.002 PHE C 225 TRP 0.008 0.001 TRP C 169 HIS 0.003 0.001 HIS K 374 Details of bonding type rmsd covalent geometry : bond 0.00372 (14768) covalent geometry : angle 0.48932 (20072) SS BOND : bond 0.00306 ( 24) SS BOND : angle 1.40958 ( 48) hydrogen bonds : bond 0.02971 ( 534) hydrogen bonds : angle 5.08782 ( 1399) link_NAG-ASN : bond 0.00013 ( 8) link_NAG-ASN : angle 1.89910 ( 24) *********************** 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 137 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.586 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: 0.8350 (t60) cc_final: 0.7843 (t60) REVERT: A 169 TRP cc_start: 0.8355 (t60) cc_final: 0.7980 (t60) REVERT: C 169 TRP cc_start: 0.8329 (t60) cc_final: 0.7989 (t60) REVERT: D 169 TRP cc_start: 0.8346 (t60) cc_final: 0.7891 (t60) REVERT: G 169 TRP cc_start: 0.8345 (t60) cc_final: 0.7918 (t60) REVERT: J 169 TRP cc_start: 0.8404 (t60) cc_final: 0.7979 (t60) REVERT: J 210 CYS cc_start: 0.7784 (m) cc_final: 0.7464 (m) REVERT: K 169 TRP cc_start: 0.8349 (t60) cc_final: 0.7903 (t60) outliers start: 9 outliers final: 8 residues processed: 137 average time/residue: 0.2377 time to fit residues: 49.9424 Evaluate side-chains 135 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 K residue 288 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 F 315 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.143719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111545 restraints weight = 114856.732| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.76 r_work: 0.3083 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 14800 Z= 0.210 Angle : 0.523 4.832 20144 Z= 0.281 Chirality : 0.045 0.145 2232 Planarity : 0.003 0.038 2568 Dihedral : 4.914 20.669 2192 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.66 % Allowed : 7.58 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.19), residues: 1848 helix: 0.05 (0.33), residues: 256 sheet: -0.85 (0.20), residues: 648 loop : -1.62 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 332 TYR 0.014 0.002 TYR F 239 PHE 0.014 0.002 PHE B 225 TRP 0.008 0.001 TRP C 169 HIS 0.003 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00486 (14768) covalent geometry : angle 0.51391 (20072) SS BOND : bond 0.00331 ( 24) SS BOND : angle 1.51941 ( 48) hydrogen bonds : bond 0.03115 ( 534) hydrogen bonds : angle 5.17984 ( 1399) link_NAG-ASN : bond 0.00042 ( 8) link_NAG-ASN : angle 1.93363 ( 24) *********************** 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 138 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.665 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: B 169 TRP cc_start: 0.8351 (t60) cc_final: 0.7764 (t60) REVERT: A 169 TRP cc_start: 0.8363 (t60) cc_final: 0.7938 (t60) REVERT: C 169 TRP cc_start: 0.8339 (t60) cc_final: 0.7949 (t60) REVERT: D 169 TRP cc_start: 0.8349 (t60) cc_final: 0.7881 (t60) REVERT: G 169 TRP cc_start: 0.8350 (t60) cc_final: 0.7884 (t60) REVERT: J 169 TRP cc_start: 0.8421 (t60) cc_final: 0.7989 (t60) REVERT: J 210 CYS cc_start: 0.7907 (m) cc_final: 0.7554 (m) REVERT: K 169 TRP cc_start: 0.8365 (t60) cc_final: 0.7869 (t60) outliers start: 10 outliers final: 5 residues processed: 138 average time/residue: 0.2296 time to fit residues: 48.7190 Evaluate side-chains 127 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain G 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 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 27 optimal weight: 0.0870 chunk 74 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 F 315 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112323 restraints weight = 119554.804| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.98 r_work: 0.3082 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14800 Z= 0.103 Angle : 0.478 4.700 20144 Z= 0.256 Chirality : 0.044 0.136 2232 Planarity : 0.003 0.033 2568 Dihedral : 4.675 18.763 2192 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.19), residues: 1848 helix: 0.13 (0.32), residues: 256 sheet: -0.76 (0.20), residues: 648 loop : -1.48 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 332 TYR 0.010 0.001 TYR C 239 PHE 0.012 0.001 PHE B 225 TRP 0.007 0.001 TRP C 169 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00234 (14768) covalent geometry : angle 0.47234 (20072) SS BOND : bond 0.00258 ( 24) SS BOND : angle 1.19277 ( 48) hydrogen bonds : bond 0.02743 ( 534) hydrogen bonds : angle 4.97771 ( 1399) link_NAG-ASN : bond 0.00182 ( 8) link_NAG-ASN : angle 1.63486 ( 24) *********************** 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 128 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 0.745 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: 0.8236 (t60) cc_final: 0.7778 (t60) REVERT: B 227 TYR cc_start: 0.8858 (t80) cc_final: 0.8619 (t80) REVERT: A 169 TRP cc_start: 0.8253 (t60) cc_final: 0.7899 (t60) REVERT: C 169 TRP cc_start: 0.8218 (t60) cc_final: 0.7840 (t60) REVERT: C 227 TYR cc_start: 0.8859 (t80) cc_final: 0.8628 (t80) REVERT: D 169 TRP cc_start: 0.8245 (t60) cc_final: 0.7842 (t60) REVERT: F 169 TRP cc_start: 0.8185 (t60) cc_final: 0.7661 (t60) REVERT: F 227 TYR cc_start: 0.8856 (t80) cc_final: 0.8629 (t80) REVERT: G 169 TRP cc_start: 0.8205 (t60) cc_final: 0.7829 (t60) REVERT: J 169 TRP cc_start: 0.8281 (t60) cc_final: 0.7879 (t60) REVERT: J 210 CYS cc_start: 0.7274 (m) cc_final: 0.6954 (m) REVERT: J 227 TYR cc_start: 0.8854 (t80) cc_final: 0.8628 (t80) REVERT: K 169 TRP cc_start: 0.8252 (t60) cc_final: 0.7882 (t60) outliers start: 4 outliers final: 1 residues processed: 128 average time/residue: 0.2253 time to fit residues: 45.0839 Evaluate side-chains 123 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 35 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 F 315 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112224 restraints weight = 109975.038| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.83 r_work: 0.3154 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1375 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= 0.133 Angle : 0.487 4.592 20144 Z= 0.261 Chirality : 0.044 0.139 2232 Planarity : 0.003 0.033 2568 Dihedral : 4.690 18.953 2192 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.33 % Allowed : 8.31 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.19), residues: 1848 helix: 0.15 (0.33), residues: 256 sheet: -0.82 (0.20), residues: 648 loop : -1.49 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 332 TYR 0.011 0.002 TYR J 239 PHE 0.012 0.001 PHE F 225 TRP 0.008 0.001 TRP C 169 HIS 0.003 0.001 HIS J 358 Details of bonding type rmsd covalent geometry : bond 0.00306 (14768) covalent geometry : angle 0.48013 (20072) SS BOND : bond 0.00277 ( 24) SS BOND : angle 1.28240 ( 48) hydrogen bonds : bond 0.02803 ( 534) hydrogen bonds : angle 4.98267 ( 1399) link_NAG-ASN : bond 0.00046 ( 8) link_NAG-ASN : angle 1.74263 ( 24) ********************** 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 128 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.752 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: 0.8339 (t60) cc_final: 0.7825 (t60) REVERT: B 227 TYR cc_start: 0.8959 (t80) cc_final: 0.8726 (t80) REVERT: A 169 TRP cc_start: 0.8346 (t60) cc_final: 0.7988 (t60) REVERT: C 169 TRP cc_start: 0.8315 (t60) cc_final: 0.7885 (t60) REVERT: C 227 TYR cc_start: 0.8969 (t80) cc_final: 0.8742 (t80) REVERT: D 169 TRP cc_start: 0.8346 (t60) cc_final: 0.7933 (t60) REVERT: F 169 TRP cc_start: 0.8307 (t60) cc_final: 0.7764 (t60) REVERT: F 227 TYR cc_start: 0.8962 (t80) cc_final: 0.8736 (t80) REVERT: G 169 TRP cc_start: 0.8308 (t60) cc_final: 0.7908 (t60) REVERT: J 169 TRP cc_start: 0.8387 (t60) cc_final: 0.7966 (t60) REVERT: J 210 CYS cc_start: 0.7792 (m) cc_final: 0.7477 (m) REVERT: J 227 TYR cc_start: 0.8957 (t80) cc_final: 0.8734 (t80) REVERT: K 169 TRP cc_start: 0.8352 (t60) cc_final: 0.7942 (t60) outliers start: 5 outliers final: 4 residues processed: 128 average time/residue: 0.2539 time to fit residues: 50.3852 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN C 315 ASN F 315 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.144787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112437 restraints weight = 106514.594| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.77 r_work: 0.3157 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 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 = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 14800 Z= 0.202 Angle : 0.920 59.199 20144 Z= 0.552 Chirality : 0.045 0.277 2232 Planarity : 0.003 0.033 2568 Dihedral : 4.688 18.954 2192 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.33 % Allowed : 8.38 % Favored : 91.29 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.19), residues: 1848 helix: 0.14 (0.33), residues: 256 sheet: -0.83 (0.20), residues: 648 loop : -1.49 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 332 TYR 0.012 0.001 TYR J 239 PHE 0.012 0.001 PHE F 225 TRP 0.007 0.001 TRP C 169 HIS 0.003 0.001 HIS J 358 Details of bonding type rmsd covalent geometry : bond 0.00404 (14768) covalent geometry : angle 0.91755 (20072) SS BOND : bond 0.00269 ( 24) SS BOND : angle 1.28422 ( 48) hydrogen bonds : bond 0.02810 ( 534) hydrogen bonds : angle 4.98235 ( 1399) link_NAG-ASN : bond 0.00044 ( 8) link_NAG-ASN : angle 1.73802 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6474.39 seconds wall clock time: 110 minutes 27.43 seconds (6627.43 seconds total)