Starting phenix.real_space_refine on Mon May 26 17:06:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s50_19717/05_2025/8s50_19717_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s50_19717/05_2025/8s50_19717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s50_19717/05_2025/8s50_19717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s50_19717/05_2025/8s50_19717.map" model { file = "/net/cci-nas-00/data/ceres_data/8s50_19717/05_2025/8s50_19717_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s50_19717/05_2025/8s50_19717_trim.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 9136 2.51 5 N 2520 2.21 5 O 2902 1.98 5 H 14016 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28654 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "A" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "C" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "D" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "F" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "G" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "J" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "K" Number of atoms: 3541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 231, 3499 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3496 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Time building chain proxies: 24.33, per 1000 atoms: 0.85 Number of scatterers: 28654 At special positions: 0 Unit cell: (98.6112, 98.6112, 139.162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 O 2902 8.00 N 2520 7.00 C 9136 6.00 H 14016 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS A 318 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS A 317 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS D 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS D 317 " distance=2.03 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 357 " distance=2.03 Simple disulfide: pdb=" SG CYS D 210 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 357 " distance=2.03 Simple disulfide: pdb=" SG CYS F 210 " - pdb=" SG CYS F 271 " distance=2.03 Simple disulfide: pdb=" SG CYS F 317 " - pdb=" SG CYS G 318 " distance=2.03 Simple disulfide: pdb=" SG CYS F 318 " - pdb=" SG CYS G 317 " distance=2.03 Simple disulfide: pdb=" SG CYS G 179 " - pdb=" SG CYS G 357 " distance=2.03 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 179 " - pdb=" SG CYS J 357 " distance=2.03 Simple disulfide: pdb=" SG CYS J 210 " - pdb=" SG CYS J 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 317 " - pdb=" SG CYS K 318 " distance=2.03 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS K 317 " distance=2.03 Simple disulfide: pdb=" SG CYS K 179 " - pdb=" SG CYS K 357 " distance=2.03 Simple disulfide: pdb=" SG CYS K 210 " - pdb=" SG CYS K 271 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 220 " " NAG B 401 " - " ASN B 220 " " NAG C 401 " - " ASN C 220 " " NAG D 401 " - " ASN D 220 " " NAG F 401 " - " ASN F 220 " " NAG G 401 " - " ASN G 220 " " NAG J 401 " - " ASN J 220 " " NAG K 401 " - " ASN K 220 " Time building additional restraints: 7.82 Conformation dependent library (CDL) restraints added in 4.3 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 16 sheets defined 13.5% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'B' and resid 151 through 173 removed outlier: 3.924A pdb=" N GLN B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 173 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.723A pdb=" N GLY B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 173 removed outlier: 3.616A pdb=" N GLN A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 173 " --> pdb=" O TRP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.765A pdb=" N GLY A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 173 removed outlier: 3.618A pdb=" N GLN C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TRP C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER C 173 " --> pdb=" O TRP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.726A pdb=" N GLY C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 173 removed outlier: 3.560A pdb=" N GLN D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TRP D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.763A pdb=" N GLY D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 173 removed outlier: 3.619A pdb=" N GLN F 158 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA F 165 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY F 168 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TRP F 169 " --> pdb=" O ALA F 165 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER F 173 " --> pdb=" O TRP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 352 removed outlier: 3.731A pdb=" N GLY F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 173 removed outlier: 3.563A pdb=" N GLN G 158 " --> pdb=" O GLU G 154 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA G 165 " --> pdb=" O ALA G 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL G 166 " --> pdb=" O ASP G 162 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY G 168 " --> pdb=" O HIS G 164 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP G 169 " --> pdb=" O ALA G 165 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER G 173 " --> pdb=" O TRP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 352 removed outlier: 3.772A pdb=" N GLY G 352 " --> pdb=" O ILE G 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 173 removed outlier: 3.533A pdb=" N GLN J 158 " --> pdb=" O GLU J 154 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA J 165 " --> pdb=" O ALA J 161 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL J 166 " --> pdb=" O ASP J 162 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY J 168 " --> pdb=" O HIS J 164 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TRP J 169 " --> pdb=" O ALA J 165 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER J 173 " --> pdb=" O TRP J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 352 removed outlier: 3.731A pdb=" N GLY J 352 " --> pdb=" O ILE J 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 173 removed outlier: 3.718A pdb=" N GLN K 158 " --> pdb=" O GLU K 154 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA K 165 " --> pdb=" O ALA K 161 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL K 166 " --> pdb=" O ASP K 162 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY K 168 " --> pdb=" O HIS K 164 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TRP K 169 " --> pdb=" O ALA K 165 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER K 173 " --> pdb=" O TRP K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 344 through 352 removed outlier: 3.758A pdb=" N GLY K 352 " --> pdb=" O ILE K 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 288 through 293 removed outlier: 6.660A pdb=" N LEU B 283 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 292 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 281 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 280 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 275 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER B 208 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE B 338 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS B 210 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B 336 " --> pdb=" O CYS B 210 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N SER B 330 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 255 through 258 removed outlier: 6.633A pdb=" N LEU B 240 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE B 223 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 308 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU B 370 " --> pdb=" O HIS B 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 293 removed outlier: 6.495A pdb=" N LEU A 283 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR A 292 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A 281 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 280 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A 275 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER A 208 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE A 338 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N CYS A 210 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE A 336 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N SER A 330 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 255 through 258 removed outlier: 6.608A pdb=" N LEU A 240 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A 223 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU A 308 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU A 370 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 288 through 293 removed outlier: 6.661A pdb=" N LEU C 283 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR C 292 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR C 281 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 280 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN C 275 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER C 208 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE C 338 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS C 210 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C 336 " --> pdb=" O CYS C 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 255 through 258 removed outlier: 6.630A pdb=" N LEU C 240 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE C 223 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU C 308 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU C 370 " --> pdb=" O HIS C 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 288 through 293 removed outlier: 6.497A pdb=" N LEU D 283 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR D 292 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR D 281 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER D 208 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE D 338 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS D 210 " --> pdb=" O PHE D 336 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE D 336 " --> pdb=" O CYS D 210 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N SER D 330 " --> pdb=" O THR D 216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 255 through 258 removed outlier: 6.608A pdb=" N LEU D 240 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE D 223 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU D 308 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU D 370 " --> pdb=" O HIS D 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 288 through 293 removed outlier: 6.670A pdb=" N LEU F 283 " --> pdb=" O ALA F 290 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR F 292 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR F 281 " --> pdb=" O THR F 292 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 280 " --> pdb=" O ASN F 275 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN F 275 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER F 208 " --> pdb=" O ILE F 338 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE F 338 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS F 210 " --> pdb=" O PHE F 336 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE F 336 " --> pdb=" O CYS F 210 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N SER F 330 " --> pdb=" O THR F 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 255 through 258 removed outlier: 6.625A pdb=" N LEU F 240 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE F 223 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU F 308 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU F 370 " --> pdb=" O HIS F 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 288 through 293 removed outlier: 6.508A pdb=" N LEU G 283 " --> pdb=" O ALA G 290 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR G 292 " --> pdb=" O THR G 281 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR G 281 " --> pdb=" O THR G 292 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 280 " --> pdb=" O ASN G 275 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN G 275 " --> pdb=" O LEU G 280 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER G 208 " --> pdb=" O ILE G 338 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE G 338 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS G 210 " --> pdb=" O PHE G 336 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE G 336 " --> pdb=" O CYS G 210 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N SER G 330 " --> pdb=" O THR G 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 255 through 258 removed outlier: 6.597A pdb=" N LEU G 240 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE G 223 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU G 308 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU G 370 " --> pdb=" O HIS G 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 288 through 293 removed outlier: 6.657A pdb=" N LEU J 283 " --> pdb=" O ALA J 290 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR J 292 " --> pdb=" O THR J 281 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR J 281 " --> pdb=" O THR J 292 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU J 280 " --> pdb=" O ASN J 275 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN J 275 " --> pdb=" O LEU J 280 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER J 208 " --> pdb=" O ILE J 338 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE J 338 " --> pdb=" O SER J 208 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N CYS J 210 " --> pdb=" O PHE J 336 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE J 336 " --> pdb=" O CYS J 210 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N SER J 330 " --> pdb=" O THR J 216 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 255 through 258 removed outlier: 6.622A pdb=" N LEU J 240 " --> pdb=" O ILE J 223 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE J 223 " --> pdb=" O LEU J 240 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU J 308 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU J 370 " --> pdb=" O HIS J 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 288 through 293 removed outlier: 6.496A pdb=" N LEU K 283 " --> pdb=" O ALA K 290 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR K 292 " --> pdb=" O THR K 281 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR K 281 " --> pdb=" O THR K 292 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU K 280 " --> pdb=" O ASN K 275 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN K 275 " --> pdb=" O LEU K 280 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER K 208 " --> pdb=" O ILE K 338 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE K 338 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N CYS K 210 " --> pdb=" O PHE K 336 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE K 336 " --> pdb=" O CYS K 210 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N SER K 330 " --> pdb=" O THR K 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 255 through 258 removed outlier: 6.607A pdb=" N LEU K 240 " --> pdb=" O ILE K 223 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE K 223 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU K 308 " --> pdb=" O VAL K 196 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU K 370 " --> pdb=" O HIS K 197 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.72 Time building geometry restraints manager: 9.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 14016 1.04 - 1.24: 1556 1.24 - 1.44: 4928 1.44 - 1.64: 8172 1.64 - 1.83: 112 Bond restraints: 28784 Sorted by residual: bond pdb=" C1 NAG J 401 " pdb=" O5 NAG J 401 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.06e+00 bond pdb=" C1 NAG G 401 " pdb=" O5 NAG G 401 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 NAG D 401 " pdb=" O5 NAG D 401 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 ... (remaining 28779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 50543 1.35 - 2.70: 1192 2.70 - 4.05: 102 4.05 - 5.40: 3 5.40 - 6.75: 8 Bond angle restraints: 51848 Sorted by residual: angle pdb=" N GLY A 320 " pdb=" CA GLY A 320 " pdb=" C GLY A 320 " ideal model delta sigma weight residual 115.08 111.24 3.84 1.64e+00 3.72e-01 5.48e+00 angle pdb=" N GLY K 320 " pdb=" CA GLY K 320 " pdb=" C GLY K 320 " ideal model delta sigma weight residual 115.08 111.25 3.83 1.64e+00 3.72e-01 5.46e+00 angle pdb=" N GLY G 320 " pdb=" CA GLY G 320 " pdb=" C GLY G 320 " ideal model delta sigma weight residual 115.08 111.35 3.73 1.64e+00 3.72e-01 5.18e+00 angle pdb=" N GLY D 320 " pdb=" CA GLY D 320 " pdb=" C GLY D 320 " ideal model delta sigma weight residual 115.08 111.38 3.70 1.64e+00 3.72e-01 5.10e+00 angle pdb=" CG ASN K 220 " pdb=" ND2 ASN K 220 " pdb="HD21 ASN K 220 " ideal model delta sigma weight residual 120.00 126.75 -6.75 3.00e+00 1.11e-01 5.06e+00 ... (remaining 51843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 12030 16.87 - 33.75: 1195 33.75 - 50.62: 289 50.62 - 67.50: 102 67.50 - 84.37: 32 Dihedral angle restraints: 13648 sinusoidal: 7432 harmonic: 6216 Sorted by residual: dihedral pdb=" CB CYS C 318 " pdb=" SG CYS C 318 " pdb=" SG CYS D 317 " pdb=" CB CYS D 317 " ideal model delta sinusoidal sigma weight residual -86.00 -170.37 84.37 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS F 318 " pdb=" SG CYS F 318 " pdb=" SG CYS G 317 " pdb=" CB CYS G 317 " ideal model delta sinusoidal sigma weight residual -86.00 -170.21 84.21 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" CB CYS B 318 " pdb=" SG CYS B 318 " pdb=" SG CYS A 317 " pdb=" CB CYS A 317 " ideal model delta sinusoidal sigma weight residual -86.00 -170.14 84.14 1 1.00e+01 1.00e-02 8.62e+01 ... (remaining 13645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1323 0.031 - 0.061: 596 0.061 - 0.092: 118 0.092 - 0.122: 143 0.122 - 0.153: 52 Chirality restraints: 2232 Sorted by residual: chirality pdb=" C1 NAG G 401 " pdb=" ND2 ASN G 220 " pdb=" C2 NAG G 401 " pdb=" O5 NAG G 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" C1 NAG D 401 " pdb=" ND2 ASN D 220 " pdb=" C2 NAG D 401 " pdb=" O5 NAG D 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 220 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 2229 not shown) Planarity restraints: 4376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 232 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO G 233 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 233 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 233 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN K 232 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO K 233 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO K 233 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 233 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 232 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO A 233 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " -0.021 5.00e-02 4.00e+02 ... (remaining 4373 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2080 2.20 - 2.80: 59625 2.80 - 3.40: 78529 3.40 - 4.00: 111282 4.00 - 4.60: 169309 Nonbonded interactions: 420825 Sorted by model distance: nonbonded pdb=" O ILE K 371 " pdb=" HH TYR K 379 " model vdw 1.599 2.450 nonbonded pdb=" OE1 GLU D 370 " pdb=" HG SER G 189 " model vdw 1.624 2.450 nonbonded pdb=" OE1 GLU G 370 " pdb=" HG SER K 189 " model vdw 1.624 2.450 nonbonded pdb=" O ILE D 371 " pdb=" HH TYR D 379 " model vdw 1.634 2.450 nonbonded pdb=" O ILE G 371 " pdb=" HH TYR G 379 " model vdw 1.635 2.450 ... (remaining 420820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'B' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'C' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'D' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'F' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'G' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'J' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) selection = (chain 'K' and (resid 151 through 265 or resid 267 through 348 or resid 350 thro \ ugh 381 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 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: 0.530 Extract box with map and model: 1.110 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 73.040 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14800 Z= 0.148 Angle : 0.583 13.528 20144 Z= 0.298 Chirality : 0.046 0.153 2232 Planarity : 0.003 0.038 2568 Dihedral : 13.595 74.861 5376 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.19), residues: 1848 helix: 0.57 (0.36), residues: 208 sheet: -0.14 (0.23), residues: 520 loop : -1.50 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 212 HIS 0.002 0.001 HIS G 374 PHE 0.008 0.001 PHE J 225 TYR 0.012 0.001 TYR K 239 ARG 0.002 0.000 ARG J 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00826 ( 8) link_NAG-ASN : angle 7.79180 ( 24) hydrogen bonds : bond 0.12145 ( 534) hydrogen bonds : angle 6.29245 ( 1399) SS BOND : bond 0.00144 ( 24) SS BOND : angle 1.38361 ( 48) covalent geometry : bond 0.00312 (14768) covalent geometry : angle 0.51396 (20072) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 2.092 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: 0.5525 time to fit residues: 141.9969 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 : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN A 254 ASN C 237 GLN D 254 ASN F 237 GLN G 254 ASN K 254 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.146472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114474 restraints weight = 119262.704| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.83 r_work: 0.3163 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14800 Z= 0.149 Angle : 0.523 4.881 20144 Z= 0.278 Chirality : 0.045 0.142 2232 Planarity : 0.003 0.035 2568 Dihedral : 4.958 22.533 2192 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.53 % Allowed : 4.79 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 1848 helix: 0.81 (0.37), residues: 208 sheet: -0.58 (0.22), residues: 576 loop : -1.50 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 212 HIS 0.002 0.001 HIS B 358 PHE 0.014 0.001 PHE J 225 TYR 0.013 0.002 TYR J 239 ARG 0.002 0.000 ARG B 157 Details of bonding type rmsd link_NAG-ASN : bond 0.00012 ( 8) link_NAG-ASN : angle 2.52557 ( 24) hydrogen bonds : bond 0.03372 ( 534) hydrogen bonds : angle 5.44633 ( 1399) SS BOND : bond 0.00159 ( 24) SS BOND : angle 1.34622 ( 48) covalent geometry : bond 0.00345 (14768) covalent geometry : angle 0.51232 (20072) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8106 (t60) cc_final: 0.7663 (t60) REVERT: A 169 TRP cc_start: 0.8119 (t60) cc_final: 0.7672 (t60) REVERT: C 162 ASP cc_start: 0.7547 (t0) cc_final: 0.7283 (t70) REVERT: G 169 TRP cc_start: 0.8087 (t60) cc_final: 0.7765 (t60) REVERT: J 169 TRP cc_start: 0.8170 (t60) cc_final: 0.7731 (t60) REVERT: K 169 TRP cc_start: 0.8112 (t60) cc_final: 0.7657 (t60) outliers start: 8 outliers final: 1 residues processed: 145 average time/residue: 0.5366 time to fit residues: 118.4275 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 288 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 96 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 137 optimal weight: 0.1980 chunk 171 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.146684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115017 restraints weight = 112707.105| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.78 r_work: 0.3167 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14800 Z= 0.133 Angle : 0.501 4.241 20144 Z= 0.269 Chirality : 0.044 0.144 2232 Planarity : 0.003 0.035 2568 Dihedral : 4.800 20.605 2192 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.07 % Allowed : 6.85 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.19), residues: 1848 helix: -0.08 (0.33), residues: 256 sheet: -0.61 (0.22), residues: 576 loop : -1.57 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.002 0.001 HIS G 374 PHE 0.014 0.001 PHE F 225 TYR 0.012 0.001 TYR J 239 ARG 0.001 0.000 ARG A 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00047 ( 8) link_NAG-ASN : angle 2.17928 ( 24) hydrogen bonds : bond 0.03138 ( 534) hydrogen bonds : angle 5.29824 ( 1399) SS BOND : bond 0.00637 ( 24) SS BOND : angle 1.59266 ( 48) covalent geometry : bond 0.00303 (14768) covalent geometry : angle 0.48981 (20072) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 2.228 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: 0.8221 (t60) cc_final: 0.7770 (t60) REVERT: B 210 CYS cc_start: 0.7692 (m) cc_final: 0.7350 (m) REVERT: B 227 TYR cc_start: 0.8938 (t80) cc_final: 0.8736 (t80) REVERT: C 162 ASP cc_start: 0.7619 (t0) cc_final: 0.7338 (t70) REVERT: C 169 TRP cc_start: 0.8343 (t60) cc_final: 0.7793 (t60) REVERT: C 210 CYS cc_start: 0.7740 (m) cc_final: 0.7400 (m) REVERT: F 210 CYS cc_start: 0.7713 (m) cc_final: 0.7374 (m) REVERT: J 169 TRP cc_start: 0.8363 (t60) cc_final: 0.7890 (t60) REVERT: J 210 CYS cc_start: 0.7713 (m) cc_final: 0.7371 (m) REVERT: K 169 TRP cc_start: 0.8279 (t60) cc_final: 0.7895 (t60) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.5666 time to fit residues: 116.6954 Evaluate side-chains 127 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 164 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.146137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114293 restraints weight = 119844.759| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.81 r_work: 0.3244 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14800 Z= 0.139 Angle : 0.491 5.105 20144 Z= 0.264 Chirality : 0.044 0.142 2232 Planarity : 0.003 0.034 2568 Dihedral : 4.742 19.487 2192 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.07 % Allowed : 8.38 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1848 helix: -0.03 (0.33), residues: 256 sheet: -0.62 (0.22), residues: 576 loop : -1.54 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 169 HIS 0.003 0.001 HIS A 269 PHE 0.014 0.001 PHE C 225 TYR 0.014 0.002 TYR C 227 ARG 0.001 0.000 ARG A 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00007 ( 8) link_NAG-ASN : angle 2.00740 ( 24) hydrogen bonds : bond 0.02957 ( 534) hydrogen bonds : angle 5.16679 ( 1399) SS BOND : bond 0.00501 ( 24) SS BOND : angle 1.55353 ( 48) covalent geometry : bond 0.00318 (14768) covalent geometry : angle 0.48060 (20072) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 2.225 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: 0.8169 (t60) cc_final: 0.7748 (t60) REVERT: B 210 CYS cc_start: 0.7197 (m) cc_final: 0.6833 (m) REVERT: B 227 TYR cc_start: 0.8838 (t80) cc_final: 0.8625 (t80) REVERT: C 162 ASP cc_start: 0.7484 (t0) cc_final: 0.7248 (t70) REVERT: C 169 TRP cc_start: 0.8173 (t60) cc_final: 0.7774 (t60) REVERT: C 210 CYS cc_start: 0.7215 (m) cc_final: 0.6858 (m) REVERT: D 169 TRP cc_start: 0.8124 (t60) cc_final: 0.7894 (t60) REVERT: F 169 TRP cc_start: 0.8163 (t60) cc_final: 0.7691 (t60) REVERT: F 210 CYS cc_start: 0.7220 (m) cc_final: 0.6861 (m) REVERT: G 169 TRP cc_start: 0.8192 (t60) cc_final: 0.7730 (t60) REVERT: G 227 TYR cc_start: 0.8723 (t80) cc_final: 0.8521 (t80) REVERT: J 169 TRP cc_start: 0.8220 (t60) cc_final: 0.7856 (t60) REVERT: J 210 CYS cc_start: 0.7235 (m) cc_final: 0.6875 (m) REVERT: K 169 TRP cc_start: 0.8125 (t60) cc_final: 0.7878 (t60) REVERT: K 227 TYR cc_start: 0.8726 (t80) cc_final: 0.8524 (t80) outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.5565 time to fit residues: 113.1554 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 : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 164 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112967 restraints weight = 118146.228| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.90 r_work: 0.3202 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.095 | | 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) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14800 Z= 0.150 Angle : 0.496 5.330 20144 Z= 0.266 Chirality : 0.044 0.144 2232 Planarity : 0.003 0.034 2568 Dihedral : 4.749 19.512 2192 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.13 % Allowed : 8.18 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.19), residues: 1848 helix: 0.01 (0.33), residues: 256 sheet: -0.67 (0.21), residues: 576 loop : -1.54 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 169 HIS 0.003 0.001 HIS A 269 PHE 0.013 0.001 PHE J 225 TYR 0.013 0.002 TYR D 227 ARG 0.002 0.000 ARG G 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 8) link_NAG-ASN : angle 1.94050 ( 24) hydrogen bonds : bond 0.02987 ( 534) hydrogen bonds : angle 5.12398 ( 1399) SS BOND : bond 0.00386 ( 24) SS BOND : angle 1.45538 ( 48) covalent geometry : bond 0.00343 (14768) covalent geometry : angle 0.48675 (20072) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 2.339 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: 0.8204 (t60) cc_final: 0.7852 (t60) REVERT: C 210 CYS cc_start: 0.7269 (m) cc_final: 0.6871 (m) REVERT: D 169 TRP cc_start: 0.8195 (t60) cc_final: 0.7918 (t60) REVERT: J 169 TRP cc_start: 0.8286 (t60) cc_final: 0.7921 (t60) REVERT: K 169 TRP cc_start: 0.8181 (t60) cc_final: 0.7943 (t60) REVERT: K 227 TYR cc_start: 0.8800 (t80) cc_final: 0.8600 (t80) outliers start: 2 outliers final: 2 residues processed: 126 average time/residue: 0.5668 time to fit residues: 110.6477 Evaluate side-chains 120 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain D residue 288 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 2 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN C 315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.144352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111397 restraints weight = 112846.823| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.89 r_work: 0.3163 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14800 Z= 0.157 Angle : 0.499 4.447 20144 Z= 0.268 Chirality : 0.044 0.145 2232 Planarity : 0.003 0.034 2568 Dihedral : 4.788 19.917 2192 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.73 % Allowed : 7.85 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.19), residues: 1848 helix: -0.00 (0.33), residues: 256 sheet: -0.70 (0.21), residues: 576 loop : -1.58 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 169 HIS 0.003 0.001 HIS A 269 PHE 0.013 0.001 PHE J 225 TYR 0.014 0.002 TYR G 227 ARG 0.001 0.000 ARG D 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00006 ( 8) link_NAG-ASN : angle 1.90443 ( 24) hydrogen bonds : bond 0.02956 ( 534) hydrogen bonds : angle 5.11049 ( 1399) SS BOND : bond 0.00349 ( 24) SS BOND : angle 1.43980 ( 48) covalent geometry : bond 0.00360 (14768) covalent geometry : angle 0.49096 (20072) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 2.426 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: 0.8206 (t60) cc_final: 0.7866 (t60) REVERT: D 169 TRP cc_start: 0.8193 (t60) cc_final: 0.7952 (t60) REVERT: J 169 TRP cc_start: 0.8267 (t60) cc_final: 0.7879 (t60) REVERT: K 169 TRP cc_start: 0.8180 (t60) cc_final: 0.7964 (t60) outliers start: 11 outliers final: 10 residues processed: 133 average time/residue: 0.5691 time to fit residues: 115.5535 Evaluate side-chains 127 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 2.252 ------------------------------------------------------------------------------- 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 F residue 288 GLU Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain J residue 288 GLU Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.144578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112841 restraints weight = 105634.146| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.70 r_work: 0.3176 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1262 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= 0.142 Angle : 0.494 4.512 20144 Z= 0.265 Chirality : 0.044 0.143 2232 Planarity : 0.003 0.036 2568 Dihedral : 4.746 19.665 2192 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.47 % Allowed : 7.91 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.19), residues: 1848 helix: 0.05 (0.33), residues: 256 sheet: -0.75 (0.20), residues: 648 loop : -1.55 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.003 0.001 HIS A 269 PHE 0.013 0.001 PHE B 225 TYR 0.012 0.002 TYR J 239 ARG 0.001 0.000 ARG A 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00067 ( 8) link_NAG-ASN : angle 1.82081 ( 24) hydrogen bonds : bond 0.02897 ( 534) hydrogen bonds : angle 5.06540 ( 1399) SS BOND : bond 0.00310 ( 24) SS BOND : angle 1.35446 ( 48) covalent geometry : bond 0.00326 (14768) covalent geometry : angle 0.48676 (20072) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 2.320 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: 0.8342 (t60) cc_final: 0.7911 (t60) REVERT: A 169 TRP cc_start: 0.8373 (t60) cc_final: 0.7854 (t60) REVERT: D 169 TRP cc_start: 0.8320 (t60) cc_final: 0.7975 (t60) REVERT: J 169 TRP cc_start: 0.8417 (t60) cc_final: 0.8006 (t60) REVERT: K 169 TRP cc_start: 0.8316 (t60) cc_final: 0.8091 (t60) outliers start: 7 outliers final: 7 residues processed: 133 average time/residue: 0.5786 time to fit residues: 119.7226 Evaluate side-chains 127 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain J residue 288 GLU Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 152 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 183 optimal weight: 0.3980 chunk 125 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.145412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113715 restraints weight = 115382.799| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.74 r_work: 0.3242 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14800 Z= 0.134 Angle : 0.485 4.232 20144 Z= 0.260 Chirality : 0.044 0.140 2232 Planarity : 0.003 0.035 2568 Dihedral : 4.706 19.429 2192 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.53 % Allowed : 7.91 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.19), residues: 1848 helix: 0.08 (0.33), residues: 256 sheet: -0.74 (0.20), residues: 648 loop : -1.52 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS B 358 PHE 0.013 0.001 PHE J 225 TYR 0.015 0.002 TYR K 227 ARG 0.001 0.000 ARG G 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 8) link_NAG-ASN : angle 1.76291 ( 24) hydrogen bonds : bond 0.02824 ( 534) hydrogen bonds : angle 5.00612 ( 1399) SS BOND : bond 0.00297 ( 24) SS BOND : angle 1.30871 ( 48) covalent geometry : bond 0.00307 (14768) covalent geometry : angle 0.47806 (20072) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8093 (t60) cc_final: 0.7821 (t60) REVERT: B 227 TYR cc_start: 0.8818 (t80) cc_final: 0.8572 (t80) REVERT: A 169 TRP cc_start: 0.8182 (t60) cc_final: 0.7763 (t60) REVERT: D 169 TRP cc_start: 0.8151 (t60) cc_final: 0.7858 (t60) REVERT: F 169 TRP cc_start: 0.8135 (t60) cc_final: 0.7759 (t60) REVERT: J 169 TRP cc_start: 0.8242 (t60) cc_final: 0.7906 (t60) REVERT: K 169 TRP cc_start: 0.8148 (t60) cc_final: 0.7922 (t60) outliers start: 8 outliers final: 8 residues processed: 134 average time/residue: 0.5687 time to fit residues: 118.6231 Evaluate side-chains 129 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain J residue 288 GLU Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 101 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.145240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114141 restraints weight = 108137.125| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.63 r_work: 0.3130 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1320 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= 0.137 Angle : 0.488 4.231 20144 Z= 0.261 Chirality : 0.044 0.140 2232 Planarity : 0.003 0.035 2568 Dihedral : 4.703 19.220 2192 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.53 % Allowed : 8.24 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1848 helix: 0.10 (0.33), residues: 256 sheet: -0.74 (0.20), residues: 648 loop : -1.52 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS A 269 PHE 0.013 0.001 PHE F 225 TYR 0.012 0.002 TYR B 239 ARG 0.001 0.000 ARG G 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 8) link_NAG-ASN : angle 1.75145 ( 24) hydrogen bonds : bond 0.02820 ( 534) hydrogen bonds : angle 4.99620 ( 1399) SS BOND : bond 0.00281 ( 24) SS BOND : angle 1.34936 ( 48) covalent geometry : bond 0.00314 (14768) covalent geometry : angle 0.48011 (20072) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8241 (t60) cc_final: 0.7897 (t60) REVERT: B 227 TYR cc_start: 0.8967 (t80) cc_final: 0.8730 (t80) REVERT: A 169 TRP cc_start: 0.8356 (t60) cc_final: 0.7799 (t60) REVERT: D 169 TRP cc_start: 0.8306 (t60) cc_final: 0.7880 (t60) REVERT: G 169 TRP cc_start: 0.8349 (t60) cc_final: 0.7855 (t60) REVERT: J 169 TRP cc_start: 0.8368 (t60) cc_final: 0.7932 (t60) REVERT: K 169 TRP cc_start: 0.8311 (t60) cc_final: 0.7910 (t60) outliers start: 8 outliers final: 8 residues processed: 130 average time/residue: 0.5726 time to fit residues: 115.4701 Evaluate side-chains 128 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain J residue 288 GLU Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 57 optimal weight: 0.0670 chunk 107 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 146 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.146110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114777 restraints weight = 121434.460| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.71 r_work: 0.3127 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 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 = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1344 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= 0.118 Angle : 0.480 4.218 20144 Z= 0.257 Chirality : 0.044 0.137 2232 Planarity : 0.003 0.034 2568 Dihedral : 4.626 18.627 2192 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.20 % Allowed : 8.58 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.19), residues: 1848 helix: 0.11 (0.33), residues: 256 sheet: -0.77 (0.20), residues: 648 loop : -1.46 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.002 0.001 HIS J 358 PHE 0.013 0.001 PHE F 225 TYR 0.011 0.002 TYR F 239 ARG 0.001 0.000 ARG G 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 8) link_NAG-ASN : angle 1.67331 ( 24) hydrogen bonds : bond 0.02735 ( 534) hydrogen bonds : angle 4.93636 ( 1399) SS BOND : bond 0.00269 ( 24) SS BOND : angle 1.27450 ( 48) covalent geometry : bond 0.00271 (14768) covalent geometry : angle 0.47308 (20072) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8239 (t60) cc_final: 0.7888 (t60) REVERT: B 227 TYR cc_start: 0.8964 (t80) cc_final: 0.8744 (t80) REVERT: A 169 TRP cc_start: 0.8341 (t60) cc_final: 0.7779 (t60) REVERT: D 169 TRP cc_start: 0.8302 (t60) cc_final: 0.7870 (t60) REVERT: F 169 TRP cc_start: 0.8268 (t60) cc_final: 0.7844 (t60) REVERT: G 169 TRP cc_start: 0.8333 (t60) cc_final: 0.7832 (t60) REVERT: J 169 TRP cc_start: 0.8369 (t60) cc_final: 0.7930 (t60) REVERT: K 169 TRP cc_start: 0.8304 (t60) cc_final: 0.7901 (t60) outliers start: 3 outliers final: 3 residues processed: 129 average time/residue: 0.5626 time to fit residues: 112.4031 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 153 optimal weight: 0.1980 chunk 154 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 0.0670 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.146438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113680 restraints weight = 112517.711| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.88 r_work: 0.3145 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14800 Z= 0.097 Angle : 0.469 4.199 20144 Z= 0.250 Chirality : 0.044 0.137 2232 Planarity : 0.003 0.031 2568 Dihedral : 4.495 17.351 2192 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.20), residues: 1848 helix: 0.18 (0.33), residues: 256 sheet: -0.70 (0.20), residues: 648 loop : -1.36 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 212 HIS 0.002 0.001 HIS A 269 PHE 0.012 0.001 PHE F 225 TYR 0.010 0.001 TYR K 227 ARG 0.001 0.000 ARG G 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 8) link_NAG-ASN : angle 1.56354 ( 24) hydrogen bonds : bond 0.02610 ( 534) hydrogen bonds : angle 4.82784 ( 1399) SS BOND : bond 0.00237 ( 24) SS BOND : angle 1.17610 ( 48) covalent geometry : bond 0.00221 (14768) covalent geometry : angle 0.46359 (20072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13400.85 seconds wall clock time: 230 minutes 20.90 seconds (13820.90 seconds total)