Starting phenix.real_space_refine on Wed May 6 00:27:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v80_43012/05_2026/8v80_43012_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v80_43012/05_2026/8v80_43012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v80_43012/05_2026/8v80_43012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v80_43012/05_2026/8v80_43012.map" model { file = "/net/cci-nas-00/data/ceres_data/8v80_43012/05_2026/8v80_43012_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v80_43012/05_2026/8v80_43012_trim.cif" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 8 Type Number sf(0) Gaussians Ca 5 9.91 5 P 10 5.49 5 S 120 5.16 5 Cl 5 4.86 5 C 11310 2.51 5 N 2635 2.21 5 O 3160 1.98 5 H 15835 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33080 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "B" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "C" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "D" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "E" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 226 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3, 'YLR': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 140 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'YLR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 10.52, per 1000 atoms: 0.32 Number of scatterers: 33080 At special positions: 0 Unit cell: (100.347, 102.505, 162.929, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 5 19.99 Cl 5 17.00 S 120 16.00 P 10 15.00 O 3160 8.00 N 2635 7.00 C 11310 6.00 H 15835 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 602 " - " ASN A 67 " " NAG B 603 " - " ASN B 67 " " NAG C 602 " - " ASN C 67 " " NAG D 602 " - " ASN D 67 " " NAG E 602 " - " ASN E 67 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN A 23 " " NAG H 1 " - " ASN B 110 " " NAG I 1 " - " ASN B 23 " " NAG J 1 " - " ASN C 110 " " NAG K 1 " - " ASN C 23 " " NAG L 1 " - " ASN D 110 " " NAG M 1 " - " ASN D 23 " " NAG N 1 " - " ASN E 110 " " NAG O 1 " - " ASN E 23 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 44.7% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.637A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.947A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 409 through 466 Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.520A pdb=" N PHE A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.793A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 227 through 230 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.947A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 409 through 466 Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.520A pdb=" N PHE B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.793A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 226 Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.947A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 409 through 466 Processing helix chain 'C' and resid 469 through 478 removed outlier: 3.520A pdb=" N PHE C 478 " --> pdb=" O VAL C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.793A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 226 Processing helix chain 'D' and resid 227 through 230 Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.947A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 409 through 466 Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.519A pdb=" N PHE D 478 " --> pdb=" O VAL D 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.793A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 226 Processing helix chain 'E' and resid 227 through 230 Processing helix chain 'E' and resid 232 through 236 Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.947A pdb=" N VAL E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 409 through 466 Processing helix chain 'E' and resid 469 through 478 removed outlier: 3.520A pdb=" N PHE E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.032A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.032A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN A 52 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE A 39 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N TRP A 54 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU A 37 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN A 56 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N SER A 58 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER A 33 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N THR A 60 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N TYR A 31 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.585A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.585A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU A 192 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR A 187 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 185 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.032A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.032A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N THR B 60 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N TYR B 31 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.585A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.585A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU B 192 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR B 187 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 185 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.032A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.032A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN C 52 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE C 39 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N TRP C 54 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU C 37 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN C 56 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N SER C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N SER C 58 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER C 33 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N THR C 60 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N TYR C 31 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.585A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.585A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU C 192 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TYR C 187 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 185 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.033A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.033A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.584A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.584A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU D 192 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TYR D 187 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 185 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.032A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.032A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.584A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.584A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU E 192 " --> pdb=" O TYR E 187 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR E 187 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 185 " --> pdb=" O TYR E 194 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.07 Time building geometry restraints manager: 3.57 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: 15800 1.04 - 1.24: 2203 1.24 - 1.44: 5407 1.44 - 1.64: 9930 1.64 - 1.84: 180 Bond restraints: 33520 Sorted by residual: bond pdb=" NZ LYS C 124 " pdb=" HZ2 LYS C 124 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS D 306 " pdb=" HZ3 LYS D 306 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS D 238 " pdb=" HZ1 LYS D 238 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS C 181 " pdb=" HZ1 LYS C 181 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS B 438 " pdb=" HZ3 LYS B 438 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 33515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 54881 2.43 - 4.85: 4963 4.85 - 7.28: 206 7.28 - 9.71: 20 9.71 - 12.13: 20 Bond angle restraints: 60090 Sorted by residual: angle pdb=" N ILE E 122 " pdb=" CA ILE E 122 " pdb=" C ILE E 122 " ideal model delta sigma weight residual 107.99 101.77 6.22 1.46e+00 4.69e-01 1.81e+01 angle pdb=" N ILE B 122 " pdb=" CA ILE B 122 " pdb=" C ILE B 122 " ideal model delta sigma weight residual 107.99 101.77 6.22 1.46e+00 4.69e-01 1.81e+01 angle pdb=" N ILE C 122 " pdb=" CA ILE C 122 " pdb=" C ILE C 122 " ideal model delta sigma weight residual 107.99 101.80 6.19 1.46e+00 4.69e-01 1.80e+01 angle pdb=" N ILE D 122 " pdb=" CA ILE D 122 " pdb=" C ILE D 122 " ideal model delta sigma weight residual 107.99 101.80 6.19 1.46e+00 4.69e-01 1.80e+01 angle pdb=" N ILE A 122 " pdb=" CA ILE A 122 " pdb=" C ILE A 122 " ideal model delta sigma weight residual 107.99 101.80 6.19 1.46e+00 4.69e-01 1.80e+01 ... (remaining 60085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.11: 16146 28.11 - 56.22: 654 56.22 - 84.33: 130 84.33 - 112.44: 50 112.44 - 140.55: 5 Dihedral angle restraints: 16985 sinusoidal: 9810 harmonic: 7175 Sorted by residual: dihedral pdb=" CA CYS E 189 " pdb=" C CYS E 189 " pdb=" N CYS E 190 " pdb=" CA CYS E 190 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual 180.00 -153.84 -26.16 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual -180.00 -153.84 -26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 16982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2325 0.075 - 0.149: 313 0.149 - 0.223: 79 0.223 - 0.298: 23 0.298 - 0.372: 10 Chirality restraints: 2750 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.84e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.78e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.77e+01 ... (remaining 2747 not shown) Planarity restraints: 4725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.255 2.00e-02 2.50e+03 2.21e-01 6.12e+02 pdb=" C7 NAG J 1 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " -0.006 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.380 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.254 2.00e-02 2.50e+03 2.21e-01 6.11e+02 pdb=" C7 NAG L 1 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.006 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.380 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.254 2.00e-02 2.50e+03 2.21e-01 6.11e+02 pdb=" C7 NAG N 1 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.006 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.380 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.181 2.00e-02 2.50e+03 ... (remaining 4722 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 427 2.08 - 2.71: 52689 2.71 - 3.34: 94353 3.34 - 3.97: 129451 3.97 - 4.60: 198606 Nonbonded interactions: 475526 Sorted by model distance: nonbonded pdb="HD21 ASN A 106 " pdb=" HG SER E 149 " model vdw 1.455 2.100 nonbonded pdb=" HG SER B 149 " pdb="HD21 ASN C 106 " model vdw 1.457 2.100 nonbonded pdb=" HG SER C 149 " pdb="HD21 ASN D 106 " model vdw 1.458 2.100 nonbonded pdb=" HG SER D 149 " pdb="HD21 ASN E 106 " model vdw 1.458 2.100 nonbonded pdb=" HG SER A 149 " pdb="HD21 ASN B 106 " model vdw 1.467 2.100 ... (remaining 475521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 478)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.170 Extract box with map and model: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 36.390 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.007 0.067 17720 Z= 0.360 Angle : 1.043 12.133 24190 Z= 0.523 Chirality : 0.064 0.372 2750 Planarity : 0.011 0.221 2845 Dihedral : 18.081 140.554 7610 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.17), residues: 1955 helix: -0.61 (0.18), residues: 785 sheet: -1.19 (0.19), residues: 440 loop : -0.60 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 206 TYR 0.020 0.003 TYR E 14 PHE 0.019 0.003 PHE B 145 TRP 0.019 0.003 TRP D 307 HIS 0.003 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00734 (17680) covalent geometry : angle 1.03622 (24080) SS BOND : bond 0.00758 ( 10) SS BOND : angle 2.02057 ( 20) hydrogen bonds : bond 0.19651 ( 845) hydrogen bonds : angle 7.76142 ( 2760) link_BETA1-4 : bond 0.00744 ( 15) link_BETA1-4 : angle 2.26854 ( 45) link_NAG-ASN : bond 0.00655 ( 15) link_NAG-ASN : angle 1.88202 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 VAL cc_start: 0.8400 (t) cc_final: 0.8154 (m) REVERT: A 252 PHE cc_start: 0.7851 (m-80) cc_final: 0.6843 (m-80) REVERT: B 252 PHE cc_start: 0.7926 (m-80) cc_final: 0.6964 (m-80) REVERT: B 436 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6775 (tm-30) REVERT: B 450 MET cc_start: 0.7339 (ttm) cc_final: 0.7079 (ttp) REVERT: C 57 MET cc_start: 0.8430 (mtt) cc_final: 0.8183 (mtt) REVERT: C 68 VAL cc_start: 0.8319 (t) cc_final: 0.8046 (p) REVERT: C 260 MET cc_start: 0.8209 (mmp) cc_final: 0.7971 (mmp) REVERT: D 237 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7598 (mt-10) REVERT: D 252 PHE cc_start: 0.7524 (m-80) cc_final: 0.6525 (m-80) REVERT: D 416 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6758 (tp30) REVERT: D 418 ARG cc_start: 0.7716 (ttm170) cc_final: 0.7423 (mtt180) REVERT: D 436 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6964 (tt0) REVERT: E 40 MET cc_start: 0.8294 (mtp) cc_final: 0.8088 (mtp) REVERT: E 68 VAL cc_start: 0.8504 (t) cc_final: 0.8184 (m) REVERT: E 274 PHE cc_start: 0.8037 (m-10) cc_final: 0.7832 (m-10) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 1.0899 time to fit residues: 288.4494 Evaluate side-chains 187 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.165254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128134 restraints weight = 54346.059| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.41 r_work: 0.3279 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17720 Z= 0.146 Angle : 0.668 6.957 24190 Z= 0.330 Chirality : 0.042 0.187 2750 Planarity : 0.005 0.071 2845 Dihedral : 15.944 123.504 3845 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.34 % Allowed : 4.71 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.17), residues: 1955 helix: 0.36 (0.17), residues: 805 sheet: -0.87 (0.20), residues: 440 loop : -0.36 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 446 TYR 0.010 0.001 TYR E 14 PHE 0.014 0.001 PHE B 99 TRP 0.009 0.001 TRP B 173 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00311 (17680) covalent geometry : angle 0.65161 (24080) SS BOND : bond 0.00795 ( 10) SS BOND : angle 1.60780 ( 20) hydrogen bonds : bond 0.04716 ( 845) hydrogen bonds : angle 5.28888 ( 2760) link_BETA1-4 : bond 0.00355 ( 15) link_BETA1-4 : angle 2.05102 ( 45) link_NAG-ASN : bond 0.00165 ( 15) link_NAG-ASN : angle 2.65587 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 214 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7742 (m-80) cc_final: 0.6829 (m-80) REVERT: B 247 LEU cc_start: 0.6852 (mp) cc_final: 0.6651 (mm) REVERT: B 252 PHE cc_start: 0.7785 (m-80) cc_final: 0.6798 (m-80) REVERT: C 40 MET cc_start: 0.8612 (mtp) cc_final: 0.8307 (mtp) REVERT: D 237 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7692 (mt-10) REVERT: D 252 PHE cc_start: 0.7367 (m-80) cc_final: 0.6427 (m-80) REVERT: D 416 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6692 (tp30) REVERT: D 436 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7340 (tt0) REVERT: E 274 PHE cc_start: 0.8239 (m-10) cc_final: 0.8030 (m-10) outliers start: 6 outliers final: 3 residues processed: 217 average time/residue: 1.1796 time to fit residues: 289.6089 Evaluate side-chains 202 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 199 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 253 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 140 optimal weight: 0.1980 chunk 151 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.165352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.127798 restraints weight = 53479.452| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.39 r_work: 0.3273 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17720 Z= 0.124 Angle : 0.593 7.375 24190 Z= 0.291 Chirality : 0.041 0.224 2750 Planarity : 0.005 0.071 2845 Dihedral : 13.313 106.654 3845 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.56 % Allowed : 5.88 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 1955 helix: 0.94 (0.17), residues: 800 sheet: -0.71 (0.21), residues: 440 loop : -0.18 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 446 TYR 0.010 0.001 TYR E 14 PHE 0.013 0.001 PHE B 99 TRP 0.007 0.001 TRP B 133 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00260 (17680) covalent geometry : angle 0.57760 (24080) SS BOND : bond 0.00752 ( 10) SS BOND : angle 1.48202 ( 20) hydrogen bonds : bond 0.04209 ( 845) hydrogen bonds : angle 4.92760 ( 2760) link_BETA1-4 : bond 0.00378 ( 15) link_BETA1-4 : angle 1.84081 ( 45) link_NAG-ASN : bond 0.00092 ( 15) link_NAG-ASN : angle 2.50884 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7684 (m-80) cc_final: 0.6690 (m-80) REVERT: B 188 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7585 (mm-30) REVERT: B 237 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7256 (mt-10) REVERT: B 247 LEU cc_start: 0.6826 (mp) cc_final: 0.6607 (mm) REVERT: B 252 PHE cc_start: 0.7876 (m-80) cc_final: 0.6828 (m-80) REVERT: B 436 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7613 (tm-30) REVERT: C 40 MET cc_start: 0.8536 (mtp) cc_final: 0.8285 (mtp) REVERT: C 304 MET cc_start: 0.7734 (ttm) cc_final: 0.7470 (ttt) REVERT: C 416 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6435 (mm-30) REVERT: D 252 PHE cc_start: 0.7401 (m-80) cc_final: 0.6361 (m-80) REVERT: D 416 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6423 (mm-30) REVERT: E 416 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6666 (tp30) outliers start: 10 outliers final: 6 residues processed: 211 average time/residue: 1.1606 time to fit residues: 276.7429 Evaluate side-chains 199 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 193 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain E residue 276 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.163228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.125251 restraints weight = 50285.402| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.37 r_work: 0.3238 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17720 Z= 0.158 Angle : 0.608 7.793 24190 Z= 0.303 Chirality : 0.041 0.244 2750 Planarity : 0.005 0.061 2845 Dihedral : 12.346 87.883 3845 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.73 % Allowed : 6.44 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.17), residues: 1955 helix: 1.19 (0.17), residues: 795 sheet: -0.75 (0.21), residues: 440 loop : -0.09 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 446 TYR 0.012 0.002 TYR E 14 PHE 0.021 0.002 PHE B 99 TRP 0.009 0.001 TRP B 133 HIS 0.008 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00338 (17680) covalent geometry : angle 0.59304 (24080) SS BOND : bond 0.00751 ( 10) SS BOND : angle 1.65656 ( 20) hydrogen bonds : bond 0.04093 ( 845) hydrogen bonds : angle 4.81500 ( 2760) link_BETA1-4 : bond 0.00426 ( 15) link_BETA1-4 : angle 1.56103 ( 45) link_NAG-ASN : bond 0.00144 ( 15) link_NAG-ASN : angle 2.66667 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7686 (m-80) cc_final: 0.6621 (m-80) REVERT: B 188 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 237 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7190 (mt-10) REVERT: B 247 LEU cc_start: 0.6932 (mp) cc_final: 0.6702 (mm) REVERT: B 252 PHE cc_start: 0.7906 (m-80) cc_final: 0.6798 (m-80) REVERT: B 436 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 445 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6355 (m-30) REVERT: C 40 MET cc_start: 0.8486 (mtp) cc_final: 0.8277 (mtp) REVERT: D 252 PHE cc_start: 0.7549 (m-80) cc_final: 0.6493 (m-80) REVERT: D 416 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6344 (mm-30) outliers start: 13 outliers final: 9 residues processed: 211 average time/residue: 1.1460 time to fit residues: 274.8873 Evaluate side-chains 204 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.161602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.122900 restraints weight = 52873.367| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.41 r_work: 0.3206 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17720 Z= 0.225 Angle : 0.667 8.836 24190 Z= 0.336 Chirality : 0.044 0.283 2750 Planarity : 0.005 0.053 2845 Dihedral : 12.545 78.199 3845 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.73 % Allowed : 7.34 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 1955 helix: 1.13 (0.17), residues: 795 sheet: -0.88 (0.20), residues: 440 loop : -0.09 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 446 TYR 0.016 0.002 TYR E 14 PHE 0.025 0.002 PHE B 99 TRP 0.011 0.002 TRP A 66 HIS 0.012 0.002 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00489 (17680) covalent geometry : angle 0.65127 (24080) SS BOND : bond 0.00753 ( 10) SS BOND : angle 1.97945 ( 20) hydrogen bonds : bond 0.04418 ( 845) hydrogen bonds : angle 4.94124 ( 2760) link_BETA1-4 : bond 0.00313 ( 15) link_BETA1-4 : angle 1.51280 ( 45) link_NAG-ASN : bond 0.00195 ( 15) link_NAG-ASN : angle 2.87073 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7715 (m-80) cc_final: 0.6639 (m-80) REVERT: B 237 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7207 (mt-10) REVERT: B 247 LEU cc_start: 0.6983 (mp) cc_final: 0.6752 (mm) REVERT: B 252 PHE cc_start: 0.7978 (m-80) cc_final: 0.7360 (m-80) REVERT: B 436 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7652 (tm-30) REVERT: B 445 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.6365 (m-30) REVERT: D 252 PHE cc_start: 0.7632 (m-80) cc_final: 0.6508 (m-80) REVERT: D 416 GLU cc_start: 0.6709 (mm-30) cc_final: 0.6370 (mm-30) REVERT: E 237 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7932 (mt-10) outliers start: 13 outliers final: 10 residues processed: 203 average time/residue: 1.1774 time to fit residues: 268.5427 Evaluate side-chains 197 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 30 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.124904 restraints weight = 49621.087| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.36 r_work: 0.3233 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17720 Z= 0.158 Angle : 0.600 7.434 24190 Z= 0.300 Chirality : 0.041 0.249 2750 Planarity : 0.005 0.048 2845 Dihedral : 12.104 71.547 3845 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.78 % Allowed : 7.56 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 1955 helix: 1.31 (0.17), residues: 795 sheet: -0.87 (0.20), residues: 440 loop : -0.02 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 446 TYR 0.012 0.002 TYR A 273 PHE 0.027 0.002 PHE A 99 TRP 0.009 0.001 TRP C 133 HIS 0.006 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00336 (17680) covalent geometry : angle 0.58588 (24080) SS BOND : bond 0.00752 ( 10) SS BOND : angle 1.68274 ( 20) hydrogen bonds : bond 0.03995 ( 845) hydrogen bonds : angle 4.78741 ( 2760) link_BETA1-4 : bond 0.00294 ( 15) link_BETA1-4 : angle 1.36850 ( 45) link_NAG-ASN : bond 0.00155 ( 15) link_NAG-ASN : angle 2.61685 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7647 (m-80) cc_final: 0.6601 (m-80) REVERT: B 237 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7162 (mt-10) REVERT: B 247 LEU cc_start: 0.6958 (mp) cc_final: 0.6733 (mm) REVERT: B 252 PHE cc_start: 0.7947 (m-80) cc_final: 0.7345 (m-80) REVERT: B 436 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 445 ASP cc_start: 0.6506 (OUTLIER) cc_final: 0.6290 (m-30) REVERT: D 252 PHE cc_start: 0.7460 (m-80) cc_final: 0.6530 (m-80) REVERT: D 416 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6552 (mm-30) REVERT: E 237 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7913 (mt-10) outliers start: 14 outliers final: 9 residues processed: 206 average time/residue: 1.1682 time to fit residues: 271.3935 Evaluate side-chains 202 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.163555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125657 restraints weight = 51573.277| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.38 r_work: 0.3245 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17720 Z= 0.138 Angle : 0.575 6.854 24190 Z= 0.286 Chirality : 0.040 0.227 2750 Planarity : 0.004 0.047 2845 Dihedral : 11.736 65.795 3845 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.73 % Allowed : 7.84 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 1955 helix: 1.50 (0.17), residues: 795 sheet: -0.86 (0.21), residues: 440 loop : 0.07 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 446 TYR 0.011 0.001 TYR A 273 PHE 0.018 0.001 PHE A 99 TRP 0.008 0.001 TRP C 133 HIS 0.006 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00296 (17680) covalent geometry : angle 0.56102 (24080) SS BOND : bond 0.00767 ( 10) SS BOND : angle 1.55854 ( 20) hydrogen bonds : bond 0.03802 ( 845) hydrogen bonds : angle 4.64983 ( 2760) link_BETA1-4 : bond 0.00292 ( 15) link_BETA1-4 : angle 1.36367 ( 45) link_NAG-ASN : bond 0.00114 ( 15) link_NAG-ASN : angle 2.50984 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7638 (m-80) cc_final: 0.6577 (m-80) REVERT: B 247 LEU cc_start: 0.6948 (mp) cc_final: 0.6724 (mm) REVERT: B 252 PHE cc_start: 0.7911 (m-80) cc_final: 0.7272 (m-80) REVERT: B 436 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7601 (tm-30) REVERT: D 252 PHE cc_start: 0.7472 (m-80) cc_final: 0.6519 (m-80) REVERT: E 237 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7895 (mt-10) outliers start: 13 outliers final: 8 residues processed: 201 average time/residue: 1.1639 time to fit residues: 266.5032 Evaluate side-chains 197 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 189 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.163322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125661 restraints weight = 48214.046| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.34 r_work: 0.3247 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17720 Z= 0.148 Angle : 0.583 7.245 24190 Z= 0.290 Chirality : 0.041 0.232 2750 Planarity : 0.005 0.055 2845 Dihedral : 11.648 66.734 3845 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.50 % Allowed : 8.12 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 1955 helix: 1.58 (0.17), residues: 795 sheet: -0.86 (0.21), residues: 440 loop : 0.09 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 446 TYR 0.012 0.002 TYR A 273 PHE 0.020 0.001 PHE A 99 TRP 0.008 0.001 TRP C 133 HIS 0.006 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00319 (17680) covalent geometry : angle 0.56848 (24080) SS BOND : bond 0.00749 ( 10) SS BOND : angle 1.62554 ( 20) hydrogen bonds : bond 0.03819 ( 845) hydrogen bonds : angle 4.64696 ( 2760) link_BETA1-4 : bond 0.00281 ( 15) link_BETA1-4 : angle 1.33954 ( 45) link_NAG-ASN : bond 0.00137 ( 15) link_NAG-ASN : angle 2.55020 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7612 (m-80) cc_final: 0.6528 (m-80) REVERT: B 247 LEU cc_start: 0.6954 (mp) cc_final: 0.6732 (mm) REVERT: B 252 PHE cc_start: 0.7918 (m-80) cc_final: 0.7276 (m-80) REVERT: B 436 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7633 (tm-30) REVERT: D 252 PHE cc_start: 0.7565 (m-80) cc_final: 0.6542 (m-80) REVERT: D 436 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7456 (tt0) REVERT: D 450 MET cc_start: 0.7938 (ttp) cc_final: 0.5964 (mpt) REVERT: E 237 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7894 (mt-10) outliers start: 9 outliers final: 8 residues processed: 196 average time/residue: 1.1548 time to fit residues: 256.1981 Evaluate side-chains 198 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 152 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 172 optimal weight: 0.2980 chunk 164 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.164461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127054 restraints weight = 49608.727| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.36 r_work: 0.3266 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17720 Z= 0.122 Angle : 0.552 6.350 24190 Z= 0.273 Chirality : 0.040 0.219 2750 Planarity : 0.004 0.050 2845 Dihedral : 11.205 67.199 3845 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.45 % Allowed : 8.29 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.18), residues: 1955 helix: 1.72 (0.17), residues: 795 sheet: -0.80 (0.21), residues: 440 loop : 0.15 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 446 TYR 0.011 0.001 TYR A 273 PHE 0.013 0.001 PHE B 99 TRP 0.008 0.001 TRP C 133 HIS 0.004 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00258 (17680) covalent geometry : angle 0.53870 (24080) SS BOND : bond 0.00768 ( 10) SS BOND : angle 1.45747 ( 20) hydrogen bonds : bond 0.03588 ( 845) hydrogen bonds : angle 4.50851 ( 2760) link_BETA1-4 : bond 0.00288 ( 15) link_BETA1-4 : angle 1.32032 ( 45) link_NAG-ASN : bond 0.00098 ( 15) link_NAG-ASN : angle 2.37402 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7541 (m-80) cc_final: 0.6428 (m-80) REVERT: B 247 LEU cc_start: 0.6933 (mp) cc_final: 0.6713 (mm) REVERT: B 252 PHE cc_start: 0.7899 (m-80) cc_final: 0.7245 (m-80) REVERT: B 436 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7630 (tm-30) REVERT: D 252 PHE cc_start: 0.7577 (m-80) cc_final: 0.6525 (m-80) REVERT: D 436 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7416 (tt0) REVERT: D 450 MET cc_start: 0.7968 (ttp) cc_final: 0.5981 (mpt) outliers start: 8 outliers final: 6 residues processed: 204 average time/residue: 1.1867 time to fit residues: 274.9235 Evaluate side-chains 196 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.162420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.124559 restraints weight = 52446.184| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.44 r_work: 0.3213 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17720 Z= 0.190 Angle : 0.625 8.181 24190 Z= 0.313 Chirality : 0.042 0.258 2750 Planarity : 0.005 0.065 2845 Dihedral : 11.677 71.308 3845 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.39 % Allowed : 8.80 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 1955 helix: 1.61 (0.17), residues: 795 sheet: -0.85 (0.21), residues: 440 loop : 0.02 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 446 TYR 0.014 0.002 TYR A 273 PHE 0.023 0.002 PHE A 99 TRP 0.009 0.002 TRP A 66 HIS 0.007 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00417 (17680) covalent geometry : angle 0.61023 (24080) SS BOND : bond 0.00743 ( 10) SS BOND : angle 1.85921 ( 20) hydrogen bonds : bond 0.04012 ( 845) hydrogen bonds : angle 4.73933 ( 2760) link_BETA1-4 : bond 0.00282 ( 15) link_BETA1-4 : angle 1.40372 ( 45) link_NAG-ASN : bond 0.00201 ( 15) link_NAG-ASN : angle 2.67209 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7614 (m-80) cc_final: 0.6502 (m-80) REVERT: B 247 LEU cc_start: 0.6940 (mp) cc_final: 0.6717 (mm) REVERT: B 252 PHE cc_start: 0.7892 (m-80) cc_final: 0.7295 (m-80) REVERT: B 436 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7619 (tm-30) REVERT: D 252 PHE cc_start: 0.7586 (m-80) cc_final: 0.7116 (m-80) REVERT: D 436 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7478 (tt0) REVERT: D 450 MET cc_start: 0.8016 (ttp) cc_final: 0.5966 (mpt) REVERT: E 450 MET cc_start: 0.8174 (ttm) cc_final: 0.6087 (mpt) outliers start: 7 outliers final: 6 residues processed: 196 average time/residue: 1.2001 time to fit residues: 265.2356 Evaluate side-chains 197 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 13 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.164150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126446 restraints weight = 51206.110| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.37 r_work: 0.3264 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17720 Z= 0.122 Angle : 0.562 6.268 24190 Z= 0.278 Chirality : 0.040 0.217 2750 Planarity : 0.005 0.094 2845 Dihedral : 11.230 72.628 3845 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.34 % Allowed : 8.91 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 1955 helix: 1.74 (0.17), residues: 795 sheet: -0.84 (0.21), residues: 440 loop : 0.13 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 446 TYR 0.011 0.001 TYR A 273 PHE 0.016 0.001 PHE B 99 TRP 0.008 0.001 TRP B 133 HIS 0.005 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00260 (17680) covalent geometry : angle 0.54879 (24080) SS BOND : bond 0.00763 ( 10) SS BOND : angle 1.48941 ( 20) hydrogen bonds : bond 0.03610 ( 845) hydrogen bonds : angle 4.55147 ( 2760) link_BETA1-4 : bond 0.00271 ( 15) link_BETA1-4 : angle 1.32299 ( 45) link_NAG-ASN : bond 0.00119 ( 15) link_NAG-ASN : angle 2.36653 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12434.79 seconds wall clock time: 210 minutes 34.79 seconds (12634.79 seconds total)