Starting phenix.real_space_refine on Mon Jul 6 09:19:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v80_43012/07_2026/8v80_43012_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v80_43012/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v80_43012/07_2026/8v80_43012_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v80_43012/07_2026/8v80_43012_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v80_43012/07_2026/8v80_43012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v80_43012/07_2026/8v80_43012.map" } 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-dev-6108/lib/python3.11/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, 182 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 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, 225 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3, 'YLR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 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, 182 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 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, 182 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 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, 139 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'YLR': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 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: 10.13, per 1000 atoms: 0.31 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: 2.97 Conformation dependent library (CDL) restraints added in 1.5 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: 0.79 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: 8.08 Time building geometry restraints manager: 4.03 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: 1.150 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: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 36.370 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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/Z covalent geometry : bond 0.00734 / 0.36 (17680) covalent geometry : angle 1.03622 / 0.52 (24080) SS BOND : bond 0.00758 / 0.41 ( 10) SS BOND : angle 2.02057 / 1.19 ( 20) hydrogen bonds : bond 0.19651 / 12.80 ( 845) hydrogen bonds : angle 7.76142 / 5.34 ( 2760) link_BETA1-4 : bond 0.00744 / 0.44 ( 15) link_BETA1-4 : angle 2.26854 / 1.52 ( 45) link_NAG-ASN : bond 0.00655 / 0.39 ( 15) link_NAG-ASN : angle 1.88202 / 1.21 ( 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 : 0.882 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: 1.0218 time to fit residues: 273.8527 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 : 0.904 ------------------------------------------------------------------------------- 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... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.164783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.127671 restraints weight = 54367.326| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.39 r_work: 0.3277 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17720 Z= 0.145 Angle : 0.662 7.316 24190 Z= 0.329 Chirality : 0.042 0.188 2750 Planarity : 0.005 0.066 2845 Dihedral : 16.287 125.017 3845 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.56 % Allowed : 4.48 % 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: -0.41 (0.17), residues: 1955 helix: 0.36 (0.17), residues: 805 sheet: -0.85 (0.20), residues: 440 loop : -0.37 (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 307 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (17680) covalent geometry : angle 0.64667 / 0.33 (24080) SS BOND : bond 0.00793 / 0.43 ( 10) SS BOND : angle 1.60280 / 0.92 ( 20) hydrogen bonds : bond 0.04795 / 3.19 ( 845) hydrogen bonds : angle 5.31929 / 3.66 ( 2760) link_BETA1-4 : bond 0.00387 / 0.25 ( 15) link_BETA1-4 : angle 2.00198 / 1.38 ( 45) link_NAG-ASN : bond 0.00174 / 0.10 ( 15) link_NAG-ASN : angle 2.60629 / 1.73 ( 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 226 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 216 time to evaluate : 0.922 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: 0.7744 (m-80) cc_final: 0.6845 (m-80) REVERT: B 252 PHE cc_start: 0.7788 (m-80) cc_final: 0.6820 (m-80) REVERT: C 40 MET cc_start: 0.8619 (mtp) cc_final: 0.8316 (mtp) REVERT: C 252 PHE cc_start: 0.7084 (m-80) cc_final: 0.6879 (m-80) REVERT: D 252 PHE cc_start: 0.7405 (m-80) cc_final: 0.6465 (m-80) REVERT: D 416 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6627 (tp30) REVERT: D 436 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7265 (tt0) REVERT: E 274 PHE cc_start: 0.8239 (m-10) cc_final: 0.8030 (m-10) outliers start: 10 outliers final: 6 residues processed: 223 average time/residue: 1.1008 time to fit residues: 281.1492 Evaluate side-chains 205 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 140 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 119 optimal weight: 0.0030 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3845 r_free = 0.3845 target = 0.163471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125385 restraints weight = 53131.536| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.39 r_work: 0.3237 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- 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 = 0.40 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1755 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= 0.161 Angle : 0.637 7.817 24190 Z= 0.314 Chirality : 0.042 0.263 2750 Planarity : 0.005 0.082 2845 Dihedral : 13.127 99.242 3845 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.56 % Allowed : 5.71 % Favored : 93.73 % 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: 0.13 (0.17), residues: 1955 helix: 0.98 (0.17), residues: 800 sheet: -0.78 (0.20), residues: 440 loop : -0.17 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 446 TYR 0.014 0.002 TYR E 14 PHE 0.021 0.002 PHE B 99 TRP 0.010 0.001 TRP B 133 HIS 0.008 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (17680) covalent geometry : angle 0.62105 / 0.31 (24080) SS BOND : bond 0.00760 / 0.41 ( 10) SS BOND : angle 1.62610 / 0.94 ( 20) hydrogen bonds : bond 0.04335 / 2.89 ( 845) hydrogen bonds : angle 4.91865 / 3.39 ( 2760) link_BETA1-4 : bond 0.00529 / 0.33 ( 15) link_BETA1-4 : angle 1.77852 / 1.16 ( 45) link_NAG-ASN : bond 0.00124 / 0.06 ( 15) link_NAG-ASN : angle 2.70821 / 1.81 ( 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 : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7711 (m-80) cc_final: 0.6636 (m-80) REVERT: B 252 PHE cc_start: 0.7948 (m-80) cc_final: 0.6843 (m-80) REVERT: C 40 MET cc_start: 0.8526 (mtp) cc_final: 0.8307 (mtp) REVERT: C 304 MET cc_start: 0.7739 (ttm) cc_final: 0.7474 (ttt) REVERT: C 416 GLU cc_start: 0.6657 (mm-30) cc_final: 0.6411 (mm-30) REVERT: D 252 PHE cc_start: 0.7425 (m-80) cc_final: 0.6352 (m-80) REVERT: D 416 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6365 (mm-30) outliers start: 10 outliers final: 5 residues processed: 210 average time/residue: 1.1375 time to fit residues: 272.4741 Evaluate side-chains 200 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 195 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 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 = 0.3857 r_free = 0.3857 target = 0.164741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127334 restraints weight = 50601.340| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.36 r_work: 0.3268 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1946 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= 0.119 Angle : 0.565 7.205 24190 Z= 0.279 Chirality : 0.040 0.223 2750 Planarity : 0.004 0.060 2845 Dihedral : 11.989 85.870 3845 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.62 % Allowed : 6.78 % Favored : 92.61 % 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: 0.39 (0.17), residues: 1955 helix: 1.26 (0.17), residues: 795 sheet: -0.79 (0.21), residues: 440 loop : 0.00 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 446 TYR 0.012 0.001 TYR A 273 PHE 0.020 0.001 PHE E 99 TRP 0.007 0.001 TRP B 133 HIS 0.007 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (17680) covalent geometry : angle 0.54983 / 0.28 (24080) SS BOND : bond 0.00755 / 0.41 ( 10) SS BOND : angle 1.46190 / 0.85 ( 20) hydrogen bonds : bond 0.03832 / 2.55 ( 845) hydrogen bonds : angle 4.69029 / 3.24 ( 2760) link_BETA1-4 : bond 0.00380 / 0.23 ( 15) link_BETA1-4 : angle 1.55287 / 1.07 ( 45) link_NAG-ASN : bond 0.00104 / 0.06 ( 15) link_NAG-ASN : angle 2.48844 / 1.66 ( 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: 11 poor density : 206 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7644 (m-80) cc_final: 0.6602 (m-80) REVERT: B 237 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7493 (mt-10) REVERT: B 252 PHE cc_start: 0.7898 (m-80) cc_final: 0.7291 (m-80) REVERT: B 439 PHE cc_start: 0.8080 (t80) cc_final: 0.7861 (t80) REVERT: C 40 MET cc_start: 0.8481 (mtp) cc_final: 0.8247 (mtp) REVERT: C 304 MET cc_start: 0.7859 (ttm) cc_final: 0.7614 (ttt) REVERT: D 252 PHE cc_start: 0.7462 (m-80) cc_final: 0.6428 (m-80) REVERT: D 416 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6338 (mm-30) outliers start: 11 outliers final: 8 residues processed: 213 average time/residue: 1.1782 time to fit residues: 288.5098 Evaluate side-chains 204 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 159 MET Chi-restraints excluded: chain C residue 276 SER 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: 0.7980 chunk 89 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 169 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 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 = 0.3846 r_free = 0.3846 target = 0.163641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.125392 restraints weight = 53120.137| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.41 r_work: 0.3240 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2046 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= 0.147 Angle : 0.584 7.504 24190 Z= 0.290 Chirality : 0.041 0.235 2750 Planarity : 0.005 0.045 2845 Dihedral : 11.798 75.411 3845 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.73 % Allowed : 7.28 % Favored : 91.99 % 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: 0.50 (0.18), residues: 1955 helix: 1.39 (0.17), residues: 795 sheet: -0.80 (0.21), residues: 440 loop : 0.07 (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 0.017 0.001 PHE B 99 TRP 0.008 0.001 TRP B 133 HIS 0.007 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (17680) covalent geometry : angle 0.57014 / 0.29 (24080) SS BOND : bond 0.00738 / 0.40 ( 10) SS BOND : angle 1.62530 / 0.95 ( 20) hydrogen bonds : bond 0.03918 / 2.61 ( 845) hydrogen bonds : angle 4.66977 / 3.22 ( 2760) link_BETA1-4 : bond 0.00338 / 0.21 ( 15) link_BETA1-4 : angle 1.38165 / 0.93 ( 45) link_NAG-ASN : bond 0.00122 / 0.06 ( 15) link_NAG-ASN : angle 2.57253 / 1.71 ( 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 213 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7626 (m-80) cc_final: 0.6578 (m-80) REVERT: B 252 PHE cc_start: 0.7919 (m-80) cc_final: 0.7301 (m-80) REVERT: C 304 MET cc_start: 0.7864 (ttm) cc_final: 0.7617 (ttt) REVERT: D 252 PHE cc_start: 0.7479 (m-80) cc_final: 0.6474 (m-80) REVERT: D 416 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6329 (mm-30) outliers start: 13 outliers final: 8 residues processed: 207 average time/residue: 1.1685 time to fit residues: 276.4288 Evaluate side-chains 200 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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=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: 4.9990 chunk 180 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 170 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3838 r_free = 0.3838 target = 0.162875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124813 restraints weight = 49606.883| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.35 r_work: 0.3232 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17720 Z= 0.172 Angle : 0.607 7.942 24190 Z= 0.303 Chirality : 0.041 0.250 2750 Planarity : 0.005 0.063 2845 Dihedral : 11.874 68.698 3845 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.62 % Allowed : 7.62 % Favored : 91.76 % 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: 0.49 (0.17), residues: 1955 helix: 1.40 (0.17), residues: 795 sheet: -0.82 (0.20), residues: 440 loop : 0.05 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 446 TYR 0.014 0.002 TYR A 273 PHE 0.020 0.002 PHE B 99 TRP 0.008 0.001 TRP A 66 HIS 0.008 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (17680) covalent geometry : angle 0.59244 / 0.30 (24080) SS BOND : bond 0.00736 / 0.40 ( 10) SS BOND : angle 1.78126 / 1.04 ( 20) hydrogen bonds : bond 0.04009 / 2.67 ( 845) hydrogen bonds : angle 4.73316 / 3.26 ( 2760) link_BETA1-4 : bond 0.00295 / 0.19 ( 15) link_BETA1-4 : angle 1.36682 / 0.92 ( 45) link_NAG-ASN : bond 0.00170 / 0.08 ( 15) link_NAG-ASN : angle 2.63706 / 1.76 ( 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 207 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7665 (m-80) cc_final: 0.6603 (m-80) REVERT: B 252 PHE cc_start: 0.7960 (m-80) cc_final: 0.7334 (m-80) REVERT: C 304 MET cc_start: 0.7917 (ttm) cc_final: 0.7669 (ttt) REVERT: D 252 PHE cc_start: 0.7501 (m-80) cc_final: 0.6490 (m-80) REVERT: D 416 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6530 (mm-30) outliers start: 11 outliers final: 8 residues processed: 202 average time/residue: 1.1293 time to fit residues: 259.7085 Evaluate side-chains 202 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3839 r_free = 0.3839 target = 0.163037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124752 restraints weight = 51405.058| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.38 r_work: 0.3231 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 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 = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17720 Z= 0.166 Angle : 0.600 7.744 24190 Z= 0.300 Chirality : 0.041 0.245 2750 Planarity : 0.005 0.047 2845 Dihedral : 11.808 68.415 3845 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: 0.54 (0.17), residues: 1955 helix: 1.48 (0.17), residues: 795 sheet: -0.83 (0.21), residues: 440 loop : 0.06 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 446 TYR 0.012 0.002 TYR A 273 PHE 0.021 0.002 PHE A 99 TRP 0.008 0.001 TRP D 148 HIS 0.007 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (17680) covalent geometry : angle 0.58559 / 0.30 (24080) SS BOND : bond 0.00744 / 0.41 ( 10) SS BOND : angle 1.74553 / 1.02 ( 20) hydrogen bonds : bond 0.03953 / 2.63 ( 845) hydrogen bonds : angle 4.70835 / 3.24 ( 2760) link_BETA1-4 : bond 0.00286 / 0.18 ( 15) link_BETA1-4 : angle 1.36778 / 0.91 ( 45) link_NAG-ASN : bond 0.00158 / 0.08 ( 15) link_NAG-ASN : angle 2.60667 / 1.74 ( 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 209 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7653 (m-80) cc_final: 0.6581 (m-80) REVERT: B 252 PHE cc_start: 0.7957 (m-80) cc_final: 0.7318 (m-80) REVERT: C 304 MET cc_start: 0.7904 (ttm) cc_final: 0.7652 (ttt) REVERT: D 252 PHE cc_start: 0.7608 (m-80) cc_final: 0.6564 (m-80) REVERT: D 436 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7544 (tt0) REVERT: E 304 MET cc_start: 0.7328 (ttp) cc_final: 0.6731 (ttp) outliers start: 13 outliers final: 8 residues processed: 204 average time/residue: 1.1991 time to fit residues: 280.1033 Evaluate side-chains 203 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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: 0.5980 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 86 optimal weight: 0.1980 chunk 98 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3857 r_free = 0.3857 target = 0.164735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127435 restraints weight = 48351.742| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.33 r_work: 0.3271 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- 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 = 0.39 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17720 Z= 0.113 Angle : 0.549 6.650 24190 Z= 0.272 Chirality : 0.040 0.215 2750 Planarity : 0.004 0.091 2845 Dihedral : 11.379 62.839 3845 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.50 % Allowed : 8.01 % Favored : 91.48 % 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: 0.73 (0.18), residues: 1955 helix: 1.67 (0.17), residues: 795 sheet: -0.78 (0.21), residues: 440 loop : 0.15 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 446 TYR 0.011 0.001 TYR A 273 PHE 0.018 0.001 PHE B 99 TRP 0.008 0.001 TRP C 133 HIS 0.005 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (17680) covalent geometry : angle 0.53667 / 0.27 (24080) SS BOND : bond 0.00761 / 0.42 ( 10) SS BOND : angle 1.43739 / 0.85 ( 20) hydrogen bonds : bond 0.03613 / 2.40 ( 845) hydrogen bonds : angle 4.54081 / 3.13 ( 2760) link_BETA1-4 : bond 0.00289 / 0.18 ( 15) link_BETA1-4 : angle 1.31353 / 0.88 ( 45) link_NAG-ASN : bond 0.00100 / 0.05 ( 15) link_NAG-ASN : angle 2.34121 / 1.56 ( 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 208 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7552 (m-80) cc_final: 0.6466 (m-80) REVERT: B 203 MET cc_start: 0.8569 (ptm) cc_final: 0.8341 (ptm) REVERT: B 252 PHE cc_start: 0.7900 (m-80) cc_final: 0.7250 (m-80) REVERT: C 304 MET cc_start: 0.7915 (ttm) cc_final: 0.7669 (ttm) REVERT: D 237 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7746 (mt-10) REVERT: D 252 PHE cc_start: 0.7574 (m-80) cc_final: 0.6551 (m-80) REVERT: D 436 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7529 (tt0) REVERT: E 304 MET cc_start: 0.7424 (ttp) cc_final: 0.6723 (ttp) outliers start: 9 outliers final: 7 residues processed: 205 average time/residue: 1.0927 time to fit residues: 256.2974 Evaluate side-chains 202 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 195 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 187 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 148 optimal weight: 0.2980 chunk 183 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3853 r_free = 0.3853 target = 0.164320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127548 restraints weight = 49463.205| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.41 r_work: 0.3248 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- 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 = 0.39 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2315 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= 0.130 Angle : 0.564 6.836 24190 Z= 0.279 Chirality : 0.040 0.223 2750 Planarity : 0.005 0.089 2845 Dihedral : 11.301 63.552 3845 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.56 % Allowed : 8.40 % Favored : 91.04 % 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: 1.71 (0.17), residues: 795 sheet: -0.78 (0.21), residues: 440 loop : 0.16 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 446 TYR 0.012 0.001 TYR A 273 PHE 0.022 0.001 PHE B 99 TRP 0.007 0.001 TRP C 133 HIS 0.005 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (17680) covalent geometry : angle 0.55067 / 0.28 (24080) SS BOND : bond 0.00753 / 0.41 ( 10) SS BOND : angle 1.53192 / 0.90 ( 20) hydrogen bonds : bond 0.03667 / 2.45 ( 845) hydrogen bonds : angle 4.53353 / 3.12 ( 2760) link_BETA1-4 : bond 0.00280 / 0.18 ( 15) link_BETA1-4 : angle 1.31482 / 0.88 ( 45) link_NAG-ASN : bond 0.00105 / 0.05 ( 15) link_NAG-ASN : angle 2.45430 / 1.64 ( 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 204 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7545 (m-80) cc_final: 0.6438 (m-80) REVERT: B 252 PHE cc_start: 0.7833 (m-80) cc_final: 0.7227 (m-80) REVERT: C 304 MET cc_start: 0.7888 (ttm) cc_final: 0.7645 (ttm) REVERT: D 237 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7836 (mt-10) REVERT: D 252 PHE cc_start: 0.7552 (m-80) cc_final: 0.6489 (m-80) REVERT: D 436 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7534 (tt0) REVERT: E 304 MET cc_start: 0.7466 (ttp) cc_final: 0.6849 (ttp) REVERT: E 450 MET cc_start: 0.8129 (ttm) cc_final: 0.6027 (mpt) outliers start: 10 outliers final: 7 residues processed: 199 average time/residue: 1.1321 time to fit residues: 256.5901 Evaluate side-chains 197 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 190 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 159 MET Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 276 SER 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: 0.9990 chunk 65 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.164496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126495 restraints weight = 52673.077| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.39 r_work: 0.3259 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17720 Z= 0.129 Angle : 0.559 6.712 24190 Z= 0.277 Chirality : 0.040 0.223 2750 Planarity : 0.005 0.093 2845 Dihedral : 11.124 64.511 3845 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.39 % Allowed : 8.57 % Favored : 91.04 % 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: 0.81 (0.18), residues: 1955 helix: 1.78 (0.17), residues: 795 sheet: -0.79 (0.21), residues: 440 loop : 0.16 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 446 TYR 0.011 0.001 TYR A 273 PHE 0.021 0.001 PHE B 99 TRP 0.007 0.001 TRP A 148 HIS 0.005 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (17680) covalent geometry : angle 0.54551 / 0.27 (24080) SS BOND : bond 0.00754 / 0.41 ( 10) SS BOND : angle 1.53967 / 0.91 ( 20) hydrogen bonds : bond 0.03618 / 2.41 ( 845) hydrogen bonds : angle 4.50431 / 3.10 ( 2760) link_BETA1-4 : bond 0.00271 / 0.17 ( 15) link_BETA1-4 : angle 1.29327 / 0.87 ( 45) link_NAG-ASN : bond 0.00124 / 0.07 ( 15) link_NAG-ASN : angle 2.41190 / 1.61 ( 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 203 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 196 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.7550 (m-80) cc_final: 0.6437 (m-80) REVERT: B 252 PHE cc_start: 0.7811 (m-80) cc_final: 0.7198 (m-80) REVERT: C 304 MET cc_start: 0.7938 (ttm) cc_final: 0.7691 (ttm) REVERT: D 237 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7788 (mt-10) REVERT: D 252 PHE cc_start: 0.7581 (m-80) cc_final: 0.6519 (m-80) REVERT: D 436 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7531 (tt0) REVERT: E 304 MET cc_start: 0.7491 (ttp) cc_final: 0.6780 (ttp) REVERT: E 450 MET cc_start: 0.8129 (ttm) cc_final: 0.6027 (mpt) outliers start: 7 outliers final: 6 residues processed: 201 average time/residue: 1.1015 time to fit residues: 253.4727 Evaluate side-chains 198 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 159 MET Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain E residue 276 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 13 optimal weight: 0.1980 chunk 89 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 55 optimal weight: 0.0170 chunk 135 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 108 optimal weight: 0.0020 overall best weight: 0.2826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN D 116 GLN E 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.166746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129837 restraints weight = 51559.742| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.36 r_work: 0.3308 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17720 Z= 0.095 Angle : 0.521 6.535 24190 Z= 0.256 Chirality : 0.039 0.202 2750 Planarity : 0.004 0.090 2845 Dihedral : 10.546 65.888 3845 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.17 % Allowed : 9.02 % 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: 1.00 (0.18), residues: 1955 helix: 1.92 (0.17), residues: 795 sheet: -0.60 (0.22), residues: 450 loop : 0.26 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 446 TYR 0.010 0.001 TYR A 117 PHE 0.011 0.001 PHE D 274 TRP 0.008 0.001 TRP C 133 HIS 0.003 0.000 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (17680) covalent geometry : angle 0.50901 / 0.25 (24080) SS BOND : bond 0.00786 / 0.43 ( 10) SS BOND : angle 1.25572 / 0.75 ( 20) hydrogen bonds : bond 0.03325 / 2.22 ( 845) hydrogen bonds : angle 4.31066 / 2.96 ( 2760) link_BETA1-4 : bond 0.00289 / 0.18 ( 15) link_BETA1-4 : angle 1.25219 / 0.85 ( 45) link_NAG-ASN : bond 0.00091 / 0.05 ( 15) link_NAG-ASN : angle 2.20807 / 1.47 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12343.50 seconds wall clock time: 209 minutes 23.60 seconds (12563.60 seconds total)