Starting phenix.real_space_refine on Sun Jun 29 09:48:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v86_43025/06_2025/8v86_43025_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v86_43025/06_2025/8v86_43025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v86_43025/06_2025/8v86_43025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v86_43025/06_2025/8v86_43025.map" model { file = "/net/cci-nas-00/data/ceres_data/8v86_43025/06_2025/8v86_43025_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v86_43025/06_2025/8v86_43025_trim.cif" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 7 Type Number sf(0) Gaussians Br 5 7.06 5 P 10 5.49 5 S 120 5.16 5 C 11255 2.51 5 N 2625 2.21 5 O 3170 1.98 5 H 15835 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33020 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: 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 27.09, per 1000 atoms: 0.82 Number of scatterers: 33020 At special positions: 0 Unit cell: (102.505, 100.347, 166.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 5 34.99 S 120 16.00 P 10 15.00 O 3170 8.00 N 2625 7.00 C 11255 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 G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 503 " - " ASN A 67 " " NAG B 505 " - " ASN B 67 " " NAG C 505 " - " ASN C 67 " " NAG D 505 " - " ASN D 67 " " NAG E 505 " - " ASN E 67 " " NAG F 1 " - " ASN A 23 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN B 23 " " NAG I 1 " - " ASN B 110 " " NAG J 1 " - " ASN C 23 " " NAG K 1 " - " ASN C 110 " " NAG L 1 " - " ASN D 23 " " NAG M 1 " - " ASN D 110 " " NAG N 1 " - " ASN E 23 " " NAG O 1 " - " ASN E 110 " Time building additional restraints: 8.65 Conformation dependent library (CDL) restraints added in 4.2 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 45.0% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.649A 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 227 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.824A pdb=" N LEU A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (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 Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.649A 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 227 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.824A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE B 259 " --> pdb=" O LEU B 255 " (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 Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.648A 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 227 Processing helix chain 'C' and resid 228 through 231 Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.824A pdb=" N LEU C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE C 259 " --> pdb=" O LEU C 255 " (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 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.648A 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 227 Processing helix chain 'D' and resid 228 through 231 Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.824A pdb=" N LEU D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE D 259 " --> pdb=" O LEU D 255 " (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 Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.648A 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 227 Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 232 through 236 Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.825A pdb=" N LEU E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE E 259 " --> pdb=" O LEU E 255 " (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 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.157A 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: 4.157A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.843A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.619A 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: 4.843A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.158A 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: 4.158A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.843A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.619A 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: 4.843A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.157A 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: 4.157A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 48 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP C 41 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR C 60 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 29 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.843A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.619A 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: 4.843A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.157A 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: 4.157A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP D 41 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR D 60 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR D 29 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.843A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.619A 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: 4.843A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.158A 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: 4.158A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 48 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP E 41 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR E 60 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR E 29 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.843A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.619A 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: 4.843A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2898 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: 14.80 Time building geometry restraints manager: 10.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 15800 1.05 - 1.26: 2605 1.26 - 1.47: 7194 1.47 - 1.69: 7661 1.69 - 1.90: 180 Bond restraints: 33440 Sorted by residual: bond pdb=" NZ LYS C 5 " pdb=" HZ2 LYS C 5 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS D 191 " pdb=" HZ3 LYS D 191 " 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 323 " pdb=" HZ3 LYS C 323 " 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 B 238 " pdb=" HZ1 LYS B 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 306 " pdb=" HZ2 LYS C 306 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 33435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 55504 2.39 - 4.78: 4241 4.78 - 7.17: 195 7.17 - 9.56: 15 9.56 - 11.95: 10 Bond angle restraints: 59965 Sorted by residual: angle pdb=" C12 POV A 505 " pdb=" C11 POV A 505 " pdb=" O12 POV A 505 " ideal model delta sigma weight residual 112.84 100.89 11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C12 POV E 502 " pdb=" C11 POV E 502 " pdb=" O12 POV E 502 " ideal model delta sigma weight residual 112.84 100.89 11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C12 POV D 502 " pdb=" C11 POV D 502 " pdb=" O12 POV D 502 " ideal model delta sigma weight residual 112.84 100.90 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C12 POV B 502 " pdb=" C11 POV B 502 " pdb=" O12 POV B 502 " ideal model delta sigma weight residual 112.84 100.92 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C12 POV C 502 " pdb=" C11 POV C 502 " pdb=" O12 POV C 502 " ideal model delta sigma weight residual 112.84 100.97 11.87 3.00e+00 1.11e-01 1.57e+01 ... (remaining 59960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.48: 16262 31.48 - 62.96: 488 62.96 - 94.44: 105 94.44 - 125.92: 30 125.92 - 157.40: 10 Dihedral angle restraints: 16895 sinusoidal: 9720 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 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+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 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N CYS A 190 " pdb=" CA CYS A 190 " ideal model delta harmonic sigma weight residual -180.00 -153.65 -26.35 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 16892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2118 0.054 - 0.107: 519 0.107 - 0.161: 78 0.161 - 0.214: 15 0.214 - 0.268: 5 Chirality restraints: 2735 Sorted by residual: 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 -2.29 -0.11 2.00e-02 2.50e+03 3.18e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.13e+01 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 -2.29 -0.11 2.00e-02 2.50e+03 3.05e+01 ... (remaining 2732 not shown) Planarity restraints: 4725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.266 2.00e-02 2.50e+03 2.29e-01 6.54e+02 pdb=" C7 NAG J 2 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " -0.014 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.388 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " 0.266 2.00e-02 2.50e+03 2.29e-01 6.54e+02 pdb=" C7 NAG L 2 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.014 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " -0.388 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.266 2.00e-02 2.50e+03 2.29e-01 6.54e+02 pdb=" C7 NAG F 2 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.014 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.388 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.193 2.00e-02 2.50e+03 ... (remaining 4722 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.11: 628 2.11 - 2.76: 59498 2.76 - 3.40: 96150 3.40 - 4.05: 137337 4.05 - 4.70: 214124 Nonbonded interactions: 507737 Sorted by model distance: nonbonded pdb="HD21 LEU E 214 " pdb="HD11 ILE E 259 " model vdw 1.458 2.440 nonbonded pdb="HD21 LEU B 214 " pdb="HD11 ILE B 259 " model vdw 1.459 2.440 nonbonded pdb="HD21 LEU C 214 " pdb="HD11 ILE C 259 " model vdw 1.459 2.440 nonbonded pdb="HD21 LEU D 214 " pdb="HD11 ILE D 259 " model vdw 1.459 2.440 nonbonded pdb="HD21 LEU A 214 " pdb="HD11 ILE A 259 " model vdw 1.460 2.440 ... (remaining 507732 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: 0.04 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: 1.180 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: 0.550 Extract box with map and model: 1.130 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 85.730 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.200 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:28.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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 : 0.006 0.066 17640 Z= 0.345 Angle : 0.896 11.954 24065 Z= 0.447 Chirality : 0.048 0.268 2735 Planarity : 0.012 0.229 2845 Dihedral : 18.070 157.396 7520 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 1955 helix: -0.73 (0.16), residues: 790 sheet: -0.64 (0.23), residues: 420 loop : -0.39 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 54 HIS 0.003 0.001 HIS B 296 PHE 0.019 0.002 PHE B 99 TYR 0.018 0.002 TYR C 117 ARG 0.004 0.001 ARG E 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 15) link_NAG-ASN : angle 4.42858 ( 45) link_BETA1-4 : bond 0.00505 ( 15) link_BETA1-4 : angle 2.56562 ( 45) hydrogen bonds : bond 0.18148 ( 891) hydrogen bonds : angle 7.21074 ( 2898) SS BOND : bond 0.00634 ( 10) SS BOND : angle 1.30479 ( 20) covalent geometry : bond 0.00650 (17600) covalent geometry : angle 0.86952 (23955) *********************** 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 243 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7283 (mt-10) REVERT: B 322 MET cc_start: 0.8770 (mtp) cc_final: 0.8535 (mtp) REVERT: C 46 ASN cc_start: 0.8060 (m110) cc_final: 0.7587 (m110) REVERT: C 97 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6874 (mt-10) REVERT: C 234 ASP cc_start: 0.7982 (m-30) cc_final: 0.7567 (m-30) REVERT: D 322 MET cc_start: 0.8624 (mtp) cc_final: 0.8258 (mtp) REVERT: E 46 ASN cc_start: 0.8173 (m110) cc_final: 0.7717 (m110) outliers start: 0 outliers final: 1 residues processed: 243 average time/residue: 2.7614 time to fit residues: 753.1172 Evaluate side-chains 207 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 296 HIS C 296 HIS D 296 HIS E 296 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.093357 restraints weight = 42541.746| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.63 r_work: 0.2818 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17640 Z= 0.148 Angle : 0.627 6.982 24065 Z= 0.313 Chirality : 0.041 0.147 2735 Planarity : 0.004 0.034 2845 Dihedral : 16.303 147.823 3757 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.62 % Allowed : 6.33 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 1955 helix: 1.06 (0.17), residues: 790 sheet: -0.01 (0.23), residues: 435 loop : -0.06 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 315 HIS 0.002 0.001 HIS C 104 PHE 0.025 0.001 PHE B 99 TYR 0.014 0.001 TYR B 117 ARG 0.003 0.001 ARG B 446 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 15) link_NAG-ASN : angle 2.65335 ( 45) link_BETA1-4 : bond 0.00308 ( 15) link_BETA1-4 : angle 1.70310 ( 45) hydrogen bonds : bond 0.06707 ( 891) hydrogen bonds : angle 5.28451 ( 2898) SS BOND : bond 0.00711 ( 10) SS BOND : angle 1.29259 ( 20) covalent geometry : bond 0.00312 (17600) covalent geometry : angle 0.61179 (23955) *********************** 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 236 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 225 time to evaluate : 6.093 Fit side-chains revert: symmetry clash REVERT: A 40 MET cc_start: 0.8679 (mmm) cc_final: 0.8382 (mtp) REVERT: A 429 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7737 (mt-10) REVERT: B 309 ARG cc_start: 0.8466 (ttm110) cc_final: 0.8194 (ttp-170) REVERT: B 322 MET cc_start: 0.8778 (mtp) cc_final: 0.8340 (mtp) REVERT: C 46 ASN cc_start: 0.8425 (m110) cc_final: 0.7966 (m110) REVERT: C 234 ASP cc_start: 0.8506 (m-30) cc_final: 0.8098 (m-30) REVERT: C 258 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7114 (mm-30) REVERT: C 260 MET cc_start: 0.7491 (mmm) cc_final: 0.7249 (mtp) REVERT: D 191 LYS cc_start: 0.8221 (tptt) cc_final: 0.7757 (mmpt) REVERT: D 322 MET cc_start: 0.8778 (mtp) cc_final: 0.8446 (mtp) REVERT: D 415 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: E 46 ASN cc_start: 0.8546 (m110) cc_final: 0.8125 (m110) outliers start: 11 outliers final: 5 residues processed: 233 average time/residue: 3.2371 time to fit residues: 856.3594 Evaluate side-chains 216 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 210 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain D residue 415 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 84 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN D 213 ASN D 293 GLN E 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.090151 restraints weight = 47341.660| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.73 r_work: 0.2761 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17640 Z= 0.222 Angle : 0.637 5.329 24065 Z= 0.325 Chirality : 0.043 0.148 2735 Planarity : 0.005 0.054 2845 Dihedral : 13.735 127.238 3755 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.74 % Allowed : 7.39 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.18), residues: 1955 helix: 1.49 (0.17), residues: 790 sheet: 0.25 (0.23), residues: 435 loop : 0.06 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 54 HIS 0.007 0.002 HIS C 297 PHE 0.021 0.002 PHE D 99 TYR 0.015 0.002 TYR E 92 ARG 0.007 0.001 ARG E 446 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 15) link_NAG-ASN : angle 2.48659 ( 45) link_BETA1-4 : bond 0.00282 ( 15) link_BETA1-4 : angle 1.71773 ( 45) hydrogen bonds : bond 0.06494 ( 891) hydrogen bonds : angle 5.00046 ( 2898) SS BOND : bond 0.00729 ( 10) SS BOND : angle 1.49345 ( 20) covalent geometry : bond 0.00512 (17600) covalent geometry : angle 0.62326 (23955) *********************** 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 251 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: A 279 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8575 (mp) REVERT: A 429 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7766 (mt-10) REVERT: B 46 ASN cc_start: 0.8593 (m110) cc_final: 0.8141 (m110) REVERT: B 191 LYS cc_start: 0.8028 (tptt) cc_final: 0.7702 (mmpt) REVERT: B 322 MET cc_start: 0.8761 (mtp) cc_final: 0.8267 (mtp) REVERT: C 44 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7424 (pm20) REVERT: C 46 ASN cc_start: 0.8539 (m110) cc_final: 0.8122 (m110) REVERT: C 258 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7121 (mm-30) REVERT: C 260 MET cc_start: 0.7575 (mmm) cc_final: 0.7298 (mtp) REVERT: C 278 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7911 (ttm) REVERT: C 309 ARG cc_start: 0.8436 (ttp-170) cc_final: 0.8116 (ttm-80) REVERT: D 44 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: D 191 LYS cc_start: 0.8258 (tptt) cc_final: 0.7801 (mmpt) REVERT: D 415 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: E 44 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: E 46 ASN cc_start: 0.8581 (m110) cc_final: 0.8160 (m110) REVERT: E 260 MET cc_start: 0.7348 (mmm) cc_final: 0.7147 (mmm) outliers start: 31 outliers final: 12 residues processed: 237 average time/residue: 2.7090 time to fit residues: 719.1376 Evaluate side-chains 230 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 192 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN D 56 GLN D 293 GLN E 26 GLN E 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.091935 restraints weight = 45066.146| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.66 r_work: 0.2798 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17640 Z= 0.168 Angle : 0.565 4.611 24065 Z= 0.292 Chirality : 0.040 0.152 2735 Planarity : 0.005 0.056 2845 Dihedral : 13.011 117.890 3755 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.96 % Allowed : 7.79 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.18), residues: 1955 helix: 1.69 (0.17), residues: 780 sheet: 0.34 (0.23), residues: 435 loop : 0.05 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 307 HIS 0.003 0.001 HIS D 295 PHE 0.019 0.001 PHE D 99 TYR 0.011 0.002 TYR D 128 ARG 0.005 0.001 ARG D 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 15) link_NAG-ASN : angle 2.45552 ( 45) link_BETA1-4 : bond 0.00312 ( 15) link_BETA1-4 : angle 1.50937 ( 45) hydrogen bonds : bond 0.05733 ( 891) hydrogen bonds : angle 4.83085 ( 2898) SS BOND : bond 0.00694 ( 10) SS BOND : angle 1.29423 ( 20) covalent geometry : bond 0.00375 (17600) covalent geometry : angle 0.55150 (23955) *********************** 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 257 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: B 46 ASN cc_start: 0.8623 (m110) cc_final: 0.8222 (m110) REVERT: B 309 ARG cc_start: 0.8461 (ttm110) cc_final: 0.8078 (ttp-170) REVERT: B 322 MET cc_start: 0.8673 (mtp) cc_final: 0.8214 (mtp) REVERT: C 46 ASN cc_start: 0.8499 (m110) cc_final: 0.8094 (m110) REVERT: C 258 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7104 (mm-30) REVERT: C 278 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7919 (ttm) REVERT: C 309 ARG cc_start: 0.8469 (ttp-170) cc_final: 0.8153 (ttm-80) REVERT: D 44 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: D 191 LYS cc_start: 0.8269 (tptt) cc_final: 0.7828 (mmpt) REVERT: D 260 MET cc_start: 0.7572 (mmm) cc_final: 0.7370 (mmm) REVERT: D 322 MET cc_start: 0.8700 (mtp) cc_final: 0.8455 (mtp) REVERT: E 44 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7782 (pm20) REVERT: E 46 ASN cc_start: 0.8569 (m110) cc_final: 0.8158 (m110) REVERT: E 234 ASP cc_start: 0.8638 (m-30) cc_final: 0.8186 (m-30) REVERT: E 278 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7874 (ttt) outliers start: 35 outliers final: 16 residues processed: 242 average time/residue: 3.7304 time to fit residues: 1044.8055 Evaluate side-chains 236 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 5.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 133 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 41 optimal weight: 0.0370 chunk 126 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 213 ASN A 293 GLN C 26 GLN D 56 GLN D 293 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.094670 restraints weight = 45300.414| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.66 r_work: 0.2833 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17640 Z= 0.108 Angle : 0.500 4.391 24065 Z= 0.257 Chirality : 0.039 0.149 2735 Planarity : 0.004 0.042 2845 Dihedral : 12.338 105.339 3755 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.06 % Allowed : 9.30 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.18), residues: 1955 helix: 2.03 (0.17), residues: 780 sheet: 0.44 (0.23), residues: 435 loop : 0.21 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 59 HIS 0.001 0.000 HIS D 295 PHE 0.011 0.001 PHE D 99 TYR 0.009 0.001 TYR E 117 ARG 0.005 0.000 ARG D 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 15) link_NAG-ASN : angle 2.34783 ( 45) link_BETA1-4 : bond 0.00336 ( 15) link_BETA1-4 : angle 1.24955 ( 45) hydrogen bonds : bond 0.04869 ( 891) hydrogen bonds : angle 4.56848 ( 2898) SS BOND : bond 0.00703 ( 10) SS BOND : angle 1.15822 ( 20) covalent geometry : bond 0.00233 (17600) covalent geometry : angle 0.48683 (23955) *********************** 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 241 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ASN cc_start: 0.8610 (m110) cc_final: 0.8236 (m110) REVERT: B 322 MET cc_start: 0.8610 (mtp) cc_final: 0.8280 (mtp) REVERT: C 258 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7061 (mm-30) REVERT: C 278 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7923 (ttm) REVERT: D 191 LYS cc_start: 0.8232 (tptt) cc_final: 0.7769 (mmpt) REVERT: D 260 MET cc_start: 0.7524 (mmm) cc_final: 0.7294 (mmm) REVERT: E 46 ASN cc_start: 0.8531 (m110) cc_final: 0.8132 (m110) REVERT: E 234 ASP cc_start: 0.8585 (m-30) cc_final: 0.8141 (m-30) REVERT: E 278 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7882 (ttt) outliers start: 19 outliers final: 5 residues processed: 234 average time/residue: 2.6173 time to fit residues: 690.0164 Evaluate side-chains 219 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 212 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain E residue 278 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 ASN C 293 GLN D 26 GLN D 56 GLN D 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.092425 restraints weight = 43013.056| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.62 r_work: 0.2804 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17640 Z= 0.183 Angle : 0.562 4.775 24065 Z= 0.289 Chirality : 0.041 0.150 2735 Planarity : 0.005 0.056 2845 Dihedral : 12.310 99.235 3755 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.46 % Allowed : 9.30 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 1955 helix: 1.91 (0.17), residues: 780 sheet: 0.37 (0.23), residues: 460 loop : 0.24 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 307 HIS 0.004 0.001 HIS C 297 PHE 0.014 0.001 PHE D 99 TYR 0.010 0.002 TYR C 194 ARG 0.009 0.001 ARG B 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 15) link_NAG-ASN : angle 2.34318 ( 45) link_BETA1-4 : bond 0.00287 ( 15) link_BETA1-4 : angle 1.40799 ( 45) hydrogen bonds : bond 0.05516 ( 891) hydrogen bonds : angle 4.69339 ( 2898) SS BOND : bond 0.00683 ( 10) SS BOND : angle 1.38126 ( 20) covalent geometry : bond 0.00421 (17600) covalent geometry : angle 0.54905 (23955) *********************** 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 244 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8114 (mp) REVERT: B 46 ASN cc_start: 0.8599 (m110) cc_final: 0.8203 (m110) REVERT: B 191 LYS cc_start: 0.8076 (tptt) cc_final: 0.7759 (mmpt) REVERT: B 322 MET cc_start: 0.8610 (mtp) cc_final: 0.8138 (mtp) REVERT: C 45 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8147 (tptp) REVERT: C 46 ASN cc_start: 0.8444 (m-40) cc_final: 0.8227 (m110) REVERT: C 212 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8073 (mp) REVERT: C 258 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7064 (mm-30) REVERT: C 278 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7903 (ttm) REVERT: C 309 ARG cc_start: 0.8388 (ttp-170) cc_final: 0.8091 (ttm-80) REVERT: D 191 LYS cc_start: 0.8218 (tptt) cc_final: 0.7767 (mmpt) REVERT: D 212 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8058 (mp) REVERT: D 260 MET cc_start: 0.7567 (mmm) cc_final: 0.7322 (mmm) REVERT: E 46 ASN cc_start: 0.8549 (m110) cc_final: 0.8148 (m110) REVERT: E 234 ASP cc_start: 0.8623 (m-30) cc_final: 0.8164 (m-30) REVERT: E 278 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.7962 (ttt) outliers start: 26 outliers final: 16 residues processed: 232 average time/residue: 2.6768 time to fit residues: 696.3594 Evaluate side-chains 237 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 278 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 61 optimal weight: 0.0270 chunk 64 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN D 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.093616 restraints weight = 52173.192| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.77 r_work: 0.2831 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17640 Z= 0.109 Angle : 0.500 4.647 24065 Z= 0.256 Chirality : 0.039 0.148 2735 Planarity : 0.004 0.060 2845 Dihedral : 11.919 106.018 3755 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.12 % Allowed : 9.69 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.18), residues: 1955 helix: 2.14 (0.17), residues: 780 sheet: 0.45 (0.24), residues: 435 loop : 0.24 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 307 HIS 0.002 0.000 HIS D 295 PHE 0.011 0.001 PHE D 99 TYR 0.008 0.001 TYR E 117 ARG 0.007 0.000 ARG B 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 15) link_NAG-ASN : angle 2.34144 ( 45) link_BETA1-4 : bond 0.00313 ( 15) link_BETA1-4 : angle 1.24807 ( 45) hydrogen bonds : bond 0.04760 ( 891) hydrogen bonds : angle 4.50586 ( 2898) SS BOND : bond 0.00682 ( 10) SS BOND : angle 1.15667 ( 20) covalent geometry : bond 0.00237 (17600) covalent geometry : angle 0.48696 (23955) *********************** 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 238 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ASN cc_start: 0.8606 (m110) cc_final: 0.8214 (m110) REVERT: B 322 MET cc_start: 0.8604 (mtp) cc_final: 0.8177 (mtp) REVERT: C 45 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8158 (tptp) REVERT: C 212 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8114 (mp) REVERT: C 258 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7064 (mm-30) REVERT: C 278 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7895 (ttm) REVERT: D 191 LYS cc_start: 0.8246 (tptt) cc_final: 0.7796 (mmpt) REVERT: D 260 MET cc_start: 0.7600 (mmm) cc_final: 0.7341 (mmm) REVERT: D 278 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7801 (ttt) REVERT: E 46 ASN cc_start: 0.8534 (m110) cc_final: 0.8121 (m110) REVERT: E 234 ASP cc_start: 0.8624 (m-30) cc_final: 0.8129 (m-30) REVERT: E 278 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7989 (ttt) outliers start: 20 outliers final: 10 residues processed: 229 average time/residue: 2.6984 time to fit residues: 692.3428 Evaluate side-chains 226 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain E residue 278 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 96 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN C 46 ASN C 293 GLN D 56 GLN E 26 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.129005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.091455 restraints weight = 49784.122| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.73 r_work: 0.2787 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17640 Z= 0.189 Angle : 0.564 4.667 24065 Z= 0.291 Chirality : 0.040 0.149 2735 Planarity : 0.005 0.049 2845 Dihedral : 11.945 110.582 3755 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.18 % Allowed : 9.64 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 1955 helix: 1.98 (0.17), residues: 780 sheet: 0.36 (0.23), residues: 460 loop : 0.25 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 307 HIS 0.004 0.001 HIS C 297 PHE 0.016 0.001 PHE D 99 TYR 0.010 0.002 TYR C 14 ARG 0.006 0.001 ARG D 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 15) link_NAG-ASN : angle 2.35936 ( 45) link_BETA1-4 : bond 0.00274 ( 15) link_BETA1-4 : angle 1.40314 ( 45) hydrogen bonds : bond 0.05470 ( 891) hydrogen bonds : angle 4.66688 ( 2898) SS BOND : bond 0.00677 ( 10) SS BOND : angle 1.41962 ( 20) covalent geometry : bond 0.00437 (17600) covalent geometry : angle 0.55091 (23955) *********************** 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 236 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ASN cc_start: 0.8615 (m110) cc_final: 0.8219 (m110) REVERT: B 191 LYS cc_start: 0.8039 (tptt) cc_final: 0.7725 (mmpt) REVERT: B 322 MET cc_start: 0.8582 (mtp) cc_final: 0.8126 (mtp) REVERT: C 45 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8210 (tttp) REVERT: C 212 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8087 (mp) REVERT: C 278 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7898 (ttm) REVERT: D 191 LYS cc_start: 0.8232 (tptt) cc_final: 0.7763 (mmpt) REVERT: D 260 MET cc_start: 0.7658 (mmm) cc_final: 0.7381 (mmm) REVERT: D 431 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: E 46 ASN cc_start: 0.8552 (m110) cc_final: 0.8136 (m110) REVERT: E 234 ASP cc_start: 0.8653 (m-30) cc_final: 0.8202 (m-30) REVERT: E 278 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8045 (ttt) outliers start: 21 outliers final: 12 residues processed: 226 average time/residue: 2.8387 time to fit residues: 718.1165 Evaluate side-chains 231 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain E residue 278 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 19 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 ASN D 56 GLN D 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.094571 restraints weight = 44979.496| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.66 r_work: 0.2841 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17640 Z= 0.110 Angle : 0.498 4.669 24065 Z= 0.255 Chirality : 0.039 0.148 2735 Planarity : 0.004 0.064 2845 Dihedral : 11.455 113.935 3755 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.95 % Allowed : 10.08 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.18), residues: 1955 helix: 2.22 (0.17), residues: 780 sheet: 0.45 (0.24), residues: 435 loop : 0.24 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 59 HIS 0.001 0.000 HIS D 295 PHE 0.008 0.001 PHE D 99 TYR 0.009 0.001 TYR B 273 ARG 0.008 0.000 ARG D 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 15) link_NAG-ASN : angle 2.34792 ( 45) link_BETA1-4 : bond 0.00312 ( 15) link_BETA1-4 : angle 1.24895 ( 45) hydrogen bonds : bond 0.04685 ( 891) hydrogen bonds : angle 4.47331 ( 2898) SS BOND : bond 0.00670 ( 10) SS BOND : angle 1.14960 ( 20) covalent geometry : bond 0.00239 (17600) covalent geometry : angle 0.48418 (23955) *********************** 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 238 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8197 (mtm-85) REVERT: B 46 ASN cc_start: 0.8596 (m110) cc_final: 0.8213 (m110) REVERT: B 322 MET cc_start: 0.8566 (mtp) cc_final: 0.8156 (mtp) REVERT: C 45 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8130 (tptp) REVERT: C 258 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7093 (mm-30) REVERT: C 278 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7880 (ttm) REVERT: D 191 LYS cc_start: 0.8259 (tptt) cc_final: 0.7797 (mmpt) REVERT: D 416 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7763 (mm-30) REVERT: E 46 ASN cc_start: 0.8520 (m110) cc_final: 0.8113 (m110) REVERT: E 234 ASP cc_start: 0.8584 (m-30) cc_final: 0.8152 (m-30) REVERT: E 278 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7974 (ttt) REVERT: E 416 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7708 (mm-30) outliers start: 17 outliers final: 11 residues processed: 230 average time/residue: 2.7983 time to fit residues: 723.6321 Evaluate side-chains 231 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain E residue 278 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 ASN C 293 GLN D 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.093905 restraints weight = 45845.242| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.67 r_work: 0.2822 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17640 Z= 0.125 Angle : 0.508 4.527 24065 Z= 0.260 Chirality : 0.039 0.146 2735 Planarity : 0.004 0.062 2845 Dihedral : 11.207 114.607 3755 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.84 % Allowed : 10.36 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 1955 helix: 2.23 (0.17), residues: 780 sheet: 0.53 (0.23), residues: 450 loop : 0.30 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 307 HIS 0.002 0.001 HIS D 295 PHE 0.014 0.001 PHE D 99 TYR 0.009 0.001 TYR C 273 ARG 0.008 0.000 ARG D 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 15) link_NAG-ASN : angle 2.29477 ( 45) link_BETA1-4 : bond 0.00285 ( 15) link_BETA1-4 : angle 1.28376 ( 45) hydrogen bonds : bond 0.04803 ( 891) hydrogen bonds : angle 4.47810 ( 2898) SS BOND : bond 0.00675 ( 10) SS BOND : angle 1.22397 ( 20) covalent geometry : bond 0.00281 (17600) covalent geometry : angle 0.49459 (23955) ********************** 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 229 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 5.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ASN cc_start: 0.8616 (m110) cc_final: 0.8233 (m110) REVERT: B 309 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7795 (ttm-80) REVERT: B 322 MET cc_start: 0.8578 (mtp) cc_final: 0.8169 (mtp) REVERT: C 45 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8097 (tptp) REVERT: C 258 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7090 (mm-30) REVERT: C 278 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7897 (ttm) REVERT: D 191 LYS cc_start: 0.8263 (tptt) cc_final: 0.7802 (mmpt) REVERT: D 431 GLU cc_start: 0.8123 (tt0) cc_final: 0.7888 (tt0) REVERT: E 46 ASN cc_start: 0.8519 (m110) cc_final: 0.8104 (m110) REVERT: E 234 ASP cc_start: 0.8596 (m-30) cc_final: 0.8101 (m-30) REVERT: E 278 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8004 (ttt) REVERT: E 416 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7658 (mm-30) outliers start: 15 outliers final: 12 residues processed: 223 average time/residue: 3.7387 time to fit residues: 947.1132 Evaluate side-chains 228 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain E residue 278 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 9 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 134 optimal weight: 0.0370 chunk 129 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN C 46 ASN D 26 GLN D 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.096393 restraints weight = 45051.158| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.66 r_work: 0.2867 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17640 Z= 0.097 Angle : 0.480 5.173 24065 Z= 0.244 Chirality : 0.038 0.146 2735 Planarity : 0.004 0.063 2845 Dihedral : 10.731 113.772 3755 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.56 % Allowed : 10.76 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.18), residues: 1955 helix: 2.43 (0.17), residues: 780 sheet: 0.59 (0.23), residues: 450 loop : 0.31 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 59 HIS 0.001 0.000 HIS D 295 PHE 0.006 0.001 PHE D 99 TYR 0.009 0.001 TYR B 273 ARG 0.007 0.000 ARG D 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 15) link_NAG-ASN : angle 2.27366 ( 45) link_BETA1-4 : bond 0.00341 ( 15) link_BETA1-4 : angle 1.20398 ( 45) hydrogen bonds : bond 0.04310 ( 891) hydrogen bonds : angle 4.32497 ( 2898) SS BOND : bond 0.00681 ( 10) SS BOND : angle 1.12478 ( 20) covalent geometry : bond 0.00212 (17600) covalent geometry : angle 0.46718 (23955) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27295.88 seconds wall clock time: 481 minutes 24.25 seconds (28884.25 seconds total)