Starting phenix.real_space_refine on Tue Aug 26 06:39:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v86_43025/08_2025/8v86_43025_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v86_43025/08_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_43025/08_2025/8v86_43025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v86_43025/08_2025/8v86_43025.map" model { file = "/net/cci-nas-00/data/ceres_data/8v86_43025/08_2025/8v86_43025_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v86_43025/08_2025/8v86_43025_trim.cif" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 9.09, per 1000 atoms: 0.28 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: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.56 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: 7.16 Time building geometry restraints manager: 3.35 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: 0.01 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: 1.300 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: 0.180 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.380 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 41.810 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (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 ARG 0.004 0.001 ARG E 185 TYR 0.018 0.002 TYR C 117 PHE 0.019 0.002 PHE B 99 TRP 0.011 0.002 TRP B 54 HIS 0.003 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00650 (17600) covalent geometry : angle 0.86952 (23955) SS BOND : bond 0.00634 ( 10) SS BOND : angle 1.30479 ( 20) hydrogen bonds : bond 0.18148 ( 891) hydrogen bonds : angle 7.21074 ( 2898) link_BETA1-4 : bond 0.00505 ( 15) link_BETA1-4 : angle 2.56562 ( 45) link_NAG-ASN : bond 0.00498 ( 15) link_NAG-ASN : angle 4.42858 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.767 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: 1.1428 time to fit residues: 310.3043 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 : 0.722 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 46 ASN E 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.093588 restraints weight = 46958.928| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.71 r_work: 0.2833 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 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 = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1296 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= 0.143 Angle : 0.623 7.060 24065 Z= 0.310 Chirality : 0.042 0.149 2735 Planarity : 0.004 0.033 2845 Dihedral : 16.124 147.953 3757 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.56 % Allowed : 6.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 1955 helix: 1.10 (0.17), residues: 790 sheet: 0.01 (0.23), residues: 435 loop : -0.03 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 418 TYR 0.015 0.001 TYR D 117 PHE 0.026 0.001 PHE C 99 TRP 0.009 0.001 TRP E 315 HIS 0.002 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00293 (17600) covalent geometry : angle 0.60795 (23955) SS BOND : bond 0.00720 ( 10) SS BOND : angle 1.30429 ( 20) hydrogen bonds : bond 0.06449 ( 891) hydrogen bonds : angle 5.24530 ( 2898) link_BETA1-4 : bond 0.00308 ( 15) link_BETA1-4 : angle 1.71025 ( 45) link_NAG-ASN : bond 0.00226 ( 15) link_NAG-ASN : angle 2.60918 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 228 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8677 (mmm) cc_final: 0.8368 (mtp) REVERT: A 429 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7738 (mt-10) REVERT: B 309 ARG cc_start: 0.8461 (ttm110) cc_final: 0.8206 (ttp-170) REVERT: B 322 MET cc_start: 0.8771 (mtp) cc_final: 0.8342 (mtp) REVERT: C 46 ASN cc_start: 0.8425 (m110) cc_final: 0.7970 (m110) REVERT: C 234 ASP cc_start: 0.8506 (m-30) cc_final: 0.8095 (m-30) REVERT: C 258 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7082 (mm-30) REVERT: C 260 MET cc_start: 0.7484 (mmm) cc_final: 0.7235 (mtp) REVERT: D 191 LYS cc_start: 0.8230 (tptt) cc_final: 0.7751 (mmpt) REVERT: D 322 MET cc_start: 0.8766 (mtp) cc_final: 0.8439 (mtp) REVERT: D 415 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: E 46 ASN cc_start: 0.8516 (m110) cc_final: 0.8091 (m110) outliers start: 10 outliers final: 4 residues processed: 235 average time/residue: 1.1588 time to fit residues: 306.3488 Evaluate side-chains 214 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 209 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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 173 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 109 optimal weight: 0.0060 chunk 182 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 133 optimal weight: 0.0000 chunk 162 optimal weight: 1.9990 overall best weight: 0.8004 ------------------------------------------------------------------------------- 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 B 26 GLN B 213 ASN C 26 GLN C 293 GLN D 26 GLN D 46 ASN D 213 ASN D 293 GLN E 26 GLN E 293 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.094892 restraints weight = 44383.078| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.64 r_work: 0.2846 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1804 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= 0.126 Angle : 0.537 5.028 24065 Z= 0.273 Chirality : 0.040 0.147 2735 Planarity : 0.004 0.055 2845 Dihedral : 13.295 131.644 3755 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.29 % Allowed : 8.01 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.18), residues: 1955 helix: 1.74 (0.17), residues: 780 sheet: 0.32 (0.23), residues: 435 loop : 0.14 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 446 TYR 0.010 0.001 TYR C 117 PHE 0.013 0.001 PHE D 99 TRP 0.010 0.001 TRP A 315 HIS 0.003 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00272 (17600) covalent geometry : angle 0.52433 (23955) SS BOND : bond 0.00706 ( 10) SS BOND : angle 1.23576 ( 20) hydrogen bonds : bond 0.05427 ( 891) hydrogen bonds : angle 4.77355 ( 2898) link_BETA1-4 : bond 0.00458 ( 15) link_BETA1-4 : angle 1.51524 ( 45) link_NAG-ASN : bond 0.00134 ( 15) link_NAG-ASN : angle 2.18739 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ASN cc_start: 0.8479 (m-40) cc_final: 0.8234 (m110) REVERT: B 322 MET cc_start: 0.8749 (mtp) cc_final: 0.8296 (mtp) REVERT: C 46 ASN cc_start: 0.8452 (m110) cc_final: 0.8005 (m110) REVERT: C 234 ASP cc_start: 0.8471 (m-30) cc_final: 0.8053 (m-30) REVERT: C 258 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7133 (mm-30) REVERT: C 309 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.8068 (ttm-80) REVERT: D 191 LYS cc_start: 0.8261 (tptt) cc_final: 0.7841 (mmpt) REVERT: D 322 MET cc_start: 0.8816 (mtp) cc_final: 0.8585 (mtp) REVERT: E 46 ASN cc_start: 0.8549 (m110) cc_final: 0.8146 (m110) outliers start: 23 outliers final: 7 residues processed: 239 average time/residue: 1.1150 time to fit residues: 297.3202 Evaluate side-chains 221 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 214 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 279 ILE 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 C residue 58 SER 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 163 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN C 296 HIS D 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.092996 restraints weight = 45045.610| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.65 r_work: 0.2818 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 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 = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17640 Z= 0.154 Angle : 0.547 5.010 24065 Z= 0.281 Chirality : 0.040 0.150 2735 Planarity : 0.004 0.059 2845 Dihedral : 12.655 122.205 3755 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.34 % Allowed : 8.46 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.18), residues: 1955 helix: 1.89 (0.17), residues: 780 sheet: 0.37 (0.23), residues: 435 loop : 0.23 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 418 TYR 0.009 0.001 TYR E 92 PHE 0.017 0.001 PHE D 99 TRP 0.008 0.001 TRP E 54 HIS 0.003 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00346 (17600) covalent geometry : angle 0.53428 (23955) SS BOND : bond 0.00700 ( 10) SS BOND : angle 1.30149 ( 20) hydrogen bonds : bond 0.05433 ( 891) hydrogen bonds : angle 4.72531 ( 2898) link_BETA1-4 : bond 0.00323 ( 15) link_BETA1-4 : angle 1.48636 ( 45) link_NAG-ASN : bond 0.00097 ( 15) link_NAG-ASN : angle 2.31913 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 LYS cc_start: 0.8035 (tptt) cc_final: 0.7722 (mmpt) REVERT: B 322 MET cc_start: 0.8678 (mtp) cc_final: 0.8272 (mtp) REVERT: C 46 ASN cc_start: 0.8507 (m110) cc_final: 0.8076 (m110) REVERT: C 258 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7065 (mm-30) REVERT: C 309 ARG cc_start: 0.8385 (ttp-170) cc_final: 0.8055 (ttm-80) REVERT: D 191 LYS cc_start: 0.8255 (tptt) cc_final: 0.7828 (mmpt) REVERT: D 260 MET cc_start: 0.7522 (mmm) cc_final: 0.7307 (mmm) REVERT: D 322 MET cc_start: 0.8821 (mtp) cc_final: 0.8577 (mtp) REVERT: E 46 ASN cc_start: 0.8539 (m110) cc_final: 0.8133 (m110) REVERT: E 234 ASP cc_start: 0.8587 (m-30) cc_final: 0.8126 (m-30) REVERT: E 278 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7890 (ttt) outliers start: 24 outliers final: 8 residues processed: 230 average time/residue: 1.1160 time to fit residues: 288.7423 Evaluate side-chains 218 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 209 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE 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 C residue 58 SER Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 278 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 96 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 293 GLN D 56 GLN D 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.094622 restraints weight = 45716.653| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.67 r_work: 0.2840 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17640 Z= 0.114 Angle : 0.502 4.651 24065 Z= 0.257 Chirality : 0.039 0.150 2735 Planarity : 0.004 0.030 2845 Dihedral : 12.181 111.384 3755 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.01 % Allowed : 9.02 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.18), residues: 1955 helix: 2.10 (0.17), residues: 780 sheet: 0.60 (0.24), residues: 425 loop : 0.26 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 446 TYR 0.007 0.001 TYR E 117 PHE 0.013 0.001 PHE D 99 TRP 0.007 0.001 TRP D 307 HIS 0.002 0.001 HIS D 295 Details of bonding type rmsd covalent geometry : bond 0.00250 (17600) covalent geometry : angle 0.48948 (23955) SS BOND : bond 0.00684 ( 10) SS BOND : angle 1.20873 ( 20) hydrogen bonds : bond 0.04904 ( 891) hydrogen bonds : angle 4.55678 ( 2898) link_BETA1-4 : bond 0.00307 ( 15) link_BETA1-4 : angle 1.27235 ( 45) link_NAG-ASN : bond 0.00072 ( 15) link_NAG-ASN : angle 2.22949 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 322 MET cc_start: 0.8660 (mtp) cc_final: 0.8278 (mtp) REVERT: C 46 ASN cc_start: 0.8504 (m110) cc_final: 0.8107 (m110) REVERT: C 258 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7067 (mm-30) REVERT: D 191 LYS cc_start: 0.8218 (tptt) cc_final: 0.7760 (mmpt) REVERT: E 46 ASN cc_start: 0.8532 (m110) cc_final: 0.8131 (m110) REVERT: E 234 ASP cc_start: 0.8529 (m-30) cc_final: 0.8077 (m-30) REVERT: E 278 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7922 (ttt) outliers start: 18 outliers final: 7 residues processed: 227 average time/residue: 1.2650 time to fit residues: 321.8500 Evaluate side-chains 223 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 464 LEU 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 165 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 169 optimal weight: 0.0770 chunk 62 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3485 r_free = 0.3485 target = 0.130967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.094075 restraints weight = 47555.039| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.70 r_work: 0.2829 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17640 Z= 0.123 Angle : 0.507 4.983 24065 Z= 0.259 Chirality : 0.039 0.148 2735 Planarity : 0.004 0.031 2845 Dihedral : 11.899 99.893 3755 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.46 % Allowed : 9.19 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.18), residues: 1955 helix: 2.16 (0.17), residues: 780 sheet: 0.59 (0.23), residues: 450 loop : 0.34 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 446 TYR 0.009 0.001 TYR C 273 PHE 0.012 0.001 PHE D 99 TRP 0.007 0.001 TRP A 307 HIS 0.002 0.001 HIS D 295 Details of bonding type rmsd covalent geometry : bond 0.00275 (17600) covalent geometry : angle 0.49500 (23955) SS BOND : bond 0.00679 ( 10) SS BOND : angle 1.23783 ( 20) hydrogen bonds : bond 0.04867 ( 891) hydrogen bonds : angle 4.51537 ( 2898) link_BETA1-4 : bond 0.00255 ( 15) link_BETA1-4 : angle 1.30377 ( 45) link_NAG-ASN : bond 0.00050 ( 15) link_NAG-ASN : angle 2.21613 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 191 LYS cc_start: 0.8096 (tptt) cc_final: 0.7776 (mmpt) REVERT: B 322 MET cc_start: 0.8642 (mtp) cc_final: 0.8180 (mtp) REVERT: C 45 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8301 (tttp) REVERT: C 46 ASN cc_start: 0.8498 (m110) cc_final: 0.8103 (m110) REVERT: C 212 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8095 (mp) REVERT: C 258 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7053 (mm-30) REVERT: D 44 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: D 191 LYS cc_start: 0.8234 (tptt) cc_final: 0.7773 (mmpt) REVERT: D 212 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8060 (mp) REVERT: D 260 MET cc_start: 0.7494 (mmm) cc_final: 0.7235 (mmm) REVERT: D 322 MET cc_start: 0.8678 (mtp) cc_final: 0.8451 (mtp) REVERT: E 46 ASN cc_start: 0.8536 (m110) cc_final: 0.8126 (m110) REVERT: E 234 ASP cc_start: 0.8539 (m-30) cc_final: 0.8091 (m-30) REVERT: E 278 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7994 (ttt) outliers start: 26 outliers final: 8 residues processed: 231 average time/residue: 1.4744 time to fit residues: 380.0781 Evaluate side-chains 227 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 B residue 58 SER 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 D residue 44 GLU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 221 ILE 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 35 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 143 optimal weight: 0.0050 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3466 r_free = 0.3466 target = 0.129483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.092923 restraints weight = 44264.542| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.64 r_work: 0.2810 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- 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 = 0.42 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 = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17640 Z= 0.175 Angle : 0.549 4.607 24065 Z= 0.283 Chirality : 0.040 0.150 2735 Planarity : 0.004 0.033 2845 Dihedral : 11.968 104.562 3755 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.18), residues: 1955 helix: 2.05 (0.17), residues: 780 sheet: 0.52 (0.23), residues: 450 loop : 0.28 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 78 TYR 0.010 0.002 TYR D 128 PHE 0.017 0.001 PHE D 99 TRP 0.009 0.001 TRP E 307 HIS 0.004 0.001 HIS D 295 Details of bonding type rmsd covalent geometry : bond 0.00404 (17600) covalent geometry : angle 0.53620 (23955) SS BOND : bond 0.00672 ( 10) SS BOND : angle 1.37448 ( 20) hydrogen bonds : bond 0.05338 ( 891) hydrogen bonds : angle 4.63731 ( 2898) link_BETA1-4 : bond 0.00263 ( 15) link_BETA1-4 : angle 1.38046 ( 45) link_NAG-ASN : bond 0.00110 ( 15) link_NAG-ASN : angle 2.32432 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8108 (mp) REVERT: B 191 LYS cc_start: 0.8075 (tptt) cc_final: 0.7759 (mmpt) REVERT: B 322 MET cc_start: 0.8614 (mtp) cc_final: 0.8123 (mtp) REVERT: C 45 LYS cc_start: 0.8587 (ttmt) cc_final: 0.8285 (tttp) REVERT: C 46 ASN cc_start: 0.8487 (m110) cc_final: 0.8098 (m110) REVERT: C 212 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8097 (mp) REVERT: C 258 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7067 (mm-30) REVERT: D 44 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: D 191 LYS cc_start: 0.8217 (tptt) cc_final: 0.7762 (mmpt) REVERT: D 212 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8058 (mp) REVERT: D 260 MET cc_start: 0.7606 (mmm) cc_final: 0.7347 (mmm) REVERT: D 322 MET cc_start: 0.8682 (mtp) cc_final: 0.8455 (mtp) REVERT: E 44 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: E 46 ASN cc_start: 0.8537 (m110) cc_final: 0.8126 (m110) REVERT: E 234 ASP cc_start: 0.8579 (m-30) cc_final: 0.8092 (m-30) REVERT: E 278 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7955 (ttt) outliers start: 21 outliers final: 11 residues processed: 226 average time/residue: 1.4971 time to fit residues: 376.1636 Evaluate side-chains 228 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 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 212 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 44 GLU 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 75 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 187 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3461 r_free = 0.3461 target = 0.129046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.092247 restraints weight = 45625.239| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.66 r_work: 0.2797 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 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 = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17640 Z= 0.184 Angle : 0.559 4.619 24065 Z= 0.288 Chirality : 0.040 0.148 2735 Planarity : 0.005 0.071 2845 Dihedral : 12.041 111.044 3755 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.34 % Allowed : 9.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.18), residues: 1955 helix: 1.95 (0.17), residues: 780 sheet: 0.35 (0.23), residues: 460 loop : 0.23 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 185 TYR 0.012 0.002 TYR D 128 PHE 0.018 0.001 PHE D 99 TRP 0.010 0.001 TRP D 307 HIS 0.004 0.001 HIS D 295 Details of bonding type rmsd covalent geometry : bond 0.00421 (17600) covalent geometry : angle 0.54545 (23955) SS BOND : bond 0.00673 ( 10) SS BOND : angle 1.38169 ( 20) hydrogen bonds : bond 0.05475 ( 891) hydrogen bonds : angle 4.68295 ( 2898) link_BETA1-4 : bond 0.00282 ( 15) link_BETA1-4 : angle 1.39919 ( 45) link_NAG-ASN : bond 0.00119 ( 15) link_NAG-ASN : angle 2.39826 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8127 (mp) REVERT: B 191 LYS cc_start: 0.8047 (tptt) cc_final: 0.7741 (mmpt) REVERT: B 212 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8038 (mp) REVERT: B 436 GLU cc_start: 0.8177 (tt0) cc_final: 0.7961 (tt0) REVERT: C 45 LYS cc_start: 0.8572 (ttmt) cc_final: 0.8270 (tttp) REVERT: C 46 ASN cc_start: 0.8490 (m110) cc_final: 0.8099 (m110) REVERT: C 212 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8127 (mp) REVERT: D 44 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: D 191 LYS cc_start: 0.8226 (tptt) cc_final: 0.7758 (mmpt) REVERT: D 212 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8101 (mp) REVERT: D 322 MET cc_start: 0.8706 (mtp) cc_final: 0.8482 (mtp) REVERT: E 44 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: E 46 ASN cc_start: 0.8542 (m110) cc_final: 0.8128 (m110) REVERT: E 234 ASP cc_start: 0.8587 (m-30) cc_final: 0.8117 (m-30) REVERT: E 278 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8029 (ttt) outliers start: 24 outliers final: 12 residues processed: 228 average time/residue: 1.4466 time to fit residues: 367.7794 Evaluate side-chains 235 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 B residue 58 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 435 SER 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 212 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 44 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 91 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3472 r_free = 0.3472 target = 0.129911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.092500 restraints weight = 50769.451| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.75 r_work: 0.2791 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 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 = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17640 Z= 0.138 Angle : 0.523 4.579 24065 Z= 0.269 Chirality : 0.039 0.149 2735 Planarity : 0.004 0.061 2845 Dihedral : 11.750 113.397 3755 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.12 % Allowed : 10.48 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.18), residues: 1955 helix: 2.10 (0.17), residues: 780 sheet: 0.51 (0.23), residues: 450 loop : 0.24 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 185 TYR 0.009 0.001 TYR D 128 PHE 0.015 0.001 PHE D 99 TRP 0.009 0.001 TRP E 307 HIS 0.003 0.001 HIS D 295 Details of bonding type rmsd covalent geometry : bond 0.00308 (17600) covalent geometry : angle 0.50981 (23955) SS BOND : bond 0.00666 ( 10) SS BOND : angle 1.23772 ( 20) hydrogen bonds : bond 0.05084 ( 891) hydrogen bonds : angle 4.58569 ( 2898) link_BETA1-4 : bond 0.00281 ( 15) link_BETA1-4 : angle 1.31785 ( 45) link_NAG-ASN : bond 0.00081 ( 15) link_NAG-ASN : angle 2.39264 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8267 (mtm-85) REVERT: B 212 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8041 (mp) REVERT: B 322 MET cc_start: 0.8580 (mtp) cc_final: 0.8315 (mtp) REVERT: B 436 GLU cc_start: 0.8260 (tt0) cc_final: 0.8023 (tt0) REVERT: C 45 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8241 (tttp) REVERT: C 46 ASN cc_start: 0.8500 (m110) cc_final: 0.8089 (m110) REVERT: C 212 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8106 (mp) REVERT: C 258 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7075 (mm-30) REVERT: D 44 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: D 191 LYS cc_start: 0.8257 (tptt) cc_final: 0.7792 (mmpt) REVERT: E 44 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: E 46 ASN cc_start: 0.8549 (m110) cc_final: 0.8137 (m110) REVERT: E 234 ASP cc_start: 0.8594 (m-30) cc_final: 0.8126 (m-30) REVERT: E 278 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8027 (ttt) outliers start: 20 outliers final: 11 residues processed: 229 average time/residue: 1.5305 time to fit residues: 390.2346 Evaluate side-chains 233 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 212 LEU Chi-restraints excluded: chain B residue 221 ILE 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 212 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 44 GLU 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 167 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3478 r_free = 0.3478 target = 0.130449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.093278 restraints weight = 47827.445| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.71 r_work: 0.2825 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- 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: 0.8436 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17640 Z= 0.125 Angle : 0.511 4.817 24065 Z= 0.262 Chirality : 0.039 0.148 2735 Planarity : 0.004 0.065 2845 Dihedral : 11.297 113.706 3755 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.90 % Allowed : 10.92 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.18), residues: 1955 helix: 2.21 (0.17), residues: 780 sheet: 0.54 (0.23), residues: 450 loop : 0.25 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 185 TYR 0.008 0.001 TYR B 273 PHE 0.013 0.001 PHE D 99 TRP 0.008 0.001 TRP D 307 HIS 0.002 0.001 HIS D 295 Details of bonding type rmsd covalent geometry : bond 0.00279 (17600) covalent geometry : angle 0.49771 (23955) SS BOND : bond 0.00669 ( 10) SS BOND : angle 1.22722 ( 20) hydrogen bonds : bond 0.04857 ( 891) hydrogen bonds : angle 4.50766 ( 2898) link_BETA1-4 : bond 0.00296 ( 15) link_BETA1-4 : angle 1.29155 ( 45) link_NAG-ASN : bond 0.00048 ( 15) link_NAG-ASN : angle 2.35012 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 322 MET cc_start: 0.8614 (mtp) cc_final: 0.8372 (mtp) REVERT: C 45 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8246 (tttp) REVERT: C 46 ASN cc_start: 0.8484 (m110) cc_final: 0.8073 (m110) REVERT: D 44 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: D 191 LYS cc_start: 0.8239 (tptt) cc_final: 0.7767 (mmpt) REVERT: E 44 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: E 46 ASN cc_start: 0.8516 (m110) cc_final: 0.8088 (m110) REVERT: E 234 ASP cc_start: 0.8544 (m-30) cc_final: 0.8080 (m-30) REVERT: E 278 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7976 (ttt) outliers start: 16 outliers final: 11 residues processed: 229 average time/residue: 1.5350 time to fit residues: 390.9991 Evaluate side-chains 231 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 217 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 D residue 44 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 44 GLU 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 134 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 47 GLN D 56 GLN D 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.095071 restraints weight = 48311.743| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.71 r_work: 0.2844 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17640 Z= 0.104 Angle : 0.491 4.768 24065 Z= 0.250 Chirality : 0.038 0.146 2735 Planarity : 0.004 0.062 2845 Dihedral : 10.833 111.562 3755 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.62 % Allowed : 11.20 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.18), residues: 1955 helix: 2.39 (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 ARG 0.008 0.000 ARG D 185 TYR 0.011 0.001 TYR E 273 PHE 0.010 0.001 PHE D 99 TRP 0.008 0.001 TRP A 59 HIS 0.001 0.000 HIS D 295 Details of bonding type rmsd covalent geometry : bond 0.00226 (17600) covalent geometry : angle 0.47717 (23955) SS BOND : bond 0.00670 ( 10) SS BOND : angle 1.15482 ( 20) hydrogen bonds : bond 0.04481 ( 891) hydrogen bonds : angle 4.39082 ( 2898) link_BETA1-4 : bond 0.00333 ( 15) link_BETA1-4 : angle 1.24323 ( 45) link_NAG-ASN : bond 0.00079 ( 15) link_NAG-ASN : angle 2.30788 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12180.07 seconds wall clock time: 206 minutes 42.33 seconds (12402.33 seconds total)