Starting phenix.real_space_refine on Mon Jul 6 10:11:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut1_42526/07_2026/8ut1_42526_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut1_42526/07_2026/8ut1_42526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ut1_42526/07_2026/8ut1_42526_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut1_42526/07_2026/8ut1_42526_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ut1_42526/07_2026/8ut1_42526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut1_42526/07_2026/8ut1_42526.map" } resolution = 2.3 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 115 5.16 5 Cl 5 4.86 5 C 11345 2.51 5 N 2630 2.21 5 O 3180 1.98 5 H 15845 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33140 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6357 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6344 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, 6345 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: 6417 Chain: "B" Number of atoms: 6357 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6344 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, 6345 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: 6417 Chain: "C" Number of atoms: 6357 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6344 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, 6345 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: 6417 Chain: "D" Number of atoms: 6357 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6344 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, 6345 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: 6417 Chain: "E" Number of atoms: 6357 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6344 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, 6345 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: 6417 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 194 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 194 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 194 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 194 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 194 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 9.64, per 1000 atoms: 0.29 Number of scatterers: 33140 At special positions: 0 Unit cell: (98.189, 102.505, 167.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 5 19.99 Cl 5 17.00 S 115 16.00 P 15 15.00 O 3180 8.00 N 2630 7.00 C 11345 6.00 H 15845 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=2.04 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=2.04 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 602 " - " ASN A 67 " " NAG B 603 " - " ASN B 67 " " NAG C 603 " - " ASN C 67 " " NAG D 603 " - " ASN D 67 " " NAG E 603 " - " ASN E 67 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN A 23 " " NAG H 1 " - " ASN B 110 " " NAG I 1 " - " ASN B 23 " " NAG J 1 " - " ASN C 110 " " NAG K 1 " - " ASN C 23 " " NAG L 1 " - " ASN D 110 " " NAG M 1 " - " ASN D 23 " " NAG N 1 " - " ASN E 110 " " NAG O 1 " - " ASN E 23 " Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.4 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 44.5% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.605A 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 removed outlier: 3.522A pdb=" N CYS A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) 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 258 removed outlier: 3.510A pdb=" N GLU A 258 " --> pdb=" O LEU A 254 " (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: 3.605A 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 removed outlier: 3.522A pdb=" N CYS B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) 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 258 removed outlier: 3.509A pdb=" N GLU B 258 " --> pdb=" O LEU B 254 " (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: 3.604A 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 removed outlier: 3.522A pdb=" N CYS C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) 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 258 removed outlier: 3.510A pdb=" N GLU C 258 " --> pdb=" O LEU C 254 " (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: 3.604A 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 removed outlier: 3.522A pdb=" N CYS D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) 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 258 removed outlier: 3.509A pdb=" N GLU D 258 " --> pdb=" O LEU D 254 " (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: 3.604A 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 removed outlier: 3.522A pdb=" N CYS E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 225 " --> pdb=" O ILE E 221 " (cutoff:3.500A) 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 258 removed outlier: 3.510A pdb=" N GLU E 258 " --> pdb=" O LEU E 254 " (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: 4.360A 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: 4.360A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.855A 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: 4.482A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.711A 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: 4.482A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU A 192 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR A 187 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.359A 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: 4.359A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.855A 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: 4.482A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.710A 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: 4.482A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU B 192 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR B 187 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.360A 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: 4.360A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL C 48 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP C 41 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR C 60 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.856A 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: 4.482A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.711A 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: 4.482A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU C 192 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR C 187 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.360A 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: 4.360A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP D 41 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR D 60 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.855A 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: 4.481A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.710A 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: 4.481A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU D 192 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR D 187 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.359A 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: 4.359A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL E 48 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP E 41 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR E 60 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 6.856A 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: 4.482A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.711A 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: 4.482A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU E 192 " --> pdb=" O TYR E 187 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR E 187 " --> pdb=" O GLU E 192 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2883 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.77 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15810 1.04 - 1.24: 2183 1.24 - 1.44: 5334 1.44 - 1.64: 10063 1.64 - 1.84: 175 Bond restraints: 33565 Sorted by residual: bond pdb=" NZ LYS E 306 " pdb=" HZ3 LYS E 306 " ideal model delta sigma weight residual 0.890 0.972 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" NZ LYS C 306 " pdb=" HZ3 LYS C 306 " 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 306 " pdb=" HZ3 LYS D 306 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS C 144 " pdb=" HZ3 LYS C 144 " 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 124 " pdb=" HZ3 LYS C 124 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 33560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 52956 1.58 - 3.16: 6420 3.16 - 4.74: 571 4.74 - 6.32: 118 6.32 - 7.90: 30 Bond angle restraints: 60095 Sorted by residual: angle pdb=" CA MET D 253 " pdb=" CB MET D 253 " pdb=" CG MET D 253 " ideal model delta sigma weight residual 114.10 119.42 -5.32 2.00e+00 2.50e-01 7.08e+00 angle pdb=" CA MET C 253 " pdb=" CB MET C 253 " pdb=" CG MET C 253 " ideal model delta sigma weight residual 114.10 119.39 -5.29 2.00e+00 2.50e-01 6.99e+00 angle pdb=" CA MET A 253 " pdb=" CB MET A 253 " pdb=" CG MET A 253 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" CA MET B 253 " pdb=" CB MET B 253 " pdb=" CG MET B 253 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.95e+00 angle pdb=" O11 POV E 605 " pdb=" P POV E 605 " pdb=" O12 POV E 605 " ideal model delta sigma weight residual 97.67 105.57 -7.90 3.00e+00 1.11e-01 6.94e+00 ... (remaining 60090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.05: 16260 31.05 - 62.11: 555 62.11 - 93.16: 100 93.16 - 124.21: 35 124.21 - 155.26: 25 Dihedral angle restraints: 16975 sinusoidal: 9800 harmonic: 7175 Sorted by residual: dihedral pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N CYS B 190 " pdb=" CA CYS B 190 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 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 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual -180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 16972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2305 0.061 - 0.123: 307 0.123 - 0.184: 110 0.184 - 0.246: 8 0.246 - 0.307: 10 Chirality restraints: 2740 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.25e+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 -2.24 -0.16 2.00e-02 2.50e+03 6.23e+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 -2.24 -0.16 2.00e-02 2.50e+03 6.23e+01 ... (remaining 2737 not shown) Planarity restraints: 4735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 78 " -0.295 9.50e-02 1.11e+02 1.04e-01 3.53e+01 pdb=" NE ARG C 78 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 78 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG C 78 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 78 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 78 " 0.061 2.00e-02 2.50e+03 pdb="HH12 ARG C 78 " -0.023 2.00e-02 2.50e+03 pdb="HH21 ARG C 78 " 0.055 2.00e-02 2.50e+03 pdb="HH22 ARG C 78 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 78 " 0.295 9.50e-02 1.11e+02 1.04e-01 3.53e+01 pdb=" NE ARG B 78 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 78 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG B 78 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 78 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 78 " -0.061 2.00e-02 2.50e+03 pdb="HH12 ARG B 78 " 0.023 2.00e-02 2.50e+03 pdb="HH21 ARG B 78 " -0.055 2.00e-02 2.50e+03 pdb="HH22 ARG B 78 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 78 " 0.294 9.50e-02 1.11e+02 1.04e-01 3.51e+01 pdb=" NE ARG A 78 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 78 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 78 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 78 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 78 " -0.061 2.00e-02 2.50e+03 pdb="HH12 ARG A 78 " 0.023 2.00e-02 2.50e+03 pdb="HH21 ARG A 78 " -0.055 2.00e-02 2.50e+03 pdb="HH22 ARG A 78 " 0.024 2.00e-02 2.50e+03 ... (remaining 4732 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 662 2.13 - 2.75: 57665 2.75 - 3.37: 91510 3.37 - 3.98: 124108 3.98 - 4.60: 189313 Nonbonded interactions: 463258 Sorted by model distance: nonbonded pdb=" HZ1 LYS C 144 " pdb=" HH TYR C 187 " model vdw 1.513 2.100 nonbonded pdb=" HZ1 LYS E 144 " pdb=" HH TYR E 187 " model vdw 1.514 2.100 nonbonded pdb=" HZ1 LYS A 144 " pdb=" HH TYR A 187 " model vdw 1.514 2.100 nonbonded pdb=" HZ1 LYS B 144 " pdb=" HH TYR B 187 " model vdw 1.514 2.100 nonbonded pdb=" HZ1 LYS D 144 " pdb=" HH TYR D 187 " model vdw 1.514 2.100 ... (remaining 463253 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 or resid 604)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 478 or (resid 604 and ( \ name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O12 or n \ ame O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P or \ name C210 or name C211)))) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 478 or (resid 604 and ( \ name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O12 or n \ ame O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P or \ name C210 or name C211)))) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 478 or (resid 604 and ( \ name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O12 or n \ ame O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P or \ name C210 or name C211)))) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 478 or (resid 604 and ( \ name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O12 or n \ ame O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P or \ name C210 or name C211)))) } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 37.090 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 0.062 17755 Z= 0.293 Angle : 0.775 7.903 24185 Z= 0.367 Chirality : 0.051 0.307 2740 Planarity : 0.007 0.110 2855 Dihedral : 19.215 155.263 7600 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.56 % Allowed : 0.00 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 1955 helix: 1.11 (0.18), residues: 800 sheet: -0.75 (0.23), residues: 440 loop : -0.34 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.002 ARG B 78 TYR 0.014 0.002 TYR D 117 PHE 0.020 0.001 PHE C 99 TRP 0.012 0.002 TRP A 307 HIS 0.002 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.29 (17715) covalent geometry : angle 0.76040 / 0.36 (24075) SS BOND : bond 0.00994 / 0.54 ( 10) SS BOND : angle 1.85945 / 1.11 ( 20) hydrogen bonds : bond 0.18056 / 11.66 ( 881) hydrogen bonds : angle 6.67987 / 4.68 ( 2883) link_BETA1-4 : bond 0.00877 / 0.52 ( 15) link_BETA1-4 : angle 2.28025 / 1.49 ( 45) link_NAG-ASN : bond 0.00323 / 0.16 ( 15) link_NAG-ASN : angle 2.51808 / 1.51 ( 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 360 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 350 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.8343 (mtp) cc_final: 0.7936 (mtp) REVERT: B 188 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7669 (mp0) REVERT: B 258 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6455 (mm-30) REVERT: B 446 ARG cc_start: 0.8427 (tpp80) cc_final: 0.8119 (tpp80) REVERT: C 252 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7533 (t80) REVERT: C 260 MET cc_start: 0.8974 (mmm) cc_final: 0.8548 (mmm) REVERT: C 322 MET cc_start: 0.8345 (mtp) cc_final: 0.8098 (mtp) REVERT: C 446 ARG cc_start: 0.8386 (tpp80) cc_final: 0.8127 (tpp80) REVERT: D 40 MET cc_start: 0.8514 (mtp) cc_final: 0.8099 (mtp) REVERT: D 446 ARG cc_start: 0.8341 (tpp80) cc_final: 0.8075 (tpp80) REVERT: E 57 MET cc_start: 0.9051 (mtm) cc_final: 0.8845 (mtp) REVERT: E 188 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7586 (mm-30) REVERT: E 260 MET cc_start: 0.9035 (mmm) cc_final: 0.8781 (mmm) REVERT: E 446 ARG cc_start: 0.8250 (tpp80) cc_final: 0.8003 (tpp80) outliers start: 10 outliers final: 6 residues processed: 360 average time/residue: 1.1425 time to fit residues: 466.8677 Evaluate side-chains 276 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 269 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN B 213 ASN B 427 GLN ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN C 293 GLN D 213 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.097048 restraints weight = 48923.561| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.66 r_work: 0.2846 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17755 Z= 0.142 Angle : 0.615 6.205 24185 Z= 0.308 Chirality : 0.042 0.148 2740 Planarity : 0.004 0.038 2855 Dihedral : 18.137 150.462 3849 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.23 % Allowed : 7.84 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 1955 helix: 1.83 (0.18), residues: 800 sheet: -0.48 (0.22), residues: 450 loop : 0.01 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 78 TYR 0.012 0.001 TYR E 294 PHE 0.013 0.001 PHE A 99 TRP 0.011 0.001 TRP C 148 HIS 0.002 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (17715) covalent geometry : angle 0.60063 / 0.31 (24075) SS BOND : bond 0.00894 / 0.49 ( 10) SS BOND : angle 1.59193 / 0.95 ( 20) hydrogen bonds : bond 0.06590 / 4.30 ( 881) hydrogen bonds : angle 5.24724 / 3.67 ( 2883) link_BETA1-4 : bond 0.00495 / 0.31 ( 15) link_BETA1-4 : angle 1.81477 / 1.30 ( 45) link_NAG-ASN : bond 0.00129 / 0.08 ( 15) link_NAG-ASN : angle 2.37361 / 1.42 ( 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 309 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 287 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7455 (mtt) cc_final: 0.7251 (mtt) REVERT: A 278 MET cc_start: 0.7864 (tpt) cc_final: 0.7638 (mmt) REVERT: A 415 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 450 MET cc_start: 0.7477 (mmt) cc_final: 0.7273 (mpm) REVERT: B 40 MET cc_start: 0.8772 (mtp) cc_final: 0.8376 (mtp) REVERT: B 188 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7928 (mt-10) REVERT: B 253 MET cc_start: 0.7557 (mtt) cc_final: 0.7346 (mtt) REVERT: C 252 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7466 (t80) REVERT: C 258 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6658 (mm-30) REVERT: C 260 MET cc_start: 0.9019 (mmm) cc_final: 0.8618 (mmm) REVERT: C 309 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7785 (ttm110) REVERT: C 322 MET cc_start: 0.8289 (mtp) cc_final: 0.8033 (mtp) REVERT: C 446 ARG cc_start: 0.8407 (tpp80) cc_final: 0.8105 (tpp80) REVERT: D 40 MET cc_start: 0.8901 (mtp) cc_final: 0.8554 (mtp) REVERT: D 265 ASP cc_start: 0.8443 (m-30) cc_final: 0.8236 (m-30) REVERT: D 309 ARG cc_start: 0.8268 (ttm110) cc_final: 0.7850 (ttm-80) REVERT: D 430 SER cc_start: 0.8725 (t) cc_final: 0.8515 (m) REVERT: D 450 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7483 (mpm) REVERT: E 57 MET cc_start: 0.9298 (mtm) cc_final: 0.9060 (mtp) REVERT: E 188 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7960 (mm-30) REVERT: E 253 MET cc_start: 0.6300 (mtp) cc_final: 0.6076 (mtp) REVERT: E 260 MET cc_start: 0.9061 (mmm) cc_final: 0.8859 (mmm) REVERT: E 278 MET cc_start: 0.8053 (tpt) cc_final: 0.7820 (mmt) REVERT: E 430 SER cc_start: 0.8761 (t) cc_final: 0.8557 (m) REVERT: E 446 ARG cc_start: 0.8451 (tpp80) cc_final: 0.8192 (tpp80) outliers start: 22 outliers final: 7 residues processed: 301 average time/residue: 1.0531 time to fit residues: 362.9811 Evaluate side-chains 284 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 275 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 173 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 0.0060 chunk 41 optimal weight: 3.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.094877 restraints weight = 51383.693| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.70 r_work: 0.2816 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17755 Z= 0.176 Angle : 0.611 5.495 24185 Z= 0.312 Chirality : 0.042 0.153 2740 Planarity : 0.005 0.048 2855 Dihedral : 16.019 145.970 3847 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.18 % Allowed : 9.80 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 1955 helix: 2.04 (0.17), residues: 800 sheet: -0.39 (0.22), residues: 450 loop : 0.08 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 78 TYR 0.016 0.002 TYR D 14 PHE 0.017 0.002 PHE D 99 TRP 0.012 0.002 TRP C 148 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (17715) covalent geometry : angle 0.59654 / 0.31 (24075) SS BOND : bond 0.01081 / 0.59 ( 10) SS BOND : angle 1.95600 / 1.17 ( 20) hydrogen bonds : bond 0.06425 / 4.19 ( 881) hydrogen bonds : angle 5.07843 / 3.55 ( 2883) link_BETA1-4 : bond 0.00492 / 0.31 ( 15) link_BETA1-4 : angle 1.84945 / 1.27 ( 45) link_NAG-ASN : bond 0.00219 / 0.13 ( 15) link_NAG-ASN : angle 2.33317 / 1.39 ( 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 311 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 290 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.7508 (mmt) cc_final: 0.7295 (mpm) REVERT: B 40 MET cc_start: 0.8798 (mtp) cc_final: 0.8388 (mtp) REVERT: B 188 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7778 (mt-10) REVERT: C 174 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8420 (t70) REVERT: C 252 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7559 (t80) REVERT: C 253 MET cc_start: 0.6240 (mtp) cc_final: 0.5921 (mtp) REVERT: C 258 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6570 (mm-30) REVERT: C 260 MET cc_start: 0.8985 (mmm) cc_final: 0.8693 (mmm) REVERT: C 278 MET cc_start: 0.8248 (mmt) cc_final: 0.7937 (mmm) REVERT: C 322 MET cc_start: 0.8341 (mtp) cc_final: 0.8074 (mtp) REVERT: C 446 ARG cc_start: 0.8477 (tpp80) cc_final: 0.8147 (tpp80) REVERT: D 40 MET cc_start: 0.8900 (mtp) cc_final: 0.8518 (mtp) REVERT: D 309 ARG cc_start: 0.8277 (ttm110) cc_final: 0.8029 (ttm-80) REVERT: D 450 MET cc_start: 0.7646 (mmt) cc_final: 0.7354 (mpm) REVERT: E 57 MET cc_start: 0.9301 (mtm) cc_final: 0.9059 (mtp) REVERT: E 174 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8488 (t70) REVERT: E 188 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8006 (mm-30) REVERT: E 446 ARG cc_start: 0.8478 (tpp80) cc_final: 0.8201 (tpp80) outliers start: 21 outliers final: 12 residues processed: 299 average time/residue: 0.9900 time to fit residues: 341.2058 Evaluate side-chains 293 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 278 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 14 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 chunk 159 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.095423 restraints weight = 51695.930| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.70 r_work: 0.2827 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 2.94 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) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17755 Z= 0.158 Angle : 0.571 5.567 24185 Z= 0.295 Chirality : 0.040 0.156 2740 Planarity : 0.005 0.041 2855 Dihedral : 15.013 140.565 3847 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.29 % Allowed : 10.64 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.18), residues: 1955 helix: 2.19 (0.17), residues: 800 sheet: -0.39 (0.22), residues: 450 loop : 0.09 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 446 TYR 0.012 0.001 TYR D 14 PHE 0.018 0.001 PHE E 319 TRP 0.010 0.001 TRP C 148 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (17715) covalent geometry : angle 0.55637 / 0.29 (24075) SS BOND : bond 0.01035 / 0.56 ( 10) SS BOND : angle 1.86408 / 1.11 ( 20) hydrogen bonds : bond 0.05766 / 3.77 ( 881) hydrogen bonds : angle 4.94163 / 3.45 ( 2883) link_BETA1-4 : bond 0.00401 / 0.26 ( 15) link_BETA1-4 : angle 1.63122 / 1.12 ( 45) link_NAG-ASN : bond 0.00155 / 0.09 ( 15) link_NAG-ASN : angle 2.37495 / 1.41 ( 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 314 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 291 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.7503 (mmt) cc_final: 0.7270 (mpm) REVERT: B 40 MET cc_start: 0.8802 (mtp) cc_final: 0.8385 (mtp) REVERT: C 174 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8369 (t70) REVERT: C 252 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7520 (t80) REVERT: C 253 MET cc_start: 0.6156 (mtp) cc_final: 0.5823 (mtp) REVERT: C 258 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6537 (mm-30) REVERT: C 260 MET cc_start: 0.8978 (mmm) cc_final: 0.8668 (mmm) REVERT: C 278 MET cc_start: 0.8271 (mmt) cc_final: 0.8061 (mmm) REVERT: C 322 MET cc_start: 0.8326 (mtp) cc_final: 0.8100 (mtp) REVERT: C 446 ARG cc_start: 0.8440 (tpp80) cc_final: 0.8086 (tpp80) REVERT: D 40 MET cc_start: 0.8881 (mtp) cc_final: 0.8509 (mtp) REVERT: D 309 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7926 (ttm-80) REVERT: D 430 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8627 (m) REVERT: D 450 MET cc_start: 0.7585 (mmt) cc_final: 0.7259 (mpm) REVERT: E 57 MET cc_start: 0.9326 (mtm) cc_final: 0.9014 (mtp) REVERT: E 174 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8420 (t70) REVERT: E 446 ARG cc_start: 0.8453 (tpp80) cc_final: 0.8157 (tpp80) outliers start: 23 outliers final: 11 residues processed: 301 average time/residue: 0.9683 time to fit residues: 337.6744 Evaluate side-chains 293 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 278 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 43 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.094977 restraints weight = 48871.864| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.66 r_work: 0.2842 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17755 Z= 0.179 Angle : 0.586 5.510 24185 Z= 0.305 Chirality : 0.041 0.162 2740 Planarity : 0.005 0.042 2855 Dihedral : 14.563 137.453 3847 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.06 % Allowed : 10.92 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.18), residues: 1955 helix: 2.28 (0.17), residues: 800 sheet: -0.38 (0.22), residues: 450 loop : 0.10 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 446 TYR 0.015 0.002 TYR D 14 PHE 0.021 0.002 PHE E 319 TRP 0.010 0.002 TRP E 66 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (17715) covalent geometry : angle 0.57194 / 0.30 (24075) SS BOND : bond 0.01126 / 0.61 ( 10) SS BOND : angle 2.01961 / 1.20 ( 20) hydrogen bonds : bond 0.05922 / 3.87 ( 881) hydrogen bonds : angle 4.94105 / 3.45 ( 2883) link_BETA1-4 : bond 0.00379 / 0.24 ( 15) link_BETA1-4 : angle 1.48253 / 0.98 ( 45) link_NAG-ASN : bond 0.00179 / 0.11 ( 15) link_NAG-ASN : angle 2.40158 / 1.43 ( 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 303 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 284 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.7506 (mmt) cc_final: 0.7274 (mpm) REVERT: B 40 MET cc_start: 0.8774 (mtp) cc_final: 0.8325 (mtp) REVERT: C 174 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8383 (t70) REVERT: C 252 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7493 (t80) REVERT: C 253 MET cc_start: 0.6044 (mtp) cc_final: 0.5724 (mtp) REVERT: C 258 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6428 (mm-30) REVERT: C 260 MET cc_start: 0.8961 (mmm) cc_final: 0.8638 (mmm) REVERT: C 322 MET cc_start: 0.8350 (mtp) cc_final: 0.8115 (mtp) REVERT: C 435 SER cc_start: 0.8527 (m) cc_final: 0.8302 (p) REVERT: D 40 MET cc_start: 0.8881 (mtp) cc_final: 0.8534 (mtp) REVERT: D 309 ARG cc_start: 0.8126 (ttm110) cc_final: 0.7833 (ttm-80) REVERT: D 450 MET cc_start: 0.7611 (mmt) cc_final: 0.7281 (mpm) REVERT: E 57 MET cc_start: 0.9325 (mtm) cc_final: 0.8996 (mtp) REVERT: E 188 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7954 (mm-30) REVERT: E 446 ARG cc_start: 0.8514 (tpp80) cc_final: 0.8209 (tpp80) outliers start: 19 outliers final: 14 residues processed: 295 average time/residue: 0.9847 time to fit residues: 336.4450 Evaluate side-chains 291 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 254 LEU 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 0 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.094805 restraints weight = 53096.682| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.72 r_work: 0.2839 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17755 Z= 0.165 Angle : 0.569 5.413 24185 Z= 0.296 Chirality : 0.040 0.163 2740 Planarity : 0.005 0.041 2855 Dihedral : 14.182 134.067 3847 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.18 % Allowed : 11.15 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.18), residues: 1955 helix: 2.34 (0.17), residues: 800 sheet: -0.39 (0.22), residues: 450 loop : 0.11 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 446 TYR 0.012 0.002 TYR D 14 PHE 0.020 0.002 PHE E 319 TRP 0.009 0.002 TRP C 85 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (17715) covalent geometry : angle 0.55502 / 0.29 (24075) SS BOND : bond 0.01086 / 0.59 ( 10) SS BOND : angle 1.91442 / 1.14 ( 20) hydrogen bonds : bond 0.05673 / 3.72 ( 881) hydrogen bonds : angle 4.88354 / 3.41 ( 2883) link_BETA1-4 : bond 0.00331 / 0.21 ( 15) link_BETA1-4 : angle 1.40675 / 0.94 ( 45) link_NAG-ASN : bond 0.00129 / 0.08 ( 15) link_NAG-ASN : angle 2.37738 / 1.42 ( 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 305 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 284 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 SER cc_start: 0.8677 (m) cc_final: 0.8456 (p) REVERT: A 450 MET cc_start: 0.7501 (mmt) cc_final: 0.7270 (mpm) REVERT: B 40 MET cc_start: 0.8784 (mtp) cc_final: 0.8342 (mtp) REVERT: C 174 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8393 (t70) REVERT: C 252 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7311 (t80) REVERT: C 253 MET cc_start: 0.5939 (mtp) cc_final: 0.5649 (mtp) REVERT: C 258 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6472 (mm-30) REVERT: C 260 MET cc_start: 0.8942 (mmm) cc_final: 0.8626 (mmm) REVERT: C 322 MET cc_start: 0.8331 (mtp) cc_final: 0.8121 (mtp) REVERT: D 40 MET cc_start: 0.8894 (mtp) cc_final: 0.8564 (mtp) REVERT: D 309 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7856 (ttm-80) REVERT: D 430 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8649 (m) REVERT: D 450 MET cc_start: 0.7623 (mmt) cc_final: 0.7291 (mpm) REVERT: E 57 MET cc_start: 0.9324 (mtm) cc_final: 0.8980 (mtp) REVERT: E 174 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8406 (t70) REVERT: E 188 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7966 (mm-30) REVERT: E 446 ARG cc_start: 0.8478 (tpp80) cc_final: 0.8169 (tpp80) outliers start: 21 outliers final: 13 residues processed: 296 average time/residue: 0.9540 time to fit residues: 328.7508 Evaluate side-chains 295 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 278 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 139 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.096797 restraints weight = 57356.275| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.79 r_work: 0.2867 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17755 Z= 0.109 Angle : 0.510 5.073 24185 Z= 0.262 Chirality : 0.038 0.142 2740 Planarity : 0.004 0.046 2855 Dihedral : 13.316 128.790 3847 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.18 % Allowed : 11.54 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.18), residues: 1955 helix: 2.55 (0.17), residues: 800 sheet: -0.33 (0.22), residues: 450 loop : 0.23 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 446 TYR 0.008 0.001 TYR E 117 PHE 0.020 0.001 PHE E 319 TRP 0.008 0.001 TRP C 148 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (17715) covalent geometry : angle 0.49622 / 0.26 (24075) SS BOND : bond 0.00876 / 0.47 ( 10) SS BOND : angle 1.38475 / 0.81 ( 20) hydrogen bonds : bond 0.04880 / 3.21 ( 881) hydrogen bonds : angle 4.63704 / 3.24 ( 2883) link_BETA1-4 : bond 0.00336 / 0.21 ( 15) link_BETA1-4 : angle 1.32005 / 0.89 ( 45) link_NAG-ASN : bond 0.00102 / 0.06 ( 15) link_NAG-ASN : angle 2.30414 / 1.37 ( 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 307 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 286 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.7567 (mmt) cc_final: 0.7327 (mpm) REVERT: B 40 MET cc_start: 0.8804 (mtp) cc_final: 0.8401 (mtp) REVERT: B 278 MET cc_start: 0.8431 (mmm) cc_final: 0.8219 (mmm) REVERT: C 174 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: C 252 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7272 (t80) REVERT: C 253 MET cc_start: 0.5902 (mtp) cc_final: 0.5663 (mtp) REVERT: C 260 MET cc_start: 0.8914 (mmm) cc_final: 0.8525 (mmm) REVERT: D 40 MET cc_start: 0.8808 (mtp) cc_final: 0.8486 (mtp) REVERT: D 253 MET cc_start: 0.6308 (mtp) cc_final: 0.5921 (mtp) REVERT: D 309 ARG cc_start: 0.8114 (ttm110) cc_final: 0.7800 (ttm-80) REVERT: D 450 MET cc_start: 0.7587 (mmt) cc_final: 0.7358 (mpm) REVERT: E 57 MET cc_start: 0.9313 (mtm) cc_final: 0.8956 (mtp) REVERT: E 188 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8005 (mm-30) REVERT: E 446 ARG cc_start: 0.8414 (tpp80) cc_final: 0.8114 (tpp80) outliers start: 21 outliers final: 15 residues processed: 299 average time/residue: 0.9728 time to fit residues: 336.7828 Evaluate side-chains 291 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 274 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 189 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 188 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.096114 restraints weight = 46286.267| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.64 r_work: 0.2836 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17755 Z= 0.150 Angle : 0.550 5.406 24185 Z= 0.284 Chirality : 0.040 0.158 2740 Planarity : 0.005 0.044 2855 Dihedral : 13.376 127.898 3847 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.06 % Allowed : 11.88 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.18), residues: 1955 helix: 2.58 (0.17), residues: 800 sheet: -0.33 (0.22), residues: 450 loop : 0.24 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 446 TYR 0.012 0.001 TYR D 14 PHE 0.021 0.001 PHE E 319 TRP 0.009 0.001 TRP C 85 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (17715) covalent geometry : angle 0.53669 / 0.28 (24075) SS BOND : bond 0.01000 / 0.54 ( 10) SS BOND : angle 1.81953 / 1.08 ( 20) hydrogen bonds : bond 0.05292 / 3.47 ( 881) hydrogen bonds : angle 4.73680 / 3.31 ( 2883) link_BETA1-4 : bond 0.00350 / 0.22 ( 15) link_BETA1-4 : angle 1.34104 / 0.88 ( 45) link_NAG-ASN : bond 0.00134 / 0.08 ( 15) link_NAG-ASN : angle 2.30178 / 1.37 ( 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 293 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 274 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.7545 (mmt) cc_final: 0.7311 (mpm) REVERT: B 40 MET cc_start: 0.8804 (mtp) cc_final: 0.8394 (mtp) REVERT: B 469 ASN cc_start: 0.8768 (m110) cc_final: 0.8439 (m110) REVERT: C 174 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8288 (m-30) REVERT: C 252 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7305 (t80) REVERT: C 253 MET cc_start: 0.5868 (mtp) cc_final: 0.5619 (mtp) REVERT: C 260 MET cc_start: 0.8920 (mmm) cc_final: 0.8565 (mmm) REVERT: D 40 MET cc_start: 0.8840 (mtp) cc_final: 0.8517 (mtp) REVERT: D 253 MET cc_start: 0.6411 (mtp) cc_final: 0.6018 (mtp) REVERT: D 309 ARG cc_start: 0.8089 (ttm110) cc_final: 0.7837 (ttm-80) REVERT: D 450 MET cc_start: 0.7559 (mmt) cc_final: 0.7333 (mpm) REVERT: E 57 MET cc_start: 0.9314 (mtm) cc_final: 0.8957 (mtp) REVERT: E 188 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7958 (mm-30) REVERT: E 446 ARG cc_start: 0.8387 (tpp80) cc_final: 0.8079 (tpp80) outliers start: 19 outliers final: 15 residues processed: 287 average time/residue: 0.9687 time to fit residues: 323.1430 Evaluate side-chains 290 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 273 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.140580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.096041 restraints weight = 51847.083| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.71 r_work: 0.2849 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17755 Z= 0.137 Angle : 0.538 5.252 24185 Z= 0.279 Chirality : 0.039 0.156 2740 Planarity : 0.005 0.047 2855 Dihedral : 13.176 127.742 3847 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.06 % Allowed : 11.82 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.18), residues: 1955 helix: 2.55 (0.17), residues: 805 sheet: -0.33 (0.22), residues: 450 loop : 0.30 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 185 TYR 0.011 0.001 TYR D 14 PHE 0.022 0.001 PHE E 319 TRP 0.008 0.001 TRP C 148 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (17715) covalent geometry : angle 0.52474 / 0.28 (24075) SS BOND : bond 0.00983 / 0.53 ( 10) SS BOND : angle 1.74065 / 1.03 ( 20) hydrogen bonds : bond 0.05140 / 3.37 ( 881) hydrogen bonds : angle 4.70740 / 3.28 ( 2883) link_BETA1-4 : bond 0.00327 / 0.21 ( 15) link_BETA1-4 : angle 1.32607 / 0.88 ( 45) link_NAG-ASN : bond 0.00103 / 0.06 ( 15) link_NAG-ASN : angle 2.31896 / 1.38 ( 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 289 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 270 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7682 (ttm-80) REVERT: A 450 MET cc_start: 0.7565 (mmt) cc_final: 0.7334 (mpm) REVERT: B 40 MET cc_start: 0.8804 (mtp) cc_final: 0.8396 (mtp) REVERT: B 469 ASN cc_start: 0.8782 (m110) cc_final: 0.8439 (m110) REVERT: C 174 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: C 252 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7312 (t80) REVERT: C 253 MET cc_start: 0.5918 (mtp) cc_final: 0.5685 (mtp) REVERT: C 260 MET cc_start: 0.8901 (mmm) cc_final: 0.8639 (mmm) REVERT: C 278 MET cc_start: 0.8316 (mmm) cc_final: 0.8111 (mmm) REVERT: D 40 MET cc_start: 0.8843 (mtp) cc_final: 0.8523 (mtp) REVERT: D 253 MET cc_start: 0.6343 (mtp) cc_final: 0.5948 (mtp) REVERT: D 450 MET cc_start: 0.7614 (mmt) cc_final: 0.7392 (mpm) REVERT: E 57 MET cc_start: 0.9315 (mtm) cc_final: 0.8963 (mtp) REVERT: E 188 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7978 (mm-30) REVERT: E 446 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8098 (tpp80) outliers start: 19 outliers final: 17 residues processed: 284 average time/residue: 0.9630 time to fit residues: 320.7519 Evaluate side-chains 287 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 268 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 130 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 147 optimal weight: 0.0470 chunk 172 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 47 optimal weight: 0.0050 chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.098611 restraints weight = 50500.022| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.69 r_work: 0.2890 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17755 Z= 0.102 Angle : 0.497 5.289 24185 Z= 0.255 Chirality : 0.038 0.141 2740 Planarity : 0.004 0.050 2855 Dihedral : 12.504 126.217 3847 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.90 % Allowed : 12.10 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.18), residues: 1955 helix: 2.73 (0.17), residues: 800 sheet: -0.29 (0.22), residues: 450 loop : 0.33 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 446 TYR 0.008 0.001 TYR E 117 PHE 0.021 0.001 PHE E 319 TRP 0.007 0.001 TRP A 59 HIS 0.002 0.000 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (17715) covalent geometry : angle 0.48418 / 0.25 (24075) SS BOND : bond 0.00849 / 0.46 ( 10) SS BOND : angle 1.28729 / 0.76 ( 20) hydrogen bonds : bond 0.04524 / 2.97 ( 881) hydrogen bonds : angle 4.49239 / 3.13 ( 2883) link_BETA1-4 : bond 0.00337 / 0.22 ( 15) link_BETA1-4 : angle 1.28524 / 0.87 ( 45) link_NAG-ASN : bond 0.00096 / 0.06 ( 15) link_NAG-ASN : angle 2.22926 / 1.33 ( 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 283 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 267 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7638 (ttm-80) REVERT: A 450 MET cc_start: 0.7482 (mmt) cc_final: 0.7248 (mpm) REVERT: B 40 MET cc_start: 0.8746 (mtp) cc_final: 0.8372 (mtp) REVERT: B 469 ASN cc_start: 0.8783 (m110) cc_final: 0.8455 (m110) REVERT: C 252 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7264 (t80) REVERT: C 253 MET cc_start: 0.5732 (mtp) cc_final: 0.5485 (mtp) REVERT: C 260 MET cc_start: 0.8890 (mmm) cc_final: 0.8650 (mmm) REVERT: D 40 MET cc_start: 0.8766 (mtp) cc_final: 0.8454 (mtp) REVERT: D 253 MET cc_start: 0.6189 (mtp) cc_final: 0.5787 (mtp) REVERT: D 309 ARG cc_start: 0.8081 (ttm110) cc_final: 0.7759 (ttm-80) REVERT: D 450 MET cc_start: 0.7524 (mmt) cc_final: 0.7311 (mpm) REVERT: E 57 MET cc_start: 0.9278 (mtm) cc_final: 0.8911 (mtp) REVERT: E 188 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7965 (mm-30) REVERT: E 435 SER cc_start: 0.8619 (m) cc_final: 0.8327 (p) outliers start: 16 outliers final: 10 residues processed: 280 average time/residue: 0.9321 time to fit residues: 302.2957 Evaluate side-chains 274 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 263 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 177 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 104 optimal weight: 0.3980 chunk 145 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.098022 restraints weight = 52234.577| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.71 r_work: 0.2887 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17755 Z= 0.107 Angle : 0.501 5.201 24185 Z= 0.257 Chirality : 0.038 0.144 2740 Planarity : 0.004 0.075 2855 Dihedral : 12.208 126.247 3847 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.62 % Allowed : 12.61 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.19), residues: 1955 helix: 2.75 (0.17), residues: 805 sheet: -0.27 (0.22), residues: 450 loop : 0.44 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 446 TYR 0.008 0.001 TYR C 14 PHE 0.021 0.001 PHE E 319 TRP 0.007 0.001 TRP C 85 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (17715) covalent geometry : angle 0.48826 / 0.25 (24075) SS BOND : bond 0.00842 / 0.46 ( 10) SS BOND : angle 1.42033 / 0.84 ( 20) hydrogen bonds : bond 0.04510 / 2.96 ( 881) hydrogen bonds : angle 4.44759 / 3.10 ( 2883) link_BETA1-4 : bond 0.00361 / 0.23 ( 15) link_BETA1-4 : angle 1.25970 / 0.84 ( 45) link_NAG-ASN : bond 0.00110 / 0.06 ( 15) link_NAG-ASN : angle 2.17132 / 1.30 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13404.03 seconds wall clock time: 227 minutes 12.56 seconds (13632.56 seconds total)