Starting phenix.real_space_refine on Tue May 5 19:33:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utb_42537/05_2026/8utb_42537_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utb_42537/05_2026/8utb_42537.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8utb_42537/05_2026/8utb_42537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utb_42537/05_2026/8utb_42537.map" model { file = "/net/cci-nas-00/data/ceres_data/8utb_42537/05_2026/8utb_42537_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utb_42537/05_2026/8utb_42537_trim.cif" } 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= 0.012 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 P 5 5.49 5 S 110 5.16 5 Cl 15 4.86 5 C 10675 2.51 5 N 2525 2.21 5 O 2990 1.98 5 F 15 1.80 5 H 15105 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31440 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 bond proxies already assigned to first conformer: 6125 Chain: "B" Number of atoms: 6067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 bond proxies already assigned to first conformer: 6125 Chain: "C" Number of atoms: 6067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 bond proxies already assigned to first conformer: 6125 Chain: "D" Number of atoms: 6067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 bond proxies already assigned to first conformer: 6125 Chain: "E" Number of atoms: 6067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 375, 6055 Classifications: {'peptide': 375} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 bond proxies already assigned to first conformer: 6125 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 142 Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'XG3': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 142 Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'XG3': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 142 Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'XG3': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 142 Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'XG3': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 142 Unusual residues: {'9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'XG3': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 9.69, per 1000 atoms: 0.31 Number of scatterers: 31440 At special positions: 0 Unit cell: (100.347, 102.505, 165.087, 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) Cl 15 17.00 S 110 16.00 P 5 15.00 F 15 9.00 O 2990 8.00 N 2525 7.00 C 10675 6.00 H 15105 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 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 23 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN B 23 " " NAG I 1 " - " ASN B 110 " " NAG J 1 " - " ASN C 23 " " NAG K 1 " - " ASN C 110 " " NAG L 1 " - " ASN D 23 " " NAG M 1 " - " ASN D 110 " " NAG N 1 " - " ASN E 23 " " NAG O 1 " - " ASN E 110 " Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.4 seconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 40.6% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.787A 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 215 through 227 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 269 through 296 removed outlier: 3.954A pdb=" N TYR A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) 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 459 Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.787A 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 215 through 227 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 237 through 260 Processing helix chain 'B' and resid 269 through 296 removed outlier: 3.954A pdb=" N TYR B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) 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 459 Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.788A 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 215 through 227 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 237 through 260 Processing helix chain 'C' and resid 269 through 296 removed outlier: 3.954A pdb=" N TYR C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) 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 459 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.787A 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 215 through 227 Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 237 through 260 Processing helix chain 'D' and resid 269 through 296 removed outlier: 3.955A pdb=" N TYR D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) 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 459 Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.787A 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 215 through 227 Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'E' and resid 269 through 296 removed outlier: 3.955A pdb=" N TYR E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) 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 459 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.074A 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: 4.074A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN A 52 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE A 39 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N TRP A 54 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A 37 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN A 56 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N SER A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N SER A 58 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER A 33 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N THR A 60 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N TYR A 31 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.564A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.735A 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: 4.564A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU A 192 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR A 187 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 185 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.073A 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: 4.073A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N THR B 60 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N TYR B 31 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.564A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.735A 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: 4.564A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU B 192 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR B 187 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 185 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.074A 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: 4.074A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 52 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE C 39 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N TRP C 54 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU C 37 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN C 56 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N SER C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N SER C 58 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER C 33 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N THR C 60 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N TYR C 31 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.564A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.735A 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: 4.564A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU C 192 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR C 187 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 185 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.073A 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: 4.073A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.564A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.735A 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: 4.564A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU D 192 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR D 187 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 185 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.073A 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: 4.073A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.564A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.735A 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: 4.564A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU E 192 " --> pdb=" O TYR E 187 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR E 187 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG E 185 " --> pdb=" O TYR E 194 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2628 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.38 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15070 1.03 - 1.23: 663 1.23 - 1.43: 6587 1.43 - 1.64: 9360 1.64 - 1.84: 175 Bond restraints: 31855 Sorted by residual: bond pdb=" O12 POV E 601 " pdb=" P POV E 601 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 9.79e+00 bond pdb=" O12 POV B 601 " pdb=" P POV B 601 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.70e+00 bond pdb=" O12 POV A 605 " pdb=" P POV A 605 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.63e+00 bond pdb=" O12 POV C 601 " pdb=" P POV C 601 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.62e+00 bond pdb=" O12 POV D 601 " pdb=" P POV D 601 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.52e+00 ... (remaining 31850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.91: 57120 5.91 - 11.83: 15 11.83 - 17.74: 0 17.74 - 23.65: 10 23.65 - 29.57: 20 Bond angle restraints: 57165 Sorted by residual: angle pdb=" CG LEU E 320 " pdb=" CD1 LEU E 320 " pdb="HD12 LEU E 320 " ideal model delta sigma weight residual 109.00 79.43 29.57 3.00e+00 1.11e-01 9.71e+01 angle pdb=" CG LEU B 320 " pdb=" CD1 LEU B 320 " pdb="HD12 LEU B 320 " ideal model delta sigma weight residual 109.00 79.44 29.56 3.00e+00 1.11e-01 9.71e+01 angle pdb=" CG LEU A 320 " pdb=" CD1 LEU A 320 " pdb="HD12 LEU A 320 " ideal model delta sigma weight residual 109.00 79.44 29.56 3.00e+00 1.11e-01 9.71e+01 angle pdb=" CG LEU C 320 " pdb=" CD1 LEU C 320 " pdb="HD12 LEU C 320 " ideal model delta sigma weight residual 109.00 79.47 29.53 3.00e+00 1.11e-01 9.69e+01 angle pdb=" CG LEU D 320 " pdb=" CD1 LEU D 320 " pdb="HD12 LEU D 320 " ideal model delta sigma weight residual 109.00 79.49 29.51 3.00e+00 1.11e-01 9.68e+01 ... (remaining 57160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.85: 15150 29.85 - 59.69: 690 59.69 - 89.54: 115 89.54 - 119.39: 55 119.39 - 149.23: 10 Dihedral angle restraints: 16020 sinusoidal: 9175 harmonic: 6845 Sorted by residual: dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual -180.00 -156.21 -23.79 0 5.00e+00 4.00e-02 2.26e+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 -156.24 -23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N CYS A 190 " pdb=" CA CYS A 190 " ideal model delta harmonic sigma weight residual 180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 16017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2058 0.054 - 0.109: 422 0.109 - 0.163: 94 0.163 - 0.217: 17 0.217 - 0.271: 19 Chirality restraints: 2610 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.84e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.82e+02 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 -2.13 -0.27 2.00e-02 2.50e+03 1.79e+02 ... (remaining 2607 not shown) Planarity restraints: 4500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " -0.193 2.00e-02 2.50e+03 1.66e-01 3.46e+02 pdb=" C7 NAG J 2 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.027 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " 0.278 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.193 2.00e-02 2.50e+03 1.66e-01 3.46e+02 pdb=" C7 NAG L 2 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " 0.028 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.278 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.193 2.00e-02 2.50e+03 1.66e-01 3.46e+02 pdb=" C7 NAG H 2 " -0.036 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.277 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.148 2.00e-02 2.50e+03 ... (remaining 4497 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 3786 2.25 - 2.84: 68014 2.84 - 3.42: 82213 3.42 - 4.01: 117596 4.01 - 4.60: 174443 Nonbonded interactions: 446052 Sorted by model distance: nonbonded pdb=" HE2 HIS A 296 " pdb=" O HOH A 702 " model vdw 1.659 2.450 nonbonded pdb=" HE2 HIS B 296 " pdb=" O HOH B 702 " model vdw 1.659 2.450 nonbonded pdb=" HE2 HIS D 296 " pdb=" O HOH D 702 " model vdw 1.659 2.450 nonbonded pdb=" HE2 HIS E 296 " pdb=" O HOH E 702 " model vdw 1.659 2.450 nonbonded pdb=" HE2 HIS C 296 " pdb=" O HOH C 702 " model vdw 1.660 2.450 ... (remaining 446047 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 459)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 459)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 459)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 459)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 459)) } 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 34.270 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 0.068 16785 Z= 0.301 Angle : 0.817 8.656 22930 Z= 0.411 Chirality : 0.053 0.271 2610 Planarity : 0.015 0.166 2715 Dihedral : 18.614 149.235 7090 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.18 (0.16), residues: 1860 helix: -1.41 (0.15), residues: 710 sheet: -0.96 (0.22), residues: 435 loop : -1.56 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.019 0.002 TYR B 31 PHE 0.018 0.002 PHE B 99 TRP 0.021 0.002 TRP D 307 HIS 0.005 0.002 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00625 (16745) covalent geometry : angle 0.78214 (22820) SS BOND : bond 0.00639 ( 10) SS BOND : angle 1.66151 ( 20) hydrogen bonds : bond 0.16591 ( 786) hydrogen bonds : angle 7.23069 ( 2628) link_BETA1-4 : bond 0.00561 ( 15) link_BETA1-4 : angle 3.97359 ( 45) link_NAG-ASN : bond 0.01389 ( 15) link_NAG-ASN : angle 3.54354 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 317 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: B 133 TRP cc_start: 0.8547 (m100) cc_final: 0.8232 (m100) REVERT: B 273 TYR cc_start: 0.7517 (t80) cc_final: 0.7265 (t80) REVERT: C 293 GLN cc_start: 0.8062 (mt0) cc_final: 0.7840 (mt0) REVERT: D 430 SER cc_start: 0.8097 (m) cc_final: 0.7803 (t) REVERT: E 430 SER cc_start: 0.8130 (m) cc_final: 0.7866 (t) outliers start: 5 outliers final: 0 residues processed: 317 average time/residue: 1.3191 time to fit residues: 463.3254 Evaluate side-chains 276 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.173257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.125659 restraints weight = 48642.734| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.09 r_work: 0.3099 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.004 0.052 16785 Z= 0.198 Angle : 0.697 7.096 22930 Z= 0.348 Chirality : 0.043 0.154 2610 Planarity : 0.005 0.067 2715 Dihedral : 16.277 141.538 3485 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.82 % Allowed : 6.22 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.29 (0.18), residues: 1860 helix: 0.81 (0.18), residues: 715 sheet: -0.38 (0.23), residues: 425 loop : -0.99 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 446 TYR 0.014 0.002 TYR A 31 PHE 0.024 0.002 PHE C 99 TRP 0.011 0.002 TRP C 307 HIS 0.005 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00430 (16745) covalent geometry : angle 0.67483 (22820) SS BOND : bond 0.00803 ( 10) SS BOND : angle 1.77812 ( 20) hydrogen bonds : bond 0.05929 ( 786) hydrogen bonds : angle 5.24069 ( 2628) link_BETA1-4 : bond 0.00316 ( 15) link_BETA1-4 : angle 2.51286 ( 45) link_NAG-ASN : bond 0.00115 ( 15) link_NAG-ASN : angle 2.95721 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 278 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 304 MET cc_start: 0.7643 (ttm) cc_final: 0.7090 (ttm) REVERT: C 260 MET cc_start: 0.7045 (ttt) cc_final: 0.6785 (tpp) REVERT: C 293 GLN cc_start: 0.8505 (mt0) cc_final: 0.8283 (mt0) REVERT: D 12 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8391 (tppt) REVERT: E 260 MET cc_start: 0.6897 (ttm) cc_final: 0.6693 (ttm) REVERT: E 430 SER cc_start: 0.8038 (m) cc_final: 0.7636 (t) outliers start: 14 outliers final: 7 residues processed: 279 average time/residue: 1.2764 time to fit residues: 396.5551 Evaluate side-chains 270 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 263 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 447 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.173941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125715 restraints weight = 48991.841| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.95 r_work: 0.3119 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16785 Z= 0.143 Angle : 0.585 5.239 22930 Z= 0.295 Chirality : 0.040 0.140 2610 Planarity : 0.004 0.054 2715 Dihedral : 13.613 130.201 3485 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.82 % Allowed : 7.04 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1860 helix: 1.61 (0.19), residues: 710 sheet: -0.36 (0.23), residues: 425 loop : -0.64 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 418 TYR 0.008 0.001 TYR D 273 PHE 0.012 0.001 PHE B 99 TRP 0.011 0.001 TRP C 307 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00308 (16745) covalent geometry : angle 0.56540 (22820) SS BOND : bond 0.00774 ( 10) SS BOND : angle 1.56700 ( 20) hydrogen bonds : bond 0.05198 ( 786) hydrogen bonds : angle 4.83553 ( 2628) link_BETA1-4 : bond 0.00367 ( 15) link_BETA1-4 : angle 2.10614 ( 45) link_NAG-ASN : bond 0.00052 ( 15) link_NAG-ASN : angle 2.56124 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 288 time to evaluate : 0.702 Fit side-chains REVERT: A 304 MET cc_start: 0.7632 (ttm) cc_final: 0.7061 (ttm) REVERT: B 249 LEU cc_start: 0.8211 (tt) cc_final: 0.7929 (tp) REVERT: B 250 THR cc_start: 0.8660 (m) cc_final: 0.8417 (m) REVERT: D 97 GLU cc_start: 0.7660 (pm20) cc_final: 0.7446 (pt0) REVERT: D 273 TYR cc_start: 0.7895 (t80) cc_final: 0.7677 (t80) REVERT: E 43 ASP cc_start: 0.8536 (t70) cc_final: 0.8267 (t0) REVERT: E 174 ASP cc_start: 0.8523 (t70) cc_final: 0.8166 (t70) REVERT: E 192 GLU cc_start: 0.8535 (tt0) cc_final: 0.7934 (tt0) REVERT: E 260 MET cc_start: 0.6900 (ttm) cc_final: 0.6685 (ttm) REVERT: E 309 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7577 (ttm-80) REVERT: E 430 SER cc_start: 0.7965 (m) cc_final: 0.7567 (t) outliers start: 14 outliers final: 3 residues processed: 288 average time/residue: 1.2096 time to fit residues: 391.2160 Evaluate side-chains 278 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 274 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 309 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 67 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.171386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.117956 restraints weight = 43688.267| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.86 r_work: 0.3075 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16785 Z= 0.193 Angle : 0.606 5.784 22930 Z= 0.311 Chirality : 0.041 0.147 2610 Planarity : 0.005 0.050 2715 Dihedral : 13.043 129.668 3485 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.70 % Allowed : 7.86 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1860 helix: 1.77 (0.19), residues: 710 sheet: -0.44 (0.22), residues: 425 loop : -0.55 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 309 TYR 0.017 0.002 TYR A 31 PHE 0.017 0.002 PHE C 99 TRP 0.013 0.002 TRP C 307 HIS 0.006 0.002 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00426 (16745) covalent geometry : angle 0.58865 (22820) SS BOND : bond 0.00775 ( 10) SS BOND : angle 1.75587 ( 20) hydrogen bonds : bond 0.05210 ( 786) hydrogen bonds : angle 4.85089 ( 2628) link_BETA1-4 : bond 0.00243 ( 15) link_BETA1-4 : angle 1.76926 ( 45) link_NAG-ASN : bond 0.00090 ( 15) link_NAG-ASN : angle 2.65653 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 280 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 304 MET cc_start: 0.7656 (ttm) cc_final: 0.7086 (ttm) REVERT: B 174 ASP cc_start: 0.8447 (t70) cc_final: 0.8163 (t70) REVERT: C 260 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.6245 (tpp) REVERT: D 273 TYR cc_start: 0.7855 (t80) cc_final: 0.7640 (t80) REVERT: E 43 ASP cc_start: 0.8564 (t70) cc_final: 0.8274 (t0) REVERT: E 174 ASP cc_start: 0.8575 (t70) cc_final: 0.8316 (t70) REVERT: E 192 GLU cc_start: 0.8626 (tt0) cc_final: 0.8010 (tt0) REVERT: E 309 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7445 (ttt-90) REVERT: E 430 SER cc_start: 0.7952 (m) cc_final: 0.7525 (t) outliers start: 12 outliers final: 5 residues processed: 280 average time/residue: 1.2580 time to fit residues: 392.3284 Evaluate side-chains 275 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 268 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 309 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 132 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 150 optimal weight: 0.1980 chunk 174 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.172024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124162 restraints weight = 53091.508| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.55 r_work: 0.3035 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16785 Z= 0.158 Angle : 0.565 5.151 22930 Z= 0.289 Chirality : 0.039 0.143 2610 Planarity : 0.004 0.047 2715 Dihedral : 12.728 129.264 3485 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.65 % Allowed : 8.21 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.64 (0.19), residues: 1860 helix: 1.97 (0.19), residues: 710 sheet: -0.45 (0.23), residues: 425 loop : -0.51 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 309 TYR 0.011 0.001 TYR C 31 PHE 0.011 0.001 PHE D 134 TRP 0.011 0.001 TRP C 307 HIS 0.004 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00341 (16745) covalent geometry : angle 0.54830 (22820) SS BOND : bond 0.00771 ( 10) SS BOND : angle 1.68038 ( 20) hydrogen bonds : bond 0.04885 ( 786) hydrogen bonds : angle 4.72084 ( 2628) link_BETA1-4 : bond 0.00235 ( 15) link_BETA1-4 : angle 1.55902 ( 45) link_NAG-ASN : bond 0.00114 ( 15) link_NAG-ASN : angle 2.52706 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 274 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 304 MET cc_start: 0.7629 (ttp) cc_final: 0.7064 (ttm) REVERT: B 304 MET cc_start: 0.7695 (ttm) cc_final: 0.7201 (ttp) REVERT: C 260 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6363 (tpp) REVERT: D 439 PHE cc_start: 0.8169 (t80) cc_final: 0.7904 (t80) REVERT: E 43 ASP cc_start: 0.8609 (t70) cc_final: 0.8319 (t0) REVERT: E 174 ASP cc_start: 0.8562 (t70) cc_final: 0.8259 (t70) REVERT: E 309 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7342 (ttt-90) outliers start: 11 outliers final: 4 residues processed: 274 average time/residue: 1.2927 time to fit residues: 395.6940 Evaluate side-chains 280 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 274 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 309 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 26 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.171013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120877 restraints weight = 47557.113| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.85 r_work: 0.3061 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16785 Z= 0.210 Angle : 0.611 5.798 22930 Z= 0.314 Chirality : 0.041 0.150 2610 Planarity : 0.005 0.047 2715 Dihedral : 12.810 129.925 3485 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.76 % Allowed : 8.15 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.70 (0.19), residues: 1860 helix: 2.04 (0.19), residues: 705 sheet: -0.47 (0.23), residues: 425 loop : -0.45 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 446 TYR 0.020 0.002 TYR C 31 PHE 0.018 0.002 PHE C 99 TRP 0.012 0.002 TRP C 307 HIS 0.006 0.002 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00466 (16745) covalent geometry : angle 0.59377 (22820) SS BOND : bond 0.00790 ( 10) SS BOND : angle 1.86181 ( 20) hydrogen bonds : bond 0.05109 ( 786) hydrogen bonds : angle 4.82149 ( 2628) link_BETA1-4 : bond 0.00158 ( 15) link_BETA1-4 : angle 1.61290 ( 45) link_NAG-ASN : bond 0.00155 ( 15) link_NAG-ASN : angle 2.67312 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 281 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 304 MET cc_start: 0.7693 (ttp) cc_final: 0.7314 (ttp) REVERT: B 174 ASP cc_start: 0.8440 (t70) cc_final: 0.8179 (t70) REVERT: B 304 MET cc_start: 0.7830 (ttm) cc_final: 0.7258 (ttp) REVERT: C 260 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6446 (tpp) REVERT: E 43 ASP cc_start: 0.8565 (t70) cc_final: 0.8289 (t0) REVERT: E 260 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6593 (ttm) REVERT: E 309 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7489 (ttm-80) outliers start: 13 outliers final: 5 residues processed: 282 average time/residue: 1.2290 time to fit residues: 386.6862 Evaluate side-chains 277 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 269 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 77 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.172267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121187 restraints weight = 45879.013| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.74 r_work: 0.3060 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16785 Z= 0.146 Angle : 0.548 5.065 22930 Z= 0.281 Chirality : 0.039 0.141 2610 Planarity : 0.004 0.045 2715 Dihedral : 11.952 128.150 3485 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.53 % Allowed : 8.50 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.80 (0.19), residues: 1860 helix: 2.14 (0.19), residues: 710 sheet: -0.45 (0.23), residues: 425 loop : -0.40 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 309 TYR 0.011 0.001 TYR C 31 PHE 0.012 0.001 PHE D 134 TRP 0.011 0.001 TRP C 148 HIS 0.003 0.001 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00316 (16745) covalent geometry : angle 0.53212 (22820) SS BOND : bond 0.00779 ( 10) SS BOND : angle 1.59855 ( 20) hydrogen bonds : bond 0.04675 ( 786) hydrogen bonds : angle 4.64303 ( 2628) link_BETA1-4 : bond 0.00200 ( 15) link_BETA1-4 : angle 1.44867 ( 45) link_NAG-ASN : bond 0.00116 ( 15) link_NAG-ASN : angle 2.45751 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 272 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.7679 (ttp) cc_final: 0.7295 (ttp) REVERT: B 304 MET cc_start: 0.7817 (ttp) cc_final: 0.7249 (ttp) REVERT: C 260 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6426 (tpp) REVERT: D 439 PHE cc_start: 0.8187 (t80) cc_final: 0.7894 (t80) REVERT: E 43 ASP cc_start: 0.8593 (t70) cc_final: 0.8328 (t0) REVERT: E 174 ASP cc_start: 0.8449 (t70) cc_final: 0.8172 (t70) REVERT: E 309 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7476 (ttm-80) outliers start: 9 outliers final: 5 residues processed: 273 average time/residue: 1.3116 time to fit residues: 401.4914 Evaluate side-chains 279 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 272 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 309 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 70 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.171230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120787 restraints weight = 50555.036| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.16 r_work: 0.3031 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16785 Z= 0.201 Angle : 0.595 5.557 22930 Z= 0.306 Chirality : 0.040 0.147 2610 Planarity : 0.005 0.046 2715 Dihedral : 11.722 128.239 3485 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.47 % Allowed : 8.86 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.82 (0.19), residues: 1860 helix: 2.17 (0.19), residues: 705 sheet: -0.47 (0.23), residues: 425 loop : -0.37 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 446 TYR 0.019 0.002 TYR C 31 PHE 0.017 0.002 PHE C 99 TRP 0.011 0.002 TRP C 148 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00446 (16745) covalent geometry : angle 0.57856 (22820) SS BOND : bond 0.00780 ( 10) SS BOND : angle 1.81172 ( 20) hydrogen bonds : bond 0.04956 ( 786) hydrogen bonds : angle 4.76806 ( 2628) link_BETA1-4 : bond 0.00148 ( 15) link_BETA1-4 : angle 1.53595 ( 45) link_NAG-ASN : bond 0.00158 ( 15) link_NAG-ASN : angle 2.61892 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 276 time to evaluate : 0.737 Fit side-chains REVERT: A 304 MET cc_start: 0.7683 (ttp) cc_final: 0.7297 (ttp) REVERT: B 304 MET cc_start: 0.7810 (ttp) cc_final: 0.7252 (ttp) REVERT: C 260 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6327 (tpp) REVERT: E 9 GLU cc_start: 0.8165 (tp30) cc_final: 0.7923 (tp30) REVERT: E 43 ASP cc_start: 0.8562 (t70) cc_final: 0.8293 (t0) REVERT: E 260 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6598 (ttm) REVERT: E 309 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7360 (ttm-80) outliers start: 8 outliers final: 5 residues processed: 277 average time/residue: 1.2586 time to fit residues: 387.9705 Evaluate side-chains 284 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 276 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 49 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.170699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120713 restraints weight = 47660.886| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.85 r_work: 0.3056 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16785 Z= 0.234 Angle : 0.628 5.750 22930 Z= 0.323 Chirality : 0.041 0.151 2610 Planarity : 0.005 0.051 2715 Dihedral : 11.647 128.287 3485 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.53 % Allowed : 8.86 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.86 (0.19), residues: 1860 helix: 2.08 (0.19), residues: 705 sheet: -0.21 (0.22), residues: 470 loop : -0.38 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 78 TYR 0.022 0.002 TYR C 31 PHE 0.017 0.002 PHE C 99 TRP 0.012 0.002 TRP C 307 HIS 0.007 0.002 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00517 (16745) covalent geometry : angle 0.61181 (22820) SS BOND : bond 0.00786 ( 10) SS BOND : angle 1.95751 ( 20) hydrogen bonds : bond 0.05133 ( 786) hydrogen bonds : angle 4.86298 ( 2628) link_BETA1-4 : bond 0.00129 ( 15) link_BETA1-4 : angle 1.60440 ( 45) link_NAG-ASN : bond 0.00233 ( 15) link_NAG-ASN : angle 2.67883 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 269 time to evaluate : 0.822 Fit side-chains REVERT: A 304 MET cc_start: 0.7645 (ttp) cc_final: 0.7281 (ttp) REVERT: B 304 MET cc_start: 0.7841 (ttp) cc_final: 0.7294 (ttp) REVERT: C 260 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6240 (tpp) REVERT: E 9 GLU cc_start: 0.8118 (tp30) cc_final: 0.7879 (tp30) REVERT: E 43 ASP cc_start: 0.8550 (t70) cc_final: 0.8278 (t0) REVERT: E 260 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6494 (ttm) REVERT: E 309 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7302 (ttm-80) outliers start: 9 outliers final: 6 residues processed: 270 average time/residue: 1.2466 time to fit residues: 376.7297 Evaluate side-chains 273 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 264 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 20 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.172415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120909 restraints weight = 44114.692| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.72 r_work: 0.3094 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16785 Z= 0.139 Angle : 0.542 4.832 22930 Z= 0.279 Chirality : 0.039 0.138 2610 Planarity : 0.004 0.044 2715 Dihedral : 11.164 125.948 3485 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.47 % Allowed : 8.97 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.91 (0.19), residues: 1860 helix: 2.22 (0.19), residues: 710 sheet: -0.49 (0.23), residues: 425 loop : -0.25 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 309 TYR 0.010 0.001 TYR C 31 PHE 0.012 0.001 PHE E 134 TRP 0.009 0.001 TRP C 148 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00297 (16745) covalent geometry : angle 0.52667 (22820) SS BOND : bond 0.00771 ( 10) SS BOND : angle 1.54210 ( 20) hydrogen bonds : bond 0.04574 ( 786) hydrogen bonds : angle 4.61489 ( 2628) link_BETA1-4 : bond 0.00219 ( 15) link_BETA1-4 : angle 1.39281 ( 45) link_NAG-ASN : bond 0.00126 ( 15) link_NAG-ASN : angle 2.40818 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 276 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 304 MET cc_start: 0.7673 (ttp) cc_final: 0.7325 (ttp) REVERT: B 304 MET cc_start: 0.7831 (ttp) cc_final: 0.7294 (ttp) REVERT: C 260 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.6238 (tpp) REVERT: D 298 ASP cc_start: 0.8474 (t0) cc_final: 0.8250 (t70) REVERT: D 439 PHE cc_start: 0.8134 (t80) cc_final: 0.7801 (t80) REVERT: E 9 GLU cc_start: 0.8095 (tp30) cc_final: 0.7855 (tp30) REVERT: E 43 ASP cc_start: 0.8546 (t70) cc_final: 0.8255 (t0) REVERT: E 174 ASP cc_start: 0.8435 (t70) cc_final: 0.8132 (t70) REVERT: E 260 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6476 (ttm) REVERT: E 309 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7269 (ttm-80) outliers start: 8 outliers final: 3 residues processed: 277 average time/residue: 1.2293 time to fit residues: 381.0947 Evaluate side-chains 275 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 269 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 309 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 111 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.171745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123341 restraints weight = 52602.934| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.45 r_work: 0.3042 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16785 Z= 0.173 Angle : 0.570 5.166 22930 Z= 0.293 Chirality : 0.040 0.142 2610 Planarity : 0.005 0.045 2715 Dihedral : 11.161 125.210 3485 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.35 % Allowed : 9.03 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.01 (0.19), residues: 1860 helix: 2.23 (0.19), residues: 710 sheet: -0.33 (0.22), residues: 475 loop : -0.17 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 446 TYR 0.017 0.002 TYR C 31 PHE 0.015 0.001 PHE C 99 TRP 0.010 0.001 TRP C 148 HIS 0.004 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00380 (16745) covalent geometry : angle 0.55431 (22820) SS BOND : bond 0.00774 ( 10) SS BOND : angle 1.67406 ( 20) hydrogen bonds : bond 0.04726 ( 786) hydrogen bonds : angle 4.66438 ( 2628) link_BETA1-4 : bond 0.00162 ( 15) link_BETA1-4 : angle 1.44813 ( 45) link_NAG-ASN : bond 0.00116 ( 15) link_NAG-ASN : angle 2.47174 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14648.43 seconds wall clock time: 247 minutes 47.48 seconds (14867.48 seconds total)