Starting phenix.real_space_refine on Tue May 5 16:08:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v8d_43035/05_2026/8v8d_43035_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v8d_43035/05_2026/8v8d_43035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v8d_43035/05_2026/8v8d_43035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v8d_43035/05_2026/8v8d_43035.map" model { file = "/net/cci-nas-00/data/ceres_data/8v8d_43035/05_2026/8v8d_43035_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v8d_43035/05_2026/8v8d_43035_trim.cif" } resolution = 3.31 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= 0.006 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 S 115 5.16 5 Cl 10 4.86 5 C 10227 2.51 5 N 2498 2.21 5 O 2836 1.98 5 H 15085 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 30774 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6060 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 6047 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 377, 6048 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 bond proxies already assigned to first conformer: 6118 Chain: "B" Number of atoms: 6036 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 6023 Classifications: {'peptide': 376} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 355} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 376, 6024 Classifications: {'peptide': 376} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 355} Chain breaks: 1 bond proxies already assigned to first conformer: 6094 Chain: "C" Number of atoms: 6060 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 6047 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 377, 6048 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 bond proxies already assigned to first conformer: 6118 Chain: "D" Number of atoms: 6080 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 6067 Classifications: {'peptide': 378} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 378, 6068 Classifications: {'peptide': 378} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 bond proxies already assigned to first conformer: 6139 Chain: "E" Number of atoms: 6080 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 6067 Classifications: {'peptide': 378} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 378, 6068 Classifications: {'peptide': 378} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 bond proxies already assigned to first conformer: 6139 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'EPJ': 1, 'I34': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' CA': 1, 'EPJ': 1, 'I34': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' CA': 1, 'EPJ': 1, 'I34': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 85 Unusual residues: {' CA': 1, 'EPJ': 1, 'I34': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.64, per 1000 atoms: 0.28 Number of scatterers: 30774 At special positions: 0 Unit cell: (89.925, 91.575, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 Cl 10 17.00 S 115 16.00 O 2836 8.00 N 2498 7.00 C 10227 6.00 H 15085 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=2.05 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=2.05 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=2.05 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 601 " - " ASN A 67 " " NAG A 602 " - " ASN A 23 " " NAG B 603 " - " ASN B 67 " " NAG B 604 " - " ASN B 23 " " NAG C 603 " - " ASN C 67 " " NAG C 604 " - " ASN C 23 " " NAG D 603 " - " ASN D 67 " " NAG D 604 " - " ASN D 23 " " NAG E 601 " - " ASN E 67 " " NAG E 602 " - " ASN E 23 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN B 110 " " NAG H 1 " - " ASN C 110 " " NAG I 1 " - " ASN D 110 " " NAG J 1 " - " ASN E 110 " Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 21 sheets defined 42.3% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.725A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 237 through 260 removed outlier: 4.088A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 426 through 465 Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.588A pdb=" N PHE A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.630A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 237 through 260 removed outlier: 4.454A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 427 through 465 Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.599A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.909A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 426 through 465 Processing helix chain 'C' and resid 466 through 468 No H-bonds generated for 'chain 'C' and resid 466 through 468' Processing helix chain 'C' and resid 469 through 478 removed outlier: 3.829A pdb=" N PHE C 478 " --> pdb=" O VAL C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.728A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 237 through 260 removed outlier: 4.291A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 425 through 465 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.750A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 227 Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 232 through 236 Processing helix chain 'E' and resid 237 through 249 Processing helix chain 'E' and resid 249 through 260 removed outlier: 3.963A pdb=" N MET E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 314 through 320 removed outlier: 3.661A pdb=" N TRP E 318 " --> pdb=" O ASN E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 465 Processing helix chain 'E' and resid 469 through 478 removed outlier: 3.507A pdb=" N PHE E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 removed outlier: 7.560A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.583A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.583A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.542A pdb=" N ASN B 110 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.542A pdb=" N ASN B 110 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.307A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.307A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.511A pdb=" N PHE C 79 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 110 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.511A pdb=" N PHE C 79 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 110 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL C 48 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASP C 41 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR C 60 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR C 29 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.450A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.450A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.556A pdb=" N ASN D 110 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.556A pdb=" N ASN D 110 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL D 48 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL D 42 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR D 50 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TRP D 54 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU D 36 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN D 56 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU D 34 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N SER D 58 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE D 32 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N THR D 60 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL D 30 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.229A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.229A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.561A pdb=" N PHE E 79 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN E 110 " --> pdb=" O HIS E 114 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.561A pdb=" N PHE E 79 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN E 110 " --> pdb=" O HIS E 114 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL E 48 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL E 42 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR E 50 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E 38 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TRP E 54 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU E 36 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLN E 56 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU E 34 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER E 58 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE E 32 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N THR E 60 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL E 30 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.599A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.599A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2496 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: 7.08 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 4798 1.05 - 1.25: 12660 1.25 - 1.45: 4928 1.45 - 1.66: 8657 1.66 - 1.86: 180 Bond restraints: 31223 Sorted by residual: bond pdb=" NE1 TRP B 54 " pdb=" HE1 TRP B 54 " ideal model delta sigma weight residual 0.860 1.083 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 66 " pdb=" HE1 TRP D 66 " ideal model delta sigma weight residual 0.860 1.083 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP C 59 " pdb=" HE1 TRP C 59 " ideal model delta sigma weight residual 0.860 1.083 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 148 " pdb=" HE1 TRP D 148 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP C 173 " pdb=" HE1 TRP C 173 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 ... (remaining 31218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.51: 56277 11.51 - 23.01: 0 23.01 - 34.52: 0 34.52 - 46.02: 1 46.02 - 57.53: 2 Bond angle restraints: 56280 Sorted by residual: angle pdb=" CA ARG A 425 " pdb=" N ARG A 425 " pdb=" H ARG A 425 " ideal model delta sigma weight residual 114.00 171.53 -57.53 3.00e+00 1.11e-01 3.68e+02 angle pdb=" CA PHE E 424 " pdb=" N PHE E 424 " pdb=" H PHE E 424 " ideal model delta sigma weight residual 114.00 161.64 -47.64 3.00e+00 1.11e-01 2.52e+02 angle pdb=" CA PHE D 424 " pdb=" N PHE D 424 " pdb=" H PHE D 424 " ideal model delta sigma weight residual 114.00 158.88 -44.88 3.00e+00 1.11e-01 2.24e+02 angle pdb=" N MET D 253 " pdb=" CA MET D 253 " pdb=" C MET D 253 " ideal model delta sigma weight residual 112.23 105.43 6.80 1.26e+00 6.30e-01 2.91e+01 angle pdb=" CA ASP B 137 " pdb=" CB ASP B 137 " pdb=" CG ASP B 137 " ideal model delta sigma weight residual 112.60 116.74 -4.14 1.00e+00 1.00e+00 1.72e+01 ... (remaining 56275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 13994 17.80 - 35.61: 810 35.61 - 53.41: 223 53.41 - 71.22: 81 71.22 - 89.02: 19 Dihedral angle restraints: 15127 sinusoidal: 8244 harmonic: 6883 Sorted by residual: dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual -180.00 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual 180.00 -154.01 -25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA CYS E 189 " pdb=" C CYS E 189 " pdb=" N CYS E 190 " pdb=" CA CYS E 190 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 15124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2098 0.070 - 0.139: 336 0.139 - 0.209: 61 0.209 - 0.278: 9 0.278 - 0.348: 7 Chirality restraints: 2511 Sorted by residual: chirality pdb=" C1 EPJ C 605 " pdb=" C2 EPJ C 605 " pdb=" C6 EPJ C 605 " pdb=" C7 EPJ C 605 " both_signs ideal model delta sigma weight residual False -2.85 -2.50 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" C1 EPJ D 605 " pdb=" C2 EPJ D 605 " pdb=" C6 EPJ D 605 " pdb=" C7 EPJ D 605 " both_signs ideal model delta sigma weight residual False -2.85 -2.50 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" C1 EPJ B 605 " pdb=" C2 EPJ B 605 " pdb=" C6 EPJ B 605 " pdb=" C7 EPJ B 605 " both_signs ideal model delta sigma weight residual False -2.85 -2.51 -0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 2508 not shown) Planarity restraints: 4483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 213 " -0.166 2.00e-02 2.50e+03 1.81e-01 4.93e+02 pdb=" CG ASN B 213 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 213 " 0.159 2.00e-02 2.50e+03 pdb=" ND2 ASN B 213 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 213 " 0.266 2.00e-02 2.50e+03 pdb="HD22 ASN B 213 " -0.271 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 213 " -0.156 2.00e-02 2.50e+03 1.74e-01 4.52e+02 pdb=" CG ASN E 213 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN E 213 " 0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN E 213 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN E 213 " 0.257 2.00e-02 2.50e+03 pdb="HD22 ASN E 213 " -0.257 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 I34 C 601 " -0.041 2.00e-02 2.50e+03 1.04e-01 2.70e+02 pdb=" C04 I34 C 601 " -0.059 2.00e-02 2.50e+03 pdb=" C05 I34 C 601 " -0.029 2.00e-02 2.50e+03 pdb=" C08 I34 C 601 " 0.007 2.00e-02 2.50e+03 pdb=" C19 I34 C 601 " 0.012 2.00e-02 2.50e+03 pdb=" C20 I34 C 601 " -0.012 2.00e-02 2.50e+03 pdb=" N09 I34 C 601 " 0.156 2.00e-02 2.50e+03 pdb=" O02 I34 C 601 " 0.215 2.00e-02 2.50e+03 pdb=" O06 I34 C 601 " -0.111 2.00e-02 2.50e+03 pdb="CL1 I34 C 601 " -0.137 2.00e-02 2.50e+03 ... (remaining 4480 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1054 2.13 - 2.74: 53043 2.74 - 3.36: 84284 3.36 - 3.98: 118450 3.98 - 4.60: 177531 Nonbonded interactions: 434362 Sorted by model distance: nonbonded pdb=" HB VAL C 131 " pdb=" HE1 MET C 260 " model vdw 1.506 2.440 nonbonded pdb=" HZ3 LYS A 5 " pdb=" HH TYR A 71 " model vdw 1.509 2.100 nonbonded pdb="HD23 LEU B 246 " pdb="HD21 LEU C 224 " model vdw 1.524 2.440 nonbonded pdb=" HA GLU C 44 " pdb="HD12 ILE C 129 " model vdw 1.562 2.440 nonbonded pdb="HG23 THR B 308 " pdb="HD12 LEU B 312 " model vdw 1.595 2.440 ... (remaining 434357 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 323 or resid 426 throug \ h 478)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 323 or resid 426 throug \ h 478)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 323 or resid 426 throug \ h 478)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 323 or resid 426 throug \ h 478)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.460 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 16168 Z= 0.305 Angle : 0.998 8.702 22083 Z= 0.518 Chirality : 0.058 0.348 2511 Planarity : 0.008 0.120 2697 Dihedral : 13.533 89.023 6145 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.12 % Allowed : 0.41 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.18), residues: 1871 helix: -0.45 (0.18), residues: 718 sheet: -1.41 (0.22), residues: 434 loop : -1.19 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 309 TYR 0.023 0.002 TYR D 273 PHE 0.021 0.002 PHE E 229 TRP 0.029 0.002 TRP D 315 HIS 0.013 0.002 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00676 (16138) covalent geometry : angle 0.99042 (22003) SS BOND : bond 0.01045 ( 10) SS BOND : angle 2.64011 ( 20) hydrogen bonds : bond 0.18071 ( 769) hydrogen bonds : angle 7.68726 ( 2496) link_BETA1-4 : bond 0.00110 ( 5) link_BETA1-4 : angle 1.11486 ( 15) link_NAG-ASN : bond 0.00156 ( 15) link_NAG-ASN : angle 2.41078 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 VAL cc_start: 0.9146 (t) cc_final: 0.8882 (t) REVERT: B 50 THR cc_start: 0.8140 (m) cc_final: 0.7846 (p) REVERT: B 253 MET cc_start: 0.6799 (mmm) cc_final: 0.6548 (mmm) REVERT: B 445 ASP cc_start: 0.7113 (m-30) cc_final: 0.6679 (m-30) REVERT: C 37 LEU cc_start: 0.7689 (mp) cc_final: 0.7149 (tp) REVERT: C 209 TYR cc_start: 0.8156 (t80) cc_final: 0.7766 (t80) REVERT: C 253 MET cc_start: 0.6889 (mmm) cc_final: 0.6577 (mtt) REVERT: C 448 CYS cc_start: 0.7580 (m) cc_final: 0.6710 (m) REVERT: E 118 LEU cc_start: 0.8165 (tt) cc_final: 0.7926 (tt) outliers start: 2 outliers final: 1 residues processed: 254 average time/residue: 0.2372 time to fit residues: 93.6559 Evaluate side-chains 207 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 253 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN B 213 ASN C 52 ASN C 272 GLN D 272 GLN D 469 ASN E 3 GLN ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.127221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.112848 restraints weight = 119621.657| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.78 r_work: 0.3563 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16168 Z= 0.156 Angle : 0.590 5.376 22083 Z= 0.307 Chirality : 0.041 0.187 2511 Planarity : 0.005 0.074 2697 Dihedral : 8.391 89.233 2573 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.05 % Allowed : 4.21 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.18), residues: 1871 helix: 0.42 (0.19), residues: 722 sheet: -1.48 (0.21), residues: 451 loop : -0.92 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 205 TYR 0.012 0.001 TYR A 294 PHE 0.015 0.001 PHE D 455 TRP 0.013 0.001 TRP A 315 HIS 0.005 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00342 (16138) covalent geometry : angle 0.58276 (22003) SS BOND : bond 0.00739 ( 10) SS BOND : angle 1.65158 ( 20) hydrogen bonds : bond 0.04471 ( 769) hydrogen bonds : angle 5.69686 ( 2496) link_BETA1-4 : bond 0.00432 ( 5) link_BETA1-4 : angle 1.22462 ( 15) link_NAG-ASN : bond 0.00121 ( 15) link_NAG-ASN : angle 1.82773 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6260 (mm-30) REVERT: B 450 MET cc_start: 0.6999 (ttp) cc_final: 0.6698 (ttp) REVERT: C 37 LEU cc_start: 0.8099 (mp) cc_final: 0.7391 (tp) REVERT: C 81 ASP cc_start: 0.7720 (t0) cc_final: 0.7499 (t0) REVERT: C 311 ILE cc_start: 0.7494 (mt) cc_final: 0.7239 (tp) REVERT: C 445 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7219 (t0) REVERT: C 448 CYS cc_start: 0.8024 (m) cc_final: 0.7358 (m) REVERT: D 445 ASP cc_start: 0.6629 (m-30) cc_final: 0.6384 (m-30) REVERT: E 118 LEU cc_start: 0.8193 (tt) cc_final: 0.7909 (tt) outliers start: 18 outliers final: 11 residues processed: 222 average time/residue: 0.2716 time to fit residues: 89.6793 Evaluate side-chains 206 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 277 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 63 optimal weight: 0.0060 chunk 157 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.126370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.111549 restraints weight = 112252.199| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.67 r_work: 0.3549 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16168 Z= 0.147 Angle : 0.541 4.626 22083 Z= 0.278 Chirality : 0.040 0.157 2511 Planarity : 0.004 0.063 2697 Dihedral : 7.699 87.087 2570 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.99 % Allowed : 5.32 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.19), residues: 1871 helix: 0.91 (0.19), residues: 717 sheet: -1.41 (0.21), residues: 462 loop : -0.61 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 98 TYR 0.018 0.001 TYR D 209 PHE 0.018 0.001 PHE E 319 TRP 0.010 0.001 TRP C 315 HIS 0.004 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00324 (16138) covalent geometry : angle 0.53370 (22003) SS BOND : bond 0.00693 ( 10) SS BOND : angle 1.29244 ( 20) hydrogen bonds : bond 0.03931 ( 769) hydrogen bonds : angle 5.24123 ( 2496) link_BETA1-4 : bond 0.00442 ( 5) link_BETA1-4 : angle 1.16057 ( 15) link_NAG-ASN : bond 0.00154 ( 15) link_NAG-ASN : angle 1.80521 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 TYR cc_start: 0.6357 (m-80) cc_final: 0.6145 (m-80) REVERT: B 97 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6283 (mm-30) REVERT: B 450 MET cc_start: 0.6997 (ttp) cc_final: 0.6656 (ttp) REVERT: C 37 LEU cc_start: 0.8192 (mp) cc_final: 0.7392 (tp) REVERT: C 311 ILE cc_start: 0.7500 (mt) cc_final: 0.7261 (tp) REVERT: C 445 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7244 (t0) REVERT: C 448 CYS cc_start: 0.8011 (m) cc_final: 0.7393 (m) outliers start: 17 outliers final: 13 residues processed: 213 average time/residue: 0.2790 time to fit residues: 88.0802 Evaluate side-chains 209 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 318 TRP Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 82 optimal weight: 0.0370 chunk 104 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS E 170 ASN E 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.124324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.109331 restraints weight = 110256.696| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.63 r_work: 0.3537 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16168 Z= 0.184 Angle : 0.543 5.449 22083 Z= 0.280 Chirality : 0.040 0.154 2511 Planarity : 0.004 0.054 2697 Dihedral : 7.388 88.850 2570 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.11 % Allowed : 6.08 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.19), residues: 1871 helix: 0.97 (0.19), residues: 717 sheet: -1.13 (0.21), residues: 464 loop : -0.49 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 205 TYR 0.017 0.001 TYR D 209 PHE 0.021 0.001 PHE E 319 TRP 0.026 0.001 TRP E 54 HIS 0.005 0.001 HIS E 296 Details of bonding type rmsd covalent geometry : bond 0.00414 (16138) covalent geometry : angle 0.53540 (22003) SS BOND : bond 0.00749 ( 10) SS BOND : angle 1.30348 ( 20) hydrogen bonds : bond 0.03805 ( 769) hydrogen bonds : angle 5.07719 ( 2496) link_BETA1-4 : bond 0.00298 ( 5) link_BETA1-4 : angle 1.08408 ( 15) link_NAG-ASN : bond 0.00166 ( 15) link_NAG-ASN : angle 1.83372 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 TYR cc_start: 0.6314 (m-80) cc_final: 0.6022 (m-80) REVERT: A 321 ARG cc_start: 0.6628 (mpt180) cc_final: 0.6266 (mtt-85) REVERT: B 97 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6410 (mm-30) REVERT: B 450 MET cc_start: 0.6987 (ttp) cc_final: 0.6628 (ttp) REVERT: C 37 LEU cc_start: 0.8347 (mp) cc_final: 0.7528 (tp) REVERT: C 448 CYS cc_start: 0.8223 (m) cc_final: 0.7681 (m) REVERT: D 253 MET cc_start: 0.8077 (mmm) cc_final: 0.7786 (mmt) REVERT: E 307 TRP cc_start: 0.5855 (m100) cc_final: 0.5609 (m100) outliers start: 19 outliers final: 15 residues processed: 205 average time/residue: 0.2865 time to fit residues: 85.8472 Evaluate side-chains 202 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 145 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.123176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.108061 restraints weight = 115066.621| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.77 r_work: 0.3495 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16168 Z= 0.226 Angle : 0.578 8.662 22083 Z= 0.300 Chirality : 0.041 0.166 2511 Planarity : 0.004 0.054 2697 Dihedral : 7.015 88.949 2570 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.05 % Allowed : 6.84 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.19), residues: 1871 helix: 0.94 (0.19), residues: 710 sheet: -1.14 (0.22), residues: 467 loop : -0.57 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 205 TYR 0.019 0.002 TYR D 209 PHE 0.013 0.001 PHE E 455 TRP 0.014 0.001 TRP C 307 HIS 0.006 0.001 HIS E 296 Details of bonding type rmsd covalent geometry : bond 0.00513 (16138) covalent geometry : angle 0.57088 (22003) SS BOND : bond 0.00723 ( 10) SS BOND : angle 1.16515 ( 20) hydrogen bonds : bond 0.03943 ( 769) hydrogen bonds : angle 5.04364 ( 2496) link_BETA1-4 : bond 0.00188 ( 5) link_BETA1-4 : angle 0.98884 ( 15) link_NAG-ASN : bond 0.00230 ( 15) link_NAG-ASN : angle 1.89277 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8328 (t70) cc_final: 0.7937 (t70) REVERT: A 321 ARG cc_start: 0.6441 (mpt180) cc_final: 0.6138 (mtt180) REVERT: A 474 VAL cc_start: 0.7999 (t) cc_final: 0.7614 (p) REVERT: C 37 LEU cc_start: 0.8274 (mp) cc_final: 0.7603 (tp) REVERT: C 153 TRP cc_start: 0.6486 (m-10) cc_final: 0.6166 (m-10) REVERT: C 448 CYS cc_start: 0.7988 (m) cc_final: 0.7448 (m) REVERT: D 185 ARG cc_start: 0.7679 (mtp-110) cc_final: 0.7381 (ttp-170) REVERT: E 260 MET cc_start: 0.6207 (mtp) cc_final: 0.5985 (mtt) outliers start: 18 outliers final: 16 residues processed: 208 average time/residue: 0.2849 time to fit residues: 88.0715 Evaluate side-chains 209 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 82 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.122490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.107149 restraints weight = 103034.393| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.49 r_work: 0.3497 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16168 Z= 0.234 Angle : 0.573 5.584 22083 Z= 0.297 Chirality : 0.041 0.164 2511 Planarity : 0.004 0.046 2697 Dihedral : 6.695 84.195 2570 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.23 % Allowed : 7.31 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.19), residues: 1871 helix: 0.92 (0.19), residues: 710 sheet: -1.16 (0.22), residues: 460 loop : -0.60 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 205 TYR 0.017 0.002 TYR D 209 PHE 0.013 0.001 PHE E 455 TRP 0.010 0.001 TRP E 437 HIS 0.006 0.001 HIS E 296 Details of bonding type rmsd covalent geometry : bond 0.00533 (16138) covalent geometry : angle 0.56577 (22003) SS BOND : bond 0.00700 ( 10) SS BOND : angle 1.15538 ( 20) hydrogen bonds : bond 0.03932 ( 769) hydrogen bonds : angle 5.01796 ( 2496) link_BETA1-4 : bond 0.00130 ( 5) link_BETA1-4 : angle 1.00274 ( 15) link_NAG-ASN : bond 0.00236 ( 15) link_NAG-ASN : angle 1.90816 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.6983 (mmt) cc_final: 0.6378 (mmt) REVERT: A 321 ARG cc_start: 0.6626 (mpt180) cc_final: 0.6209 (mtt-85) REVERT: A 474 VAL cc_start: 0.8075 (t) cc_final: 0.7710 (p) REVERT: C 37 LEU cc_start: 0.8380 (mp) cc_final: 0.7617 (tp) REVERT: C 153 TRP cc_start: 0.6549 (m-10) cc_final: 0.6129 (m-10) REVERT: C 445 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7578 (t0) REVERT: C 448 CYS cc_start: 0.8202 (m) cc_final: 0.7727 (m) REVERT: D 185 ARG cc_start: 0.7648 (mtp-110) cc_final: 0.7352 (ttp-170) REVERT: E 40 MET cc_start: 0.7907 (mtt) cc_final: 0.7621 (mtt) REVERT: E 260 MET cc_start: 0.6374 (mtp) cc_final: 0.6174 (mtt) outliers start: 21 outliers final: 16 residues processed: 208 average time/residue: 0.2919 time to fit residues: 88.7689 Evaluate side-chains 205 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 3.9990 chunk 132 optimal weight: 0.1980 chunk 11 optimal weight: 6.9990 chunk 171 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.124422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.109698 restraints weight = 111900.581| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.65 r_work: 0.3524 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16168 Z= 0.124 Angle : 0.508 4.660 22083 Z= 0.261 Chirality : 0.039 0.153 2511 Planarity : 0.004 0.045 2697 Dihedral : 6.305 84.122 2570 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.88 % Allowed : 7.66 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1871 helix: 1.19 (0.19), residues: 713 sheet: -1.01 (0.22), residues: 454 loop : -0.42 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.019 0.001 TYR D 209 PHE 0.012 0.001 PHE E 319 TRP 0.010 0.001 TRP E 437 HIS 0.006 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00276 (16138) covalent geometry : angle 0.50115 (22003) SS BOND : bond 0.00671 ( 10) SS BOND : angle 1.16958 ( 20) hydrogen bonds : bond 0.03605 ( 769) hydrogen bonds : angle 4.77288 ( 2496) link_BETA1-4 : bond 0.00307 ( 5) link_BETA1-4 : angle 0.99687 ( 15) link_NAG-ASN : bond 0.00147 ( 15) link_NAG-ASN : angle 1.73245 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8318 (t70) cc_final: 0.7945 (t70) REVERT: A 260 MET cc_start: 0.6831 (mmt) cc_final: 0.6212 (mmt) REVERT: A 280 ILE cc_start: 0.6528 (mm) cc_final: 0.6139 (mt) REVERT: A 321 ARG cc_start: 0.6463 (mpt180) cc_final: 0.6146 (mtt-85) REVERT: A 474 VAL cc_start: 0.7963 (t) cc_final: 0.7621 (p) REVERT: B 97 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6358 (mm-30) REVERT: C 37 LEU cc_start: 0.8229 (mp) cc_final: 0.7489 (tp) REVERT: C 448 CYS cc_start: 0.7878 (m) cc_final: 0.7363 (m) REVERT: C 472 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7310 (mm-30) REVERT: D 185 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.7405 (ttp-170) REVERT: E 40 MET cc_start: 0.7666 (mtt) cc_final: 0.7371 (mtt) REVERT: E 253 MET cc_start: 0.7236 (mmm) cc_final: 0.6915 (mmm) outliers start: 15 outliers final: 15 residues processed: 202 average time/residue: 0.2608 time to fit residues: 78.9404 Evaluate side-chains 202 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 34 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 113 optimal weight: 0.0000 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.122816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.108131 restraints weight = 108150.701| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.60 r_work: 0.3497 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16168 Z= 0.184 Angle : 0.528 4.497 22083 Z= 0.273 Chirality : 0.039 0.158 2511 Planarity : 0.004 0.045 2697 Dihedral : 6.269 86.165 2570 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.76 % Allowed : 7.95 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.19), residues: 1871 helix: 1.20 (0.19), residues: 713 sheet: -1.03 (0.22), residues: 458 loop : -0.36 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 205 TYR 0.017 0.001 TYR D 209 PHE 0.011 0.001 PHE A 134 TRP 0.013 0.001 TRP E 437 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00419 (16138) covalent geometry : angle 0.52026 (22003) SS BOND : bond 0.00679 ( 10) SS BOND : angle 1.13743 ( 20) hydrogen bonds : bond 0.03678 ( 769) hydrogen bonds : angle 4.79223 ( 2496) link_BETA1-4 : bond 0.00146 ( 5) link_BETA1-4 : angle 1.02066 ( 15) link_NAG-ASN : bond 0.00178 ( 15) link_NAG-ASN : angle 1.81710 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.6852 (mmt) cc_final: 0.6274 (mmt) REVERT: A 280 ILE cc_start: 0.6557 (mm) cc_final: 0.6346 (mm) REVERT: A 321 ARG cc_start: 0.6481 (mpt180) cc_final: 0.6156 (mtt-85) REVERT: A 474 VAL cc_start: 0.8021 (t) cc_final: 0.7631 (p) REVERT: B 97 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6363 (mm-30) REVERT: C 37 LEU cc_start: 0.8252 (mp) cc_final: 0.7491 (tp) REVERT: C 448 CYS cc_start: 0.7882 (m) cc_final: 0.7367 (m) REVERT: D 185 ARG cc_start: 0.7616 (mtp-110) cc_final: 0.7359 (ttp-170) REVERT: E 40 MET cc_start: 0.7792 (mtt) cc_final: 0.7486 (mtt) REVERT: E 253 MET cc_start: 0.7315 (mmm) cc_final: 0.7062 (mmm) outliers start: 13 outliers final: 13 residues processed: 198 average time/residue: 0.2858 time to fit residues: 83.9110 Evaluate side-chains 202 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.124821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.110073 restraints weight = 109477.239| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.65 r_work: 0.3521 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16168 Z= 0.118 Angle : 0.492 4.984 22083 Z= 0.252 Chirality : 0.039 0.149 2511 Planarity : 0.004 0.052 2697 Dihedral : 5.950 85.655 2570 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.76 % Allowed : 8.07 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 1871 helix: 1.41 (0.19), residues: 713 sheet: -0.97 (0.22), residues: 455 loop : -0.20 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.019 0.001 TYR D 209 PHE 0.014 0.001 PHE E 319 TRP 0.015 0.001 TRP E 437 HIS 0.005 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00264 (16138) covalent geometry : angle 0.48470 (22003) SS BOND : bond 0.00663 ( 10) SS BOND : angle 1.13264 ( 20) hydrogen bonds : bond 0.03456 ( 769) hydrogen bonds : angle 4.62153 ( 2496) link_BETA1-4 : bond 0.00249 ( 5) link_BETA1-4 : angle 0.95605 ( 15) link_NAG-ASN : bond 0.00139 ( 15) link_NAG-ASN : angle 1.67507 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8305 (t70) cc_final: 0.7900 (t70) REVERT: A 260 MET cc_start: 0.6697 (mmt) cc_final: 0.6117 (mmt) REVERT: A 280 ILE cc_start: 0.6487 (mm) cc_final: 0.6264 (mm) REVERT: A 321 ARG cc_start: 0.6475 (mpt180) cc_final: 0.6162 (mtt-85) REVERT: A 474 VAL cc_start: 0.8001 (t) cc_final: 0.7664 (p) REVERT: B 97 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6358 (mm-30) REVERT: C 37 LEU cc_start: 0.8247 (mp) cc_final: 0.7503 (tp) REVERT: C 448 CYS cc_start: 0.7847 (m) cc_final: 0.7344 (m) REVERT: C 472 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7398 (mm-30) REVERT: D 185 ARG cc_start: 0.7619 (mtp-110) cc_final: 0.7237 (ttt180) REVERT: D 253 MET cc_start: 0.7890 (mmt) cc_final: 0.7621 (mmt) REVERT: E 40 MET cc_start: 0.7681 (mtt) cc_final: 0.7369 (mtt) REVERT: E 253 MET cc_start: 0.7229 (mmm) cc_final: 0.7020 (mmm) outliers start: 13 outliers final: 13 residues processed: 198 average time/residue: 0.2640 time to fit residues: 78.9912 Evaluate side-chains 204 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 173 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.123297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.109146 restraints weight = 114948.532| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.62 r_work: 0.3512 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16168 Z= 0.166 Angle : 0.512 4.519 22083 Z= 0.265 Chirality : 0.039 0.156 2511 Planarity : 0.004 0.045 2697 Dihedral : 5.958 86.674 2570 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.76 % Allowed : 8.18 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 1871 helix: 1.33 (0.19), residues: 719 sheet: -0.99 (0.22), residues: 453 loop : -0.15 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 98 TYR 0.017 0.001 TYR D 209 PHE 0.012 0.001 PHE E 319 TRP 0.019 0.001 TRP E 437 HIS 0.005 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00379 (16138) covalent geometry : angle 0.50531 (22003) SS BOND : bond 0.00679 ( 10) SS BOND : angle 1.11630 ( 20) hydrogen bonds : bond 0.03552 ( 769) hydrogen bonds : angle 4.66514 ( 2496) link_BETA1-4 : bond 0.00117 ( 5) link_BETA1-4 : angle 1.00024 ( 15) link_NAG-ASN : bond 0.00165 ( 15) link_NAG-ASN : angle 1.77281 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8408 (t70) cc_final: 0.8018 (t70) REVERT: A 260 MET cc_start: 0.6884 (mmt) cc_final: 0.6310 (mmt) REVERT: A 280 ILE cc_start: 0.6593 (mm) cc_final: 0.6351 (mm) REVERT: A 321 ARG cc_start: 0.6724 (mpt180) cc_final: 0.6262 (mtt-85) REVERT: A 474 VAL cc_start: 0.8098 (t) cc_final: 0.7773 (p) REVERT: B 97 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6555 (mm-30) REVERT: C 37 LEU cc_start: 0.8406 (mp) cc_final: 0.7661 (tp) REVERT: C 448 CYS cc_start: 0.8137 (m) cc_final: 0.7676 (m) REVERT: D 185 ARG cc_start: 0.7627 (mtp-110) cc_final: 0.7210 (ttt180) REVERT: D 253 MET cc_start: 0.8132 (mmt) cc_final: 0.7833 (mmt) REVERT: E 40 MET cc_start: 0.7972 (mtt) cc_final: 0.7690 (mtt) outliers start: 13 outliers final: 12 residues processed: 203 average time/residue: 0.2852 time to fit residues: 85.2494 Evaluate side-chains 203 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 65 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 111 optimal weight: 0.0370 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.125050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.110019 restraints weight = 106115.297| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.58 r_work: 0.3549 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16168 Z= 0.099 Angle : 0.476 4.524 22083 Z= 0.243 Chirality : 0.039 0.146 2511 Planarity : 0.004 0.044 2697 Dihedral : 5.609 81.330 2570 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.64 % Allowed : 8.42 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1871 helix: 1.58 (0.19), residues: 719 sheet: -0.91 (0.23), residues: 451 loop : -0.00 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.020 0.001 TYR D 209 PHE 0.015 0.001 PHE E 319 TRP 0.018 0.001 TRP E 437 HIS 0.005 0.000 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00220 (16138) covalent geometry : angle 0.46898 (22003) SS BOND : bond 0.00671 ( 10) SS BOND : angle 1.15798 ( 20) hydrogen bonds : bond 0.03321 ( 769) hydrogen bonds : angle 4.46809 ( 2496) link_BETA1-4 : bond 0.00331 ( 5) link_BETA1-4 : angle 0.95618 ( 15) link_NAG-ASN : bond 0.00167 ( 15) link_NAG-ASN : angle 1.59346 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7084.88 seconds wall clock time: 120 minutes 46.17 seconds (7246.17 seconds total)