Starting phenix.real_space_refine on Fri Jul 3 09:05:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp8_36471/07_2026/8jp8_36471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp8_36471/07_2026/8jp8_36471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jp8_36471/07_2026/8jp8_36471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp8_36471/07_2026/8jp8_36471.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jp8_36471/07_2026/8jp8_36471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp8_36471/07_2026/8jp8_36471.map" } resolution = 3.39 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= 0.012 sd= 0.115 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: 6 Type Number sf(0) Gaussians Ca 16 9.91 5 Zn 4 6.06 5 S 36 5.16 5 C 8466 2.51 5 N 2346 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13500 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2619 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 309} Chain: "B" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 297} Chain breaks: 1 Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "E" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2619 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 309} Chain: "F" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 297} Chain breaks: 1 Chain: "G" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 3.19, per 1000 atoms: 0.24 Number of scatterers: 13500 At special positions: 0 Unit cell: (119.52, 116.532, 128.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 16 19.99 S 36 16.00 O 2632 8.00 N 2346 7.00 C 8466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 230 " distance=2.03 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 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 691.5 milliseconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 16 sheets defined 32.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.736A pdb=" N ASP A 181 " --> pdb=" O HIS A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.761A pdb=" N LYS A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 309 removed outlier: 4.175A pdb=" N LYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 362 removed outlier: 3.944A pdb=" N ASN A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.512A pdb=" N ASN B 180 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP B 181 " --> pdb=" O HIS B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing helix chain 'B' and resid 282 through 309 removed outlier: 3.606A pdb=" N LYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 362 removed outlier: 3.540A pdb=" N ARG B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.707A pdb=" N ILE C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 81 removed outlier: 3.512A pdb=" N ASP C 81 " --> pdb=" O PHE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 113 through 129 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 48 through 56 removed outlier: 3.562A pdb=" N ILE D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 113 through 128 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'E' and resid 177 through 181 removed outlier: 3.735A pdb=" N ASP E 181 " --> pdb=" O HIS E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 removed outlier: 3.760A pdb=" N LYS E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 309 removed outlier: 4.182A pdb=" N LYS E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU E 306 " --> pdb=" O LYS E 302 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE E 307 " --> pdb=" O LYS E 303 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 364 removed outlier: 3.987A pdb=" N ASN E 339 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE E 341 " --> pdb=" O GLY E 337 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER E 364 " --> pdb=" O ARG E 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.514A pdb=" N ASN F 180 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP F 181 " --> pdb=" O HIS F 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 177 through 181' Processing helix chain 'F' and resid 282 through 309 removed outlier: 3.607A pdb=" N LYS F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU F 306 " --> pdb=" O LYS F 302 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE F 307 " --> pdb=" O LYS F 303 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 362 removed outlier: 3.595A pdb=" N ARG F 361 " --> pdb=" O ASP F 357 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 47 Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.706A pdb=" N ILE G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 80 Processing helix chain 'G' and resid 89 through 98 Processing helix chain 'G' and resid 113 through 129 Processing helix chain 'G' and resid 137 through 142 Processing helix chain 'H' and resid 42 through 47 Processing helix chain 'H' and resid 48 through 56 removed outlier: 3.560A pdb=" N ILE H 52 " --> pdb=" O ASP H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 80 Processing helix chain 'H' and resid 89 through 98 Processing helix chain 'H' and resid 113 through 128 Processing helix chain 'H' and resid 137 through 142 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 53 removed outlier: 4.587A pdb=" N THR A 264 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LYS A 49 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N PHE A 262 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 10.662A pdb=" N SER A 51 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N LEU A 260 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 12.165A pdb=" N LYS A 53 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 14.742A pdb=" N ASP A 258 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N HIS A 257 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 53 removed outlier: 4.587A pdb=" N THR A 264 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LYS A 49 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N PHE A 262 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 10.662A pdb=" N SER A 51 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N LEU A 260 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 12.165A pdb=" N LYS A 53 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 14.742A pdb=" N ASP A 258 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS A 257 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR A 113 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL A 259 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG A 111 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 202 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE A 216 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N PHE A 229 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.705A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.705A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 249 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY A 122 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 123 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 53 removed outlier: 4.661A pdb=" N THR B 264 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LYS B 49 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE B 262 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N SER B 51 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N LEU B 260 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N LYS B 53 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 14.502A pdb=" N ASP B 258 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N HIS B 257 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 53 removed outlier: 4.661A pdb=" N THR B 264 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LYS B 49 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE B 262 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N SER B 51 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N LEU B 260 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N LYS B 53 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 14.502A pdb=" N ASP B 258 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS B 257 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR B 113 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL B 259 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG B 111 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 261 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ILE B 216 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE B 229 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.754A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.754A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 249 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY B 122 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 123 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 43 through 53 removed outlier: 4.578A pdb=" N THR E 264 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N LYS E 49 " --> pdb=" O PHE E 262 " (cutoff:3.500A) removed outlier: 10.755A pdb=" N PHE E 262 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N SER E 51 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N LEU E 260 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 12.209A pdb=" N LYS E 53 " --> pdb=" O ASP E 258 " (cutoff:3.500A) removed outlier: 14.828A pdb=" N ASP E 258 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N HIS E 257 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 43 through 53 removed outlier: 4.578A pdb=" N THR E 264 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N LYS E 49 " --> pdb=" O PHE E 262 " (cutoff:3.500A) removed outlier: 10.755A pdb=" N PHE E 262 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N SER E 51 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N LEU E 260 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 12.209A pdb=" N LYS E 53 " --> pdb=" O ASP E 258 " (cutoff:3.500A) removed outlier: 14.828A pdb=" N ASP E 258 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N HIS E 257 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR E 113 " --> pdb=" O HIS E 257 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL E 259 " --> pdb=" O ARG E 111 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG E 111 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 202 " --> pdb=" O ASN E 217 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE E 216 " --> pdb=" O PHE E 229 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE E 229 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.710A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.710A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA E 249 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY E 122 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 123 " --> pdb=" O PHE E 151 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 43 through 53 removed outlier: 4.640A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 11.999A pdb=" N LYS F 53 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 14.553A pdb=" N ASP F 258 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N HIS F 257 " --> pdb=" O VAL F 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 43 through 53 removed outlier: 4.640A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 11.999A pdb=" N LYS F 53 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 14.553A pdb=" N ASP F 258 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS F 257 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N THR F 113 " --> pdb=" O HIS F 257 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL F 259 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG F 111 " --> pdb=" O VAL F 259 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER F 261 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE F 216 " --> pdb=" O PHE F 229 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N PHE F 229 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.690A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.690A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA F 249 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY F 122 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 123 " --> pdb=" O PHE F 151 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1866 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: 1.95 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4627 1.35 - 1.47: 3096 1.47 - 1.59: 6007 1.59 - 1.71: 0 1.71 - 1.83: 64 Bond restraints: 13794 Sorted by residual: bond pdb=" N ILE B 125 " pdb=" CA ILE B 125 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.67e+00 bond pdb=" N LEU A 133 " pdb=" CA LEU A 133 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.81e+00 bond pdb=" N GLU E 134 " pdb=" CA GLU E 134 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.27e-02 6.20e+03 7.58e+00 bond pdb=" N GLU A 134 " pdb=" CA GLU A 134 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.23e-02 6.61e+03 6.49e+00 bond pdb=" N LEU E 133 " pdb=" CA LEU E 133 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.36e+00 ... (remaining 13789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 18471 2.28 - 4.57: 138 4.57 - 6.85: 15 6.85 - 9.13: 3 9.13 - 11.41: 3 Bond angle restraints: 18630 Sorted by residual: angle pdb=" CB MET B 354 " pdb=" CG MET B 354 " pdb=" SD MET B 354 " ideal model delta sigma weight residual 112.70 124.11 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C ILE F 125 " pdb=" N TRP F 126 " pdb=" CA TRP F 126 " ideal model delta sigma weight residual 122.74 117.27 5.47 1.54e+00 4.22e-01 1.26e+01 angle pdb=" N TRP B 126 " pdb=" CA TRP B 126 " pdb=" C TRP B 126 " ideal model delta sigma weight residual 109.24 114.53 -5.29 1.67e+00 3.59e-01 1.00e+01 angle pdb=" CA GLN A 131 " pdb=" C GLN A 131 " pdb=" O GLN A 131 " ideal model delta sigma weight residual 121.02 117.46 3.56 1.15e+00 7.56e-01 9.57e+00 angle pdb=" N TRP F 126 " pdb=" CA TRP F 126 " pdb=" C TRP F 126 " ideal model delta sigma weight residual 108.76 113.94 -5.18 1.69e+00 3.50e-01 9.38e+00 ... (remaining 18625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 7191 17.13 - 34.26: 787 34.26 - 51.40: 165 51.40 - 68.53: 84 68.53 - 85.66: 21 Dihedral angle restraints: 8248 sinusoidal: 3432 harmonic: 4816 Sorted by residual: dihedral pdb=" CA TRP E 126 " pdb=" C TRP E 126 " pdb=" N TYR E 127 " pdb=" CA TYR E 127 " ideal model delta harmonic sigma weight residual 180.00 160.07 19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CB CYS B 190 " pdb=" SG CYS B 190 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual -86.00 -118.92 32.92 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" CB CYS F 190 " pdb=" SG CYS F 190 " pdb=" SG CYS F 230 " pdb=" CB CYS F 230 " ideal model delta sinusoidal sigma weight residual -86.00 -118.86 32.86 1 1.00e+01 1.00e-02 1.54e+01 ... (remaining 8245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1299 0.037 - 0.075: 431 0.075 - 0.112: 128 0.112 - 0.149: 51 0.149 - 0.186: 7 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CA GLN A 131 " pdb=" N GLN A 131 " pdb=" C GLN A 131 " pdb=" CB GLN A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA GLN E 131 " pdb=" N GLN E 131 " pdb=" C GLN E 131 " pdb=" CB GLN E 131 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA ILE B 125 " pdb=" N ILE B 125 " pdb=" C ILE B 125 " pdb=" CB ILE B 125 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 1913 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 130 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C ASN A 130 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN A 130 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 131 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 130 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ASN E 130 " 0.031 2.00e-02 2.50e+03 pdb=" O ASN E 130 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN E 131 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 124 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.73e+00 pdb=" C ALA B 124 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA B 124 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE B 125 " 0.008 2.00e-02 2.50e+03 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 137 2.40 - 3.02: 7135 3.02 - 3.65: 20334 3.65 - 4.27: 30011 4.27 - 4.90: 51959 Nonbonded interactions: 109576 Sorted by model distance: nonbonded pdb=" OD1 ASP A 155 " pdb=" OD1 ASN A 162 " model vdw 1.774 3.040 nonbonded pdb=" OD1 ASP B 155 " pdb=" OD1 ASN B 162 " model vdw 1.778 3.040 nonbonded pdb=" OD1 ASP E 155 " pdb=" OD1 ASN E 162 " model vdw 1.822 3.040 nonbonded pdb=" OD1 ASP F 155 " pdb=" OD1 ASN F 162 " model vdw 1.834 3.040 nonbonded pdb=" CD2 HIS H 101 " pdb="ZN ZN H 703 " model vdw 1.971 2.450 ... (remaining 109571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'B' selection = (chain 'E' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } 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=1.00 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.120 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.002 0.035 13798 Z= 0.126 Angle : 0.517 11.414 18638 Z= 0.280 Chirality : 0.044 0.186 1916 Planarity : 0.003 0.031 2510 Dihedral : 16.263 85.662 5140 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.07 % Allowed : 12.72 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.20 (0.20), residues: 1650 helix: 1.46 (0.23), residues: 492 sheet: 0.73 (0.30), residues: 364 loop : -1.02 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 360 TYR 0.012 0.001 TYR D 76 PHE 0.013 0.001 PHE E 52 TRP 0.015 0.001 TRP A 126 HIS 0.007 0.001 HIS H 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.13 (13794) covalent geometry : angle 0.51602 / 0.28 (18630) SS BOND : bond 0.00144 / 0.09 ( 4) SS BOND : angle 1.86326 / 1.02 ( 8) hydrogen bonds : bond 0.11199 / 7.78 ( 606) hydrogen bonds : angle 5.04473 / 3.54 ( 1866) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 397 time to evaluate : 0.501 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.9165 (mm) cc_final: 0.8944 (mm) REVERT: A 218 ASN cc_start: 0.6771 (t0) cc_final: 0.6430 (p0) REVERT: A 226 ASP cc_start: 0.7509 (t70) cc_final: 0.7238 (t0) REVERT: A 297 GLN cc_start: 0.9236 (mt0) cc_final: 0.8875 (mt0) REVERT: A 349 ASN cc_start: 0.8430 (t0) cc_final: 0.8100 (t0) REVERT: B 77 SER cc_start: 0.8867 (m) cc_final: 0.8584 (t) REVERT: B 297 GLN cc_start: 0.8802 (pt0) cc_final: 0.8255 (pt0) REVERT: C 70 GLN cc_start: 0.8977 (pp30) cc_final: 0.8065 (pp30) REVERT: C 71 GLU cc_start: 0.8978 (tp30) cc_final: 0.8477 (tp30) REVERT: C 73 GLN cc_start: 0.8596 (pt0) cc_final: 0.8352 (pp30) REVERT: C 81 ASP cc_start: 0.8214 (t70) cc_final: 0.8003 (t0) REVERT: C 127 ASP cc_start: 0.8121 (m-30) cc_final: 0.7899 (m-30) REVERT: C 132 ASN cc_start: 0.8882 (t0) cc_final: 0.8466 (t0) REVERT: D 49 GLN cc_start: 0.8917 (tp-100) cc_final: 0.7654 (tp-100) REVERT: D 53 MET cc_start: 0.8935 (mmm) cc_final: 0.8524 (mmp) REVERT: D 86 ASN cc_start: 0.7824 (m-40) cc_final: 0.7142 (t0) REVERT: D 132 ASN cc_start: 0.8031 (t0) cc_final: 0.7692 (t0) REVERT: E 218 ASN cc_start: 0.7090 (t0) cc_final: 0.6790 (m110) REVERT: E 295 HIS cc_start: 0.9173 (t-90) cc_final: 0.8836 (t-90) REVERT: F 207 TYR cc_start: 0.8711 (t80) cc_final: 0.8458 (t80) REVERT: F 223 ASP cc_start: 0.7926 (t0) cc_final: 0.7657 (t0) REVERT: H 78 LYS cc_start: 0.9294 (tptt) cc_final: 0.9045 (tppt) REVERT: H 132 ASN cc_start: 0.8790 (t0) cc_final: 0.8413 (t0) REVERT: H 135 TYR cc_start: 0.7824 (m-80) cc_final: 0.7109 (m-80) outliers start: 1 outliers final: 1 residues processed: 398 average time/residue: 0.1230 time to fit residues: 69.2571 Evaluate side-chains 256 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0040 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 0.5730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN A 235 ASN A 351 GLN B 235 ASN B 241 GLN B 311 HIS B 333 GLN B 342 HIS C 70 GLN C 73 GLN C 75 HIS C 80 HIS D 55 HIS D 73 GLN D 80 HIS D 101 HIS E 43 HIS E 59 GLN E 79 GLN E 162 ASN E 342 HIS E 351 GLN F 162 ASN F 235 ASN F 241 GLN F 333 GLN F 342 HIS G 49 GLN G 70 GLN G 73 GLN G 80 HIS H 73 GLN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.168615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114775 restraints weight = 19975.893| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.09 r_work: 0.3214 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13798 Z= 0.113 Angle : 0.538 10.737 18638 Z= 0.283 Chirality : 0.044 0.173 1916 Planarity : 0.003 0.062 2510 Dihedral : 4.163 59.109 1790 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.28 % Allowed : 16.60 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.41 (0.20), residues: 1650 helix: 1.73 (0.23), residues: 502 sheet: 0.88 (0.29), residues: 348 loop : -0.99 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 350 TYR 0.021 0.001 TYR D 76 PHE 0.023 0.001 PHE E 323 TRP 0.011 0.001 TRP A 126 HIS 0.012 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (13794) covalent geometry : angle 0.53686 / 0.28 (18630) SS BOND : bond 0.00245 / 0.16 ( 4) SS BOND : angle 1.62327 / 0.88 ( 8) hydrogen bonds : bond 0.03230 / 2.19 ( 606) hydrogen bonds : angle 4.06525 / 2.80 ( 1866) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 0.451 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: 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 118 ILE cc_start: 0.9164 (mm) cc_final: 0.8909 (mm) REVERT: A 218 ASN cc_start: 0.6889 (t0) cc_final: 0.6554 (p0) REVERT: A 224 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7786 (tptt) REVERT: A 226 ASP cc_start: 0.7774 (t70) cc_final: 0.7470 (t0) REVERT: A 349 ASN cc_start: 0.8521 (t0) cc_final: 0.8216 (t0) REVERT: B 77 SER cc_start: 0.8897 (m) cc_final: 0.8669 (t) REVERT: B 223 ASP cc_start: 0.8187 (t0) cc_final: 0.7987 (t0) REVERT: B 224 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7702 (tptt) REVERT: C 70 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8166 (pp30) REVERT: C 73 GLN cc_start: 0.8541 (pt0) cc_final: 0.8328 (pp30) REVERT: C 94 SER cc_start: 0.8983 (t) cc_final: 0.8455 (p) REVERT: C 97 ILE cc_start: 0.9210 (mm) cc_final: 0.8953 (pt) REVERT: C 132 ASN cc_start: 0.8752 (t0) cc_final: 0.8402 (t0) REVERT: C 138 TYR cc_start: 0.8501 (t80) cc_final: 0.8222 (t80) REVERT: D 49 GLN cc_start: 0.9187 (tp-100) cc_final: 0.8618 (tp-100) REVERT: D 77 PHE cc_start: 0.8388 (t80) cc_final: 0.8053 (t80) REVERT: D 113 SER cc_start: 0.8737 (t) cc_final: 0.8193 (t) REVERT: D 119 ASN cc_start: 0.8245 (m-40) cc_final: 0.7939 (m110) REVERT: D 132 ASN cc_start: 0.7983 (t0) cc_final: 0.7395 (t0) REVERT: D 140 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7908 (pt0) REVERT: E 218 ASN cc_start: 0.6901 (t0) cc_final: 0.6683 (m110) REVERT: F 207 TYR cc_start: 0.8764 (t80) cc_final: 0.8483 (t80) REVERT: F 289 TYR cc_start: 0.8815 (m-80) cc_final: 0.8500 (m-10) REVERT: G 47 HIS cc_start: 0.9185 (m-70) cc_final: 0.8602 (m-70) REVERT: G 75 HIS cc_start: 0.9029 (OUTLIER) cc_final: 0.8624 (t-90) REVERT: G 86 ASN cc_start: 0.8371 (m-40) cc_final: 0.8103 (m-40) REVERT: G 140 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7624 (mt-10) REVERT: H 78 LYS cc_start: 0.9224 (tptt) cc_final: 0.8925 (tppt) REVERT: H 112 MET cc_start: 0.7871 (tpp) cc_final: 0.7559 (tpp) REVERT: H 132 ASN cc_start: 0.8761 (t0) cc_final: 0.8249 (t0) REVERT: H 135 TYR cc_start: 0.7628 (m-80) cc_final: 0.6487 (m-80) outliers start: 33 outliers final: 20 residues processed: 298 average time/residue: 0.1108 time to fit residues: 48.2754 Evaluate side-chains 269 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 137 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 311 HIS C 70 GLN C 75 HIS C 86 ASN E 43 HIS E 156 ASN G 49 GLN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.160327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106872 restraints weight = 19272.849| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.90 r_work: 0.3066 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13798 Z= 0.132 Angle : 0.538 10.689 18638 Z= 0.283 Chirality : 0.044 0.164 1916 Planarity : 0.003 0.073 2510 Dihedral : 4.122 53.962 1790 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.35 % Allowed : 17.84 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.21), residues: 1650 helix: 1.75 (0.24), residues: 502 sheet: 0.55 (0.29), residues: 360 loop : -0.89 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 90 TYR 0.017 0.001 TYR D 76 PHE 0.025 0.001 PHE B 293 TRP 0.010 0.001 TRP A 126 HIS 0.008 0.001 HIS D 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (13794) covalent geometry : angle 0.53596 / 0.28 (18630) SS BOND : bond 0.00220 / 0.13 ( 4) SS BOND : angle 2.11124 / 1.01 ( 8) hydrogen bonds : bond 0.03232 / 2.17 ( 606) hydrogen bonds : angle 3.99589 / 2.75 ( 1866) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 0.537 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: 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 118 ILE cc_start: 0.9228 (mm) cc_final: 0.8904 (mm) REVERT: A 218 ASN cc_start: 0.6922 (t0) cc_final: 0.6370 (p0) REVERT: A 224 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7841 (tptt) REVERT: A 225 ASN cc_start: 0.8297 (t0) cc_final: 0.8057 (t0) REVERT: A 349 ASN cc_start: 0.8386 (t0) cc_final: 0.8066 (t0) REVERT: B 77 SER cc_start: 0.9056 (m) cc_final: 0.8699 (t) REVERT: B 223 ASP cc_start: 0.8208 (t0) cc_final: 0.7831 (t0) REVERT: B 224 LYS cc_start: 0.8370 (mtmt) cc_final: 0.7522 (tptt) REVERT: B 347 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 352 LEU cc_start: 0.8235 (tt) cc_final: 0.8005 (tt) REVERT: C 70 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8923 (pm20) REVERT: C 73 GLN cc_start: 0.8537 (pt0) cc_final: 0.8308 (pp30) REVERT: C 94 SER cc_start: 0.8887 (t) cc_final: 0.8372 (p) REVERT: C 132 ASN cc_start: 0.8989 (t0) cc_final: 0.8571 (t0) REVERT: C 138 TYR cc_start: 0.8726 (t80) cc_final: 0.8256 (t80) REVERT: D 49 GLN cc_start: 0.9246 (tp-100) cc_final: 0.7893 (tp-100) REVERT: D 77 PHE cc_start: 0.8260 (t80) cc_final: 0.7996 (t80) REVERT: D 79 MET cc_start: 0.8105 (tmm) cc_final: 0.7569 (ppp) REVERT: D 80 HIS cc_start: 0.8098 (m90) cc_final: 0.7616 (m-70) REVERT: D 132 ASN cc_start: 0.8354 (t0) cc_final: 0.7740 (t0) REVERT: D 140 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8043 (pt0) REVERT: E 180 ASN cc_start: 0.8847 (m-40) cc_final: 0.8583 (m110) REVERT: E 218 ASN cc_start: 0.7159 (t0) cc_final: 0.6604 (m110) REVERT: F 258 ASP cc_start: 0.8157 (m-30) cc_final: 0.7942 (m-30) REVERT: F 336 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7543 (mt-10) REVERT: G 47 HIS cc_start: 0.9238 (m-70) cc_final: 0.8701 (m-70) REVERT: G 49 GLN cc_start: 0.9015 (tp40) cc_final: 0.8645 (tp-100) REVERT: G 75 HIS cc_start: 0.9066 (OUTLIER) cc_final: 0.8699 (t-90) REVERT: G 86 ASN cc_start: 0.8370 (m-40) cc_final: 0.8154 (m-40) REVERT: G 128 ASP cc_start: 0.8327 (m-30) cc_final: 0.8111 (m-30) REVERT: G 140 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7702 (mt-10) REVERT: H 78 LYS cc_start: 0.9202 (tptt) cc_final: 0.8857 (tppt) REVERT: H 86 ASN cc_start: 0.8906 (m-40) cc_final: 0.8567 (m-40) REVERT: H 112 MET cc_start: 0.7906 (tpp) cc_final: 0.7705 (tpp) REVERT: H 115 ASP cc_start: 0.8442 (p0) cc_final: 0.8190 (p0) REVERT: H 119 ASN cc_start: 0.8679 (t0) cc_final: 0.8336 (m110) REVERT: H 132 ASN cc_start: 0.8995 (t0) cc_final: 0.8427 (t0) REVERT: H 135 TYR cc_start: 0.7640 (m-80) cc_final: 0.6548 (m-80) REVERT: H 140 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7149 (mt-10) REVERT: H 143 LYS cc_start: 0.9225 (tppt) cc_final: 0.8811 (tppt) outliers start: 34 outliers final: 22 residues processed: 276 average time/residue: 0.1135 time to fit residues: 46.0857 Evaluate side-chains 255 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 137 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 71 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 162 optimal weight: 30.0000 chunk 69 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.0670 chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 297 GLN B 311 HIS C 75 HIS C 80 HIS D 49 GLN E 43 HIS E 257 HIS F 191 GLN F 235 ASN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.159472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100074 restraints weight = 19240.988| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.80 r_work: 0.3026 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13798 Z= 0.132 Angle : 0.537 10.650 18638 Z= 0.280 Chirality : 0.044 0.153 1916 Planarity : 0.003 0.059 2510 Dihedral : 4.142 52.045 1790 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.97 % Allowed : 18.19 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.34 (0.21), residues: 1650 helix: 1.65 (0.24), residues: 496 sheet: 0.59 (0.29), residues: 356 loop : -0.86 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 340 TYR 0.017 0.001 TYR A 362 PHE 0.024 0.001 PHE B 293 TRP 0.009 0.001 TRP A 126 HIS 0.010 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13794) covalent geometry : angle 0.53478 / 0.28 (18630) SS BOND : bond 0.00193 / 0.11 ( 4) SS BOND : angle 2.23088 / 1.06 ( 8) hydrogen bonds : bond 0.03210 / 2.15 ( 606) hydrogen bonds : angle 3.99453 / 2.76 ( 1866) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 256 time to evaluate : 0.511 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.9226 (mm) cc_final: 0.8921 (mm) REVERT: A 218 ASN cc_start: 0.6952 (t0) cc_final: 0.6390 (p0) REVERT: A 224 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7784 (tptt) REVERT: A 306 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8649 (pm20) REVERT: A 335 PHE cc_start: 0.9094 (t80) cc_final: 0.8877 (t80) REVERT: A 336 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8183 (mm-30) REVERT: A 349 ASN cc_start: 0.8411 (t0) cc_final: 0.8109 (t0) REVERT: B 77 SER cc_start: 0.9063 (m) cc_final: 0.8719 (t) REVERT: B 223 ASP cc_start: 0.8290 (t0) cc_final: 0.7878 (t0) REVERT: B 224 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7452 (tptt) REVERT: B 347 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7822 (tm-30) REVERT: B 350 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7175 (ttp80) REVERT: C 71 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8746 (tp30) REVERT: C 94 SER cc_start: 0.8868 (t) cc_final: 0.8401 (p) REVERT: C 132 ASN cc_start: 0.9035 (t0) cc_final: 0.8660 (t0) REVERT: D 49 GLN cc_start: 0.9224 (tp40) cc_final: 0.8544 (tp-100) REVERT: D 53 MET cc_start: 0.8975 (mmm) cc_final: 0.8359 (mmm) REVERT: D 79 MET cc_start: 0.8067 (tmm) cc_final: 0.7450 (ppp) REVERT: D 80 HIS cc_start: 0.8031 (m90) cc_final: 0.7372 (m90) REVERT: D 119 ASN cc_start: 0.8019 (m-40) cc_final: 0.7583 (m110) REVERT: D 132 ASN cc_start: 0.8420 (t0) cc_final: 0.7847 (t0) REVERT: E 171 ASN cc_start: 0.9065 (m110) cc_final: 0.8564 (t0) REVERT: E 180 ASN cc_start: 0.8891 (m-40) cc_final: 0.8603 (m110) REVERT: F 258 ASP cc_start: 0.8216 (m-30) cc_final: 0.7958 (m-30) REVERT: G 41 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6863 (tt) REVERT: G 47 HIS cc_start: 0.9298 (m-70) cc_final: 0.8725 (m-70) REVERT: G 67 MET cc_start: 0.8217 (mpp) cc_final: 0.7820 (pmm) REVERT: G 73 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8168 (pp30) REVERT: G 74 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8509 (mm) REVERT: G 75 HIS cc_start: 0.9109 (OUTLIER) cc_final: 0.8777 (t-90) REVERT: G 86 ASN cc_start: 0.8442 (m-40) cc_final: 0.8239 (m-40) REVERT: G 130 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8478 (mtpt) REVERT: G 140 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7711 (mt-10) REVERT: H 53 MET cc_start: 0.9382 (mmm) cc_final: 0.9168 (mmm) REVERT: H 62 LYS cc_start: 0.9058 (tttt) cc_final: 0.8789 (mmtm) REVERT: H 78 LYS cc_start: 0.9197 (tptt) cc_final: 0.8796 (tppt) REVERT: H 86 ASN cc_start: 0.8928 (m-40) cc_final: 0.8717 (m-40) REVERT: H 112 MET cc_start: 0.7817 (tpp) cc_final: 0.7591 (tpp) REVERT: H 115 ASP cc_start: 0.8487 (p0) cc_final: 0.8077 (p0) REVERT: H 116 GLU cc_start: 0.8535 (mp0) cc_final: 0.8171 (mp0) REVERT: H 119 ASN cc_start: 0.8672 (t0) cc_final: 0.8364 (m110) REVERT: H 132 ASN cc_start: 0.8998 (t0) cc_final: 0.8471 (t0) REVERT: H 135 TYR cc_start: 0.7740 (m-80) cc_final: 0.6721 (m-80) REVERT: H 137 ASP cc_start: 0.7976 (t0) cc_final: 0.6910 (p0) REVERT: H 140 GLU cc_start: 0.7831 (mt-10) cc_final: 0.6475 (mt-10) REVERT: H 143 LYS cc_start: 0.9253 (tppt) cc_final: 0.8815 (tppt) outliers start: 43 outliers final: 25 residues processed: 289 average time/residue: 0.1103 time to fit residues: 47.1755 Evaluate side-chains 269 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 40 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 127 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 297 GLN D 61 ASN E 43 HIS E 131 GLN G 49 GLN G 61 ASN G 80 HIS ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.160726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107043 restraints weight = 19389.077| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.07 r_work: 0.3002 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13798 Z= 0.146 Angle : 0.546 8.322 18638 Z= 0.288 Chirality : 0.045 0.162 1916 Planarity : 0.003 0.053 2510 Dihedral : 4.207 51.908 1790 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.53 % Allowed : 18.05 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.33 (0.21), residues: 1650 helix: 1.65 (0.24), residues: 494 sheet: 0.55 (0.29), residues: 356 loop : -0.86 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 126 TYR 0.027 0.001 TYR C 138 PHE 0.035 0.001 PHE B 296 TRP 0.009 0.001 TRP A 126 HIS 0.016 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (13794) covalent geometry : angle 0.54463 / 0.29 (18630) SS BOND : bond 0.00198 / 0.11 ( 4) SS BOND : angle 2.24090 / 1.06 ( 8) hydrogen bonds : bond 0.03209 / 2.14 ( 606) hydrogen bonds : angle 3.98958 / 2.75 ( 1866) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 251 time to evaluate : 0.462 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: 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 118 ILE cc_start: 0.9248 (mm) cc_final: 0.8870 (mm) REVERT: A 209 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: A 218 ASN cc_start: 0.6863 (t0) cc_final: 0.6329 (p0) REVERT: A 224 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7814 (tptt) REVERT: A 306 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8637 (pm20) REVERT: A 335 PHE cc_start: 0.9124 (t80) cc_final: 0.8912 (t80) REVERT: A 336 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8206 (mm-30) REVERT: A 349 ASN cc_start: 0.8437 (t0) cc_final: 0.8155 (t0) REVERT: B 77 SER cc_start: 0.9078 (m) cc_final: 0.8740 (t) REVERT: B 223 ASP cc_start: 0.8316 (t0) cc_final: 0.7911 (t0) REVERT: B 224 LYS cc_start: 0.8335 (mtmt) cc_final: 0.7445 (tptt) REVERT: B 347 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 350 ARG cc_start: 0.7399 (ttp80) cc_final: 0.6896 (mtm110) REVERT: C 56 LEU cc_start: 0.9330 (tp) cc_final: 0.8869 (mt) REVERT: C 70 GLN cc_start: 0.9107 (pp30) cc_final: 0.8838 (pp30) REVERT: C 71 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8606 (tp30) REVERT: C 94 SER cc_start: 0.8876 (t) cc_final: 0.8580 (p) REVERT: C 132 ASN cc_start: 0.9065 (t0) cc_final: 0.8704 (t0) REVERT: D 49 GLN cc_start: 0.9373 (tp40) cc_final: 0.8427 (tp-100) REVERT: D 53 MET cc_start: 0.9069 (mmm) cc_final: 0.8492 (mmm) REVERT: D 67 MET cc_start: 0.7329 (tmm) cc_final: 0.6883 (pmm) REVERT: D 79 MET cc_start: 0.8013 (tmm) cc_final: 0.7394 (ppp) REVERT: D 80 HIS cc_start: 0.8106 (m90) cc_final: 0.7369 (m90) REVERT: D 119 ASN cc_start: 0.8177 (m-40) cc_final: 0.7772 (m110) REVERT: D 126 ARG cc_start: 0.8999 (mtm110) cc_final: 0.8794 (mtm110) REVERT: D 132 ASN cc_start: 0.8558 (t0) cc_final: 0.8011 (t0) REVERT: E 171 ASN cc_start: 0.9088 (m110) cc_final: 0.8525 (t0) REVERT: E 180 ASN cc_start: 0.8906 (m-40) cc_final: 0.8600 (m110) REVERT: F 258 ASP cc_start: 0.8251 (m-30) cc_final: 0.7994 (m-30) REVERT: F 289 TYR cc_start: 0.8855 (m-80) cc_final: 0.8570 (m-10) REVERT: G 47 HIS cc_start: 0.9329 (m-70) cc_final: 0.8511 (m-70) REVERT: G 49 GLN cc_start: 0.8829 (tp40) cc_final: 0.8158 (tp-100) REVERT: G 67 MET cc_start: 0.8205 (mpp) cc_final: 0.7478 (ttm) REVERT: G 75 HIS cc_start: 0.9118 (OUTLIER) cc_final: 0.8835 (t-90) REVERT: G 86 ASN cc_start: 0.8510 (m-40) cc_final: 0.8168 (m-40) REVERT: G 130 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8559 (mtpt) REVERT: G 140 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7773 (mt-10) REVERT: H 78 LYS cc_start: 0.9173 (tptt) cc_final: 0.8761 (tppt) REVERT: H 86 ASN cc_start: 0.8951 (m-40) cc_final: 0.8670 (m-40) REVERT: H 112 MET cc_start: 0.7809 (tpp) cc_final: 0.7540 (tpp) REVERT: H 115 ASP cc_start: 0.8456 (p0) cc_final: 0.8061 (p0) REVERT: H 116 GLU cc_start: 0.8521 (mp0) cc_final: 0.8019 (mp0) REVERT: H 119 ASN cc_start: 0.8698 (t0) cc_final: 0.8385 (m110) REVERT: H 132 ASN cc_start: 0.9004 (t0) cc_final: 0.8464 (t0) REVERT: H 135 TYR cc_start: 0.7701 (m-80) cc_final: 0.6645 (m-80) REVERT: H 140 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7142 (mt-10) REVERT: H 143 LYS cc_start: 0.9266 (tppt) cc_final: 0.8830 (tppt) outliers start: 51 outliers final: 30 residues processed: 290 average time/residue: 0.1142 time to fit residues: 48.7848 Evaluate side-chains 275 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 242 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 139 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 152 optimal weight: 0.0040 chunk 67 optimal weight: 0.0370 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 162 optimal weight: 40.0000 chunk 10 optimal weight: 1.9990 overall best weight: 0.5472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN D 61 ASN E 43 HIS E 131 GLN E 308 GLN ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.162042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100978 restraints weight = 19739.633| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.97 r_work: 0.3048 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13798 Z= 0.104 Angle : 0.557 13.798 18638 Z= 0.286 Chirality : 0.044 0.214 1916 Planarity : 0.003 0.047 2510 Dihedral : 4.095 50.667 1790 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.49 % Allowed : 19.16 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.21), residues: 1650 helix: 1.70 (0.24), residues: 470 sheet: 0.90 (0.29), residues: 336 loop : -0.88 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 126 TYR 0.016 0.001 TYR C 138 PHE 0.028 0.001 PHE B 293 TRP 0.011 0.001 TRP B 126 HIS 0.006 0.001 HIS G 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (13794) covalent geometry : angle 0.55521 / 0.28 (18630) SS BOND : bond 0.00166 / 0.09 ( 4) SS BOND : angle 2.14172 / 1.07 ( 8) hydrogen bonds : bond 0.03042 / 1.98 ( 606) hydrogen bonds : angle 3.84357 / 2.64 ( 1866) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.532 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: A 218 ASN cc_start: 0.6862 (t0) cc_final: 0.6360 (p0) REVERT: A 224 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7749 (tptt) REVERT: A 336 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8161 (mm-30) REVERT: A 349 ASN cc_start: 0.8304 (t0) cc_final: 0.8039 (t0) REVERT: B 77 SER cc_start: 0.9027 (m) cc_final: 0.8659 (t) REVERT: B 223 ASP cc_start: 0.8245 (t0) cc_final: 0.7832 (t0) REVERT: B 224 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7369 (tptt) REVERT: B 347 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7833 (tm-30) REVERT: B 352 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8046 (tt) REVERT: C 56 LEU cc_start: 0.9343 (tp) cc_final: 0.9096 (tt) REVERT: C 70 GLN cc_start: 0.9102 (pp30) cc_final: 0.8638 (pp30) REVERT: C 71 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8607 (tp30) REVERT: C 76 TYR cc_start: 0.8322 (t80) cc_final: 0.8102 (t80) REVERT: C 94 SER cc_start: 0.8890 (t) cc_final: 0.8603 (p) REVERT: C 132 ASN cc_start: 0.9040 (t0) cc_final: 0.8672 (t0) REVERT: D 49 GLN cc_start: 0.9468 (tp40) cc_final: 0.8872 (tp-100) REVERT: D 67 MET cc_start: 0.7342 (tmm) cc_final: 0.7105 (pmm) REVERT: D 79 MET cc_start: 0.7970 (tmm) cc_final: 0.7260 (ppp) REVERT: D 80 HIS cc_start: 0.7983 (m90) cc_final: 0.7677 (m170) REVERT: D 119 ASN cc_start: 0.8149 (m-40) cc_final: 0.7683 (m110) REVERT: D 126 ARG cc_start: 0.8999 (mtm110) cc_final: 0.8497 (ptp-110) REVERT: D 132 ASN cc_start: 0.8592 (t0) cc_final: 0.8074 (t0) REVERT: E 171 ASN cc_start: 0.9094 (m110) cc_final: 0.8534 (t0) REVERT: E 180 ASN cc_start: 0.8915 (m-40) cc_final: 0.8625 (m110) REVERT: F 234 GLU cc_start: 0.7956 (pp20) cc_final: 0.7655 (tm-30) REVERT: F 235 ASN cc_start: 0.8640 (m110) cc_final: 0.8322 (m110) REVERT: F 258 ASP cc_start: 0.8186 (m-30) cc_final: 0.7946 (m-30) REVERT: F 289 TYR cc_start: 0.8896 (m-80) cc_final: 0.8566 (m-10) REVERT: G 47 HIS cc_start: 0.9062 (m-70) cc_final: 0.8551 (m-70) REVERT: G 49 GLN cc_start: 0.8955 (tp40) cc_final: 0.8482 (tp-100) REVERT: G 73 GLN cc_start: 0.8351 (pt0) cc_final: 0.7827 (pp30) REVERT: G 75 HIS cc_start: 0.9114 (OUTLIER) cc_final: 0.8892 (t70) REVERT: G 86 ASN cc_start: 0.8509 (m-40) cc_final: 0.8179 (m-40) REVERT: G 130 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8521 (mtpt) REVERT: G 140 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7720 (mt-10) REVERT: H 78 LYS cc_start: 0.9155 (tptt) cc_final: 0.8739 (tppt) REVERT: H 112 MET cc_start: 0.7773 (tpp) cc_final: 0.7552 (tpp) REVERT: H 132 ASN cc_start: 0.8990 (t0) cc_final: 0.8446 (t0) REVERT: H 135 TYR cc_start: 0.7679 (m-80) cc_final: 0.6600 (m-80) REVERT: H 137 ASP cc_start: 0.7978 (t0) cc_final: 0.7007 (p0) REVERT: H 140 GLU cc_start: 0.7654 (mt-10) cc_final: 0.6513 (mt-10) outliers start: 36 outliers final: 22 residues processed: 277 average time/residue: 0.1129 time to fit residues: 46.3454 Evaluate side-chains 262 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 150 optimal weight: 0.0070 chunk 100 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 139 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 ASN A 297 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN E 43 HIS E 131 GLN ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 GLN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.159413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105036 restraints weight = 19653.835| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.73 r_work: 0.2967 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13798 Z= 0.161 Angle : 0.597 14.819 18638 Z= 0.309 Chirality : 0.046 0.239 1916 Planarity : 0.003 0.048 2510 Dihedral : 4.237 50.899 1790 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.21 % Allowed : 19.99 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.22 (0.21), residues: 1650 helix: 1.37 (0.24), residues: 504 sheet: 0.57 (0.29), residues: 358 loop : -0.85 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 350 TYR 0.019 0.001 TYR G 138 PHE 0.027 0.002 PHE B 293 TRP 0.008 0.001 TRP A 126 HIS 0.007 0.001 HIS G 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (13794) covalent geometry : angle 0.59474 / 0.31 (18630) SS BOND : bond 0.00204 / 0.11 ( 4) SS BOND : angle 2.38264 / 1.14 ( 8) hydrogen bonds : bond 0.03453 / 2.26 ( 606) hydrogen bonds : angle 4.03563 / 2.79 ( 1866) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 250 time to evaluate : 0.525 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: 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 209 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: A 218 ASN cc_start: 0.6919 (t0) cc_final: 0.6379 (p0) REVERT: A 224 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7869 (tptt) REVERT: A 336 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8244 (mm-30) REVERT: A 349 ASN cc_start: 0.8383 (t0) cc_final: 0.8101 (t0) REVERT: B 77 SER cc_start: 0.9133 (m) cc_final: 0.8783 (t) REVERT: B 223 ASP cc_start: 0.8357 (t0) cc_final: 0.7893 (t0) REVERT: B 224 LYS cc_start: 0.8334 (mtmt) cc_final: 0.7355 (tptt) REVERT: B 347 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 350 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7073 (ptt-90) REVERT: C 56 LEU cc_start: 0.9475 (tp) cc_final: 0.9195 (tt) REVERT: C 70 GLN cc_start: 0.9142 (pp30) cc_final: 0.8763 (pp30) REVERT: C 71 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8775 (tp30) REVERT: C 94 SER cc_start: 0.8909 (t) cc_final: 0.8630 (p) REVERT: C 132 ASN cc_start: 0.9114 (t0) cc_final: 0.8758 (t0) REVERT: D 49 GLN cc_start: 0.9496 (tp40) cc_final: 0.9243 (tp-100) REVERT: D 79 MET cc_start: 0.8011 (tmm) cc_final: 0.7273 (ppp) REVERT: D 80 HIS cc_start: 0.8100 (m90) cc_final: 0.7629 (m170) REVERT: D 119 ASN cc_start: 0.8193 (m-40) cc_final: 0.7703 (m110) REVERT: D 126 ARG cc_start: 0.9005 (mtm110) cc_final: 0.8519 (ptp-110) REVERT: D 132 ASN cc_start: 0.8690 (t0) cc_final: 0.8194 (t0) REVERT: E 171 ASN cc_start: 0.9104 (m110) cc_final: 0.8499 (t0) REVERT: E 180 ASN cc_start: 0.8923 (m-40) cc_final: 0.8654 (m110) REVERT: F 258 ASP cc_start: 0.8296 (m-30) cc_final: 0.8033 (m-30) REVERT: F 289 TYR cc_start: 0.8936 (m-80) cc_final: 0.8653 (m-10) REVERT: G 47 HIS cc_start: 0.9138 (m-70) cc_final: 0.8557 (m-70) REVERT: G 49 GLN cc_start: 0.8828 (tp40) cc_final: 0.8466 (tp-100) REVERT: G 73 GLN cc_start: 0.8544 (pt0) cc_final: 0.7944 (pp30) REVERT: G 74 LEU cc_start: 0.8979 (mt) cc_final: 0.8776 (mt) REVERT: G 75 HIS cc_start: 0.9151 (OUTLIER) cc_final: 0.8850 (t-90) REVERT: G 130 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8664 (mtpt) REVERT: G 140 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7523 (mt-10) REVERT: H 53 MET cc_start: 0.9228 (mmm) cc_final: 0.9020 (mmm) REVERT: H 112 MET cc_start: 0.7787 (tpp) cc_final: 0.7584 (tpp) REVERT: H 132 ASN cc_start: 0.9019 (t0) cc_final: 0.8446 (t0) REVERT: H 137 ASP cc_start: 0.8012 (t0) cc_final: 0.7030 (p0) REVERT: H 140 GLU cc_start: 0.7807 (mt-10) cc_final: 0.6568 (mt-10) outliers start: 32 outliers final: 24 residues processed: 274 average time/residue: 0.1086 time to fit residues: 43.9535 Evaluate side-chains 267 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 116 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 100 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN C 49 GLN E 43 HIS E 308 GLN ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN H 55 HIS H 73 GLN H 101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.161254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102913 restraints weight = 19495.703| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.29 r_work: 0.3028 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13798 Z= 0.116 Angle : 0.587 15.209 18638 Z= 0.300 Chirality : 0.045 0.264 1916 Planarity : 0.003 0.047 2510 Dihedral : 4.123 49.685 1790 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.94 % Allowed : 20.75 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.26 (0.21), residues: 1650 helix: 1.38 (0.24), residues: 504 sheet: 0.61 (0.29), residues: 358 loop : -0.83 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 350 TYR 0.016 0.001 TYR H 76 PHE 0.025 0.001 PHE B 293 TRP 0.011 0.001 TRP F 126 HIS 0.007 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13794) covalent geometry : angle 0.58553 / 0.30 (18630) SS BOND : bond 0.00179 / 0.10 ( 4) SS BOND : angle 2.20095 / 1.06 ( 8) hydrogen bonds : bond 0.03192 / 2.07 ( 606) hydrogen bonds : angle 3.90453 / 2.71 ( 1866) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.519 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: A 218 ASN cc_start: 0.6907 (t0) cc_final: 0.6385 (p0) REVERT: A 224 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7966 (tttp) REVERT: A 289 TYR cc_start: 0.9253 (m-10) cc_final: 0.9053 (m-10) REVERT: A 336 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8213 (mm-30) REVERT: A 349 ASN cc_start: 0.8294 (t0) cc_final: 0.8038 (t0) REVERT: B 77 SER cc_start: 0.9076 (m) cc_final: 0.8711 (t) REVERT: B 223 ASP cc_start: 0.8328 (t0) cc_final: 0.7875 (t0) REVERT: B 224 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7357 (tptt) REVERT: B 347 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 350 ARG cc_start: 0.7380 (ttp80) cc_final: 0.7115 (ptt-90) REVERT: C 70 GLN cc_start: 0.9149 (pp30) cc_final: 0.8770 (pp30) REVERT: C 71 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8763 (tp30) REVERT: C 132 ASN cc_start: 0.9084 (t0) cc_final: 0.8726 (t0) REVERT: D 49 GLN cc_start: 0.9498 (tp40) cc_final: 0.9004 (tp-100) REVERT: D 79 MET cc_start: 0.8034 (tmm) cc_final: 0.7255 (ppp) REVERT: D 80 HIS cc_start: 0.8130 (m90) cc_final: 0.7744 (m170) REVERT: D 119 ASN cc_start: 0.8184 (m-40) cc_final: 0.7684 (m110) REVERT: D 126 ARG cc_start: 0.8988 (mtm110) cc_final: 0.8516 (ptp-110) REVERT: D 132 ASN cc_start: 0.8684 (t0) cc_final: 0.8228 (t0) REVERT: E 171 ASN cc_start: 0.9085 (m110) cc_final: 0.8505 (t0) REVERT: E 180 ASN cc_start: 0.8953 (m-40) cc_final: 0.8684 (m110) REVERT: F 258 ASP cc_start: 0.8228 (m-30) cc_final: 0.7965 (m-30) REVERT: F 289 TYR cc_start: 0.8954 (m-80) cc_final: 0.8684 (m-10) REVERT: G 47 HIS cc_start: 0.9097 (m-70) cc_final: 0.8421 (m-70) REVERT: G 49 GLN cc_start: 0.8766 (tp40) cc_final: 0.8411 (tp-100) REVERT: G 73 GLN cc_start: 0.8523 (pt0) cc_final: 0.7912 (pp30) REVERT: G 130 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8645 (mtpt) REVERT: G 140 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7476 (mt-10) REVERT: H 53 MET cc_start: 0.9187 (mmm) cc_final: 0.8913 (mmm) REVERT: H 112 MET cc_start: 0.7778 (tpp) cc_final: 0.7532 (tpp) REVERT: H 132 ASN cc_start: 0.9009 (t0) cc_final: 0.8446 (t0) REVERT: H 137 ASP cc_start: 0.7996 (t0) cc_final: 0.6936 (p0) REVERT: H 140 GLU cc_start: 0.7720 (mt-10) cc_final: 0.6420 (mt-10) outliers start: 28 outliers final: 23 residues processed: 270 average time/residue: 0.1122 time to fit residues: 44.7366 Evaluate side-chains 265 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 116 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 52 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 145 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN C 49 GLN D 70 GLN E 43 HIS E 308 GLN ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS G 86 ASN H 70 GLN H 80 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.159747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104517 restraints weight = 19693.881| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.12 r_work: 0.3001 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13798 Z= 0.144 Angle : 0.611 15.900 18638 Z= 0.312 Chirality : 0.045 0.248 1916 Planarity : 0.003 0.047 2510 Dihedral : 4.198 49.197 1790 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.21 % Allowed : 20.82 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 (0.21), residues: 1650 helix: 1.41 (0.24), residues: 480 sheet: 0.48 (0.28), residues: 368 loop : -0.76 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 340 TYR 0.014 0.001 TYR B 48 PHE 0.021 0.001 PHE B 293 TRP 0.008 0.001 TRP A 126 HIS 0.012 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13794) covalent geometry : angle 0.60953 / 0.31 (18630) SS BOND : bond 0.00207 / 0.12 ( 4) SS BOND : angle 2.23760 / 1.06 ( 8) hydrogen bonds : bond 0.03392 / 2.20 ( 606) hydrogen bonds : angle 4.03810 / 2.80 ( 1866) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 245 time to evaluate : 0.439 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: 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 209 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: A 218 ASN cc_start: 0.6886 (t0) cc_final: 0.6359 (p0) REVERT: A 224 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7989 (tttp) REVERT: A 336 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8203 (mm-30) REVERT: A 349 ASN cc_start: 0.8349 (t0) cc_final: 0.8073 (t0) REVERT: B 77 SER cc_start: 0.9109 (m) cc_final: 0.8768 (t) REVERT: B 223 ASP cc_start: 0.8354 (t0) cc_final: 0.7896 (t0) REVERT: B 224 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7322 (tptt) REVERT: B 347 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7905 (tm-30) REVERT: C 70 GLN cc_start: 0.9174 (pp30) cc_final: 0.8733 (pp30) REVERT: C 71 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8785 (tp30) REVERT: C 132 ASN cc_start: 0.9122 (t0) cc_final: 0.8776 (t0) REVERT: D 53 MET cc_start: 0.9167 (mmm) cc_final: 0.8662 (mmp) REVERT: D 79 MET cc_start: 0.8100 (tmm) cc_final: 0.7358 (ppp) REVERT: D 80 HIS cc_start: 0.8118 (m90) cc_final: 0.7536 (m90) REVERT: D 92 GLU cc_start: 0.6402 (mt-10) cc_final: 0.6156 (mt-10) REVERT: D 119 ASN cc_start: 0.8159 (m-40) cc_final: 0.7590 (m110) REVERT: D 126 ARG cc_start: 0.8985 (mtm110) cc_final: 0.8513 (ptp-110) REVERT: D 132 ASN cc_start: 0.8726 (t0) cc_final: 0.8297 (t0) REVERT: E 171 ASN cc_start: 0.9090 (m110) cc_final: 0.8510 (t0) REVERT: E 180 ASN cc_start: 0.8962 (m-40) cc_final: 0.8697 (m-40) REVERT: F 258 ASP cc_start: 0.8251 (m-30) cc_final: 0.7982 (m-30) REVERT: F 289 TYR cc_start: 0.8949 (m-80) cc_final: 0.8670 (m-10) REVERT: G 47 HIS cc_start: 0.9060 (m-70) cc_final: 0.8367 (m-70) REVERT: G 49 GLN cc_start: 0.8719 (tp40) cc_final: 0.8149 (tp-100) REVERT: G 140 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7494 (mt-10) REVERT: H 53 MET cc_start: 0.9181 (mmm) cc_final: 0.8936 (mmm) REVERT: H 78 LYS cc_start: 0.9211 (tptp) cc_final: 0.8783 (tppt) REVERT: H 101 HIS cc_start: 0.8036 (t70) cc_final: 0.7633 (t70) REVERT: H 112 MET cc_start: 0.7743 (tpp) cc_final: 0.7495 (tpp) REVERT: H 132 ASN cc_start: 0.9006 (t0) cc_final: 0.8465 (t0) REVERT: H 137 ASP cc_start: 0.8027 (t0) cc_final: 0.6997 (p0) REVERT: H 140 GLU cc_start: 0.7821 (mt-10) cc_final: 0.6518 (mt-10) outliers start: 32 outliers final: 26 residues processed: 270 average time/residue: 0.1049 time to fit residues: 41.7119 Evaluate side-chains 263 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 HIS Chi-restraints excluded: chain H residue 116 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 59 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 138 optimal weight: 0.0050 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN H 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.159962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104309 restraints weight = 19646.708| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.10 r_work: 0.2999 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13798 Z= 0.142 Angle : 0.639 16.129 18638 Z= 0.328 Chirality : 0.045 0.248 1916 Planarity : 0.003 0.047 2510 Dihedral : 4.222 48.608 1790 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.80 % Allowed : 21.16 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 (0.21), residues: 1650 helix: 1.37 (0.24), residues: 480 sheet: 0.46 (0.28), residues: 368 loop : -0.76 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 350 TYR 0.015 0.001 TYR B 48 PHE 0.025 0.001 PHE B 293 TRP 0.009 0.001 TRP F 126 HIS 0.006 0.001 HIS G 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (13794) covalent geometry : angle 0.63728 / 0.33 (18630) SS BOND : bond 0.00227 / 0.13 ( 4) SS BOND : angle 2.23011 / 1.05 ( 8) hydrogen bonds : bond 0.03450 / 2.21 ( 606) hydrogen bonds : angle 4.06433 / 2.82 ( 1866) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.520 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: A 218 ASN cc_start: 0.6893 (t0) cc_final: 0.6364 (p0) REVERT: A 224 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7914 (tttp) REVERT: A 336 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8207 (mm-30) REVERT: A 349 ASN cc_start: 0.8284 (t0) cc_final: 0.8026 (t0) REVERT: B 77 SER cc_start: 0.9110 (m) cc_final: 0.8774 (t) REVERT: B 223 ASP cc_start: 0.8362 (t0) cc_final: 0.7900 (t0) REVERT: B 224 LYS cc_start: 0.8331 (mtmt) cc_final: 0.7312 (tptt) REVERT: B 350 ARG cc_start: 0.7438 (ttp80) cc_final: 0.7183 (ptt-90) REVERT: C 71 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8870 (tp30) REVERT: C 132 ASN cc_start: 0.9122 (t0) cc_final: 0.8790 (t0) REVERT: D 49 GLN cc_start: 0.9288 (tp-100) cc_final: 0.8758 (tp-100) REVERT: D 53 MET cc_start: 0.9094 (mmm) cc_final: 0.8660 (mmp) REVERT: D 67 MET cc_start: 0.7386 (tmm) cc_final: 0.6967 (mpp) REVERT: D 79 MET cc_start: 0.8133 (tmm) cc_final: 0.7395 (ppp) REVERT: D 80 HIS cc_start: 0.8082 (m90) cc_final: 0.7498 (m90) REVERT: D 116 GLU cc_start: 0.8808 (pm20) cc_final: 0.8543 (pm20) REVERT: D 119 ASN cc_start: 0.8151 (m-40) cc_final: 0.7584 (m110) REVERT: D 126 ARG cc_start: 0.8985 (mtm110) cc_final: 0.8497 (ptp-110) REVERT: D 132 ASN cc_start: 0.8719 (t0) cc_final: 0.8303 (t0) REVERT: E 171 ASN cc_start: 0.9096 (m110) cc_final: 0.8510 (t0) REVERT: E 180 ASN cc_start: 0.8925 (m-40) cc_final: 0.8671 (m-40) REVERT: E 354 MET cc_start: 0.8189 (tpp) cc_final: 0.7879 (tmm) REVERT: F 258 ASP cc_start: 0.8266 (m-30) cc_final: 0.8003 (m-30) REVERT: F 289 TYR cc_start: 0.8947 (m-80) cc_final: 0.8691 (m-10) REVERT: G 47 HIS cc_start: 0.9048 (m-70) cc_final: 0.8350 (m-70) REVERT: G 140 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7486 (mt-10) REVERT: H 53 MET cc_start: 0.9185 (mmm) cc_final: 0.8896 (mmm) REVERT: H 78 LYS cc_start: 0.9137 (tptp) cc_final: 0.8689 (tppt) REVERT: H 101 HIS cc_start: 0.7861 (t70) cc_final: 0.7408 (t70) REVERT: H 112 MET cc_start: 0.7746 (tpp) cc_final: 0.7498 (tpp) REVERT: H 132 ASN cc_start: 0.8998 (t0) cc_final: 0.8449 (t0) REVERT: H 137 ASP cc_start: 0.8054 (t0) cc_final: 0.7099 (p0) REVERT: H 140 GLU cc_start: 0.7814 (mt-10) cc_final: 0.6522 (mt-10) outliers start: 26 outliers final: 24 residues processed: 258 average time/residue: 0.1109 time to fit residues: 42.0333 Evaluate side-chains 258 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 80 HIS Chi-restraints excluded: chain H residue 116 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 20 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN E 43 HIS E 131 GLN E 308 GLN ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103206 restraints weight = 19458.716| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.21 r_work: 0.2933 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13798 Z= 0.255 Angle : 0.703 16.299 18638 Z= 0.367 Chirality : 0.048 0.237 1916 Planarity : 0.004 0.057 2510 Dihedral : 4.522 49.737 1790 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.28 % Allowed : 20.95 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.06 (0.21), residues: 1650 helix: 1.09 (0.24), residues: 484 sheet: 0.22 (0.28), residues: 368 loop : -0.85 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 111 TYR 0.018 0.002 TYR B 48 PHE 0.025 0.002 PHE B 293 TRP 0.011 0.002 TRP A 67 HIS 0.014 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.26 (13794) covalent geometry : angle 0.70088 / 0.37 (18630) SS BOND : bond 0.00297 / 0.17 ( 4) SS BOND : angle 2.46334 / 1.16 ( 8) hydrogen bonds : bond 0.03941 / 2.60 ( 606) hydrogen bonds : angle 4.44738 / 3.10 ( 1866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3269.03 seconds wall clock time: 56 minutes 44.31 seconds (3404.31 seconds total)