Starting phenix.real_space_refine on Sat Aug 23 16:23:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp8_36471/08_2025/8jp8_36471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp8_36471/08_2025/8jp8_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_36471/08_2025/8jp8_36471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp8_36471/08_2025/8jp8_36471.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jp8_36471/08_2025/8jp8_36471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp8_36471/08_2025/8jp8_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-2.0-5787/lib/python3.9/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.66, per 1000 atoms: 0.20 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: 0.98 Conformation dependent library (CDL) restraints added in 590.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.29 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: 1.92 Time building geometry restraints manager: 1.26 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: 0.630 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.240 Find NCS groups from input model: 0.180 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 aren 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 covalent geometry : bond 0.00220 (13794) covalent geometry : angle 0.51602 (18630) SS BOND : bond 0.00144 ( 4) SS BOND : angle 1.86326 ( 8) hydrogen bonds : bond 0.11199 ( 606) hydrogen bonds : angle 5.04473 ( 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 : 0.424 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: 0.8877 (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: 0.1161 time to fit residues: 65.0330 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 : 0.474 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 235 ASN A 351 GLN 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 80 HIS D 101 HIS E 43 HIS E 59 GLN E 79 GLN E 342 HIS E 351 GLN 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.167493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112167 restraints weight = 20040.670| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.97 r_work: 0.3233 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13798 Z= 0.112 Angle : 0.532 10.558 18638 Z= 0.280 Chirality : 0.044 0.174 1916 Planarity : 0.003 0.063 2510 Dihedral : 4.133 59.096 1790 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.21 % Allowed : 17.36 % Favored : 80.43 % 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 aren not related in a simple way. whole: 0.40 (0.20), residues: 1650 helix: 1.70 (0.23), residues: 502 sheet: 0.89 (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 0.022 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 covalent geometry : bond 0.00244 (13794) covalent geometry : angle 0.53115 (18630) SS BOND : bond 0.00229 ( 4) SS BOND : angle 1.65958 ( 8) hydrogen bonds : bond 0.03285 ( 606) hydrogen bonds : angle 4.07009 ( 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 307 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 0.336 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.9151 (mm) cc_final: 0.8899 (mm) REVERT: A 218 ASN cc_start: 0.6892 (t0) cc_final: 0.6552 (p0) REVERT: A 224 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7805 (tptt) REVERT: A 226 ASP cc_start: 0.7723 (t70) cc_final: 0.7421 (t0) REVERT: A 349 ASN cc_start: 0.8510 (t0) cc_final: 0.8208 (t0) REVERT: B 77 SER cc_start: 0.8893 (m) cc_final: 0.8666 (t) REVERT: B 224 LYS cc_start: 0.8238 (mtmt) cc_final: 0.7723 (tptt) REVERT: C 70 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8177 (pp30) REVERT: C 94 SER cc_start: 0.8964 (t) cc_final: 0.8460 (p) REVERT: C 132 ASN cc_start: 0.8813 (t0) cc_final: 0.8305 (t0) REVERT: C 138 TYR cc_start: 0.8549 (t80) cc_final: 0.8130 (t80) REVERT: D 77 PHE cc_start: 0.8401 (t80) cc_final: 0.8077 (t80) REVERT: D 113 SER cc_start: 0.8699 (t) cc_final: 0.8348 (t) REVERT: D 119 ASN cc_start: 0.8218 (m-40) cc_final: 0.7920 (m110) REVERT: D 132 ASN cc_start: 0.8056 (t0) cc_final: 0.7519 (t0) REVERT: E 171 ASN cc_start: 0.8803 (m110) cc_final: 0.8533 (t0) REVERT: E 218 ASN cc_start: 0.6914 (t0) cc_final: 0.6698 (m110) REVERT: F 207 TYR cc_start: 0.8753 (t80) cc_final: 0.8470 (t80) REVERT: F 289 TYR cc_start: 0.8802 (m-80) cc_final: 0.8499 (m-10) REVERT: G 47 HIS cc_start: 0.9137 (m-70) cc_final: 0.8557 (m-70) REVERT: G 75 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8568 (t-90) REVERT: G 92 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6535 (mt-10) REVERT: H 78 LYS cc_start: 0.9233 (tptt) cc_final: 0.8912 (tppt) REVERT: H 112 MET cc_start: 0.7945 (tpp) cc_final: 0.7652 (tpp) REVERT: H 132 ASN cc_start: 0.8700 (t0) cc_final: 0.8227 (t0) REVERT: H 135 TYR cc_start: 0.7700 (m-80) cc_final: 0.6944 (m-80) outliers start: 32 outliers final: 19 residues processed: 295 average time/residue: 0.1037 time to fit residues: 44.5357 Evaluate side-chains 262 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 121 ASP 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 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 F residue 118 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 75 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 40.0000 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 74 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 311 HIS C 75 HIS D 73 GLN E 43 HIS E 257 HIS F 191 GLN G 49 GLN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 HIS H 80 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.160336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106116 restraints weight = 19236.474| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.98 r_work: 0.3024 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2986 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= 0.150 Angle : 0.542 11.038 18638 Z= 0.287 Chirality : 0.045 0.168 1916 Planarity : 0.004 0.074 2510 Dihedral : 4.154 53.488 1790 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.42 % Allowed : 17.77 % 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 aren not related in a simple way. whole: 0.34 (0.21), residues: 1650 helix: 1.64 (0.23), residues: 506 sheet: 0.56 (0.29), residues: 356 loop : -0.88 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 340 TYR 0.017 0.002 TYR D 76 PHE 0.025 0.002 PHE B 293 TRP 0.011 0.001 TRP A 126 HIS 0.014 0.001 HIS D 55 Details of bonding type rmsd covalent geometry : bond 0.00343 (13794) covalent geometry : angle 0.54023 (18630) SS BOND : bond 0.00358 ( 4) SS BOND : angle 2.29679 ( 8) hydrogen bonds : bond 0.03326 ( 606) hydrogen bonds : angle 4.07394 ( 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 288 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 0.562 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: 0.9236 (mm) cc_final: 0.8958 (mm) REVERT: A 218 ASN cc_start: 0.6865 (t0) cc_final: 0.6313 (p0) REVERT: A 224 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7822 (tptt) REVERT: A 225 ASN cc_start: 0.8332 (t0) cc_final: 0.8095 (t0) REVERT: A 349 ASN cc_start: 0.8453 (t0) cc_final: 0.8124 (t0) REVERT: B 77 SER cc_start: 0.9089 (m) cc_final: 0.8740 (t) REVERT: B 223 ASP cc_start: 0.8172 (t0) cc_final: 0.7926 (t0) REVERT: B 224 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7510 (tptt) REVERT: B 347 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7832 (tm-30) REVERT: C 94 SER cc_start: 0.8919 (t) cc_final: 0.8389 (p) REVERT: C 132 ASN cc_start: 0.9069 (t0) cc_final: 0.8578 (t0) REVERT: D 53 MET cc_start: 0.9154 (mmm) cc_final: 0.8784 (mmp) REVERT: D 77 PHE cc_start: 0.8283 (t80) cc_final: 0.8046 (t80) REVERT: D 79 MET cc_start: 0.8137 (tmm) cc_final: 0.7594 (ppp) REVERT: D 80 HIS cc_start: 0.8120 (m90) cc_final: 0.7661 (m-70) REVERT: D 132 ASN cc_start: 0.8351 (t0) cc_final: 0.7729 (t0) REVERT: E 171 ASN cc_start: 0.9015 (m110) cc_final: 0.8520 (t0) REVERT: F 258 ASP cc_start: 0.8229 (m-30) cc_final: 0.7991 (m-30) REVERT: G 47 HIS cc_start: 0.9245 (m-70) cc_final: 0.8713 (m-70) REVERT: G 49 GLN cc_start: 0.9032 (tp40) cc_final: 0.8629 (tp-100) REVERT: G 75 HIS cc_start: 0.9064 (OUTLIER) cc_final: 0.8710 (t-90) REVERT: G 92 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6737 (mt-10) REVERT: G 127 ASP cc_start: 0.8477 (m-30) cc_final: 0.8234 (m-30) REVERT: G 128 ASP cc_start: 0.8432 (m-30) cc_final: 0.7845 (m-30) REVERT: G 140 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7655 (mt-10) REVERT: H 62 LYS cc_start: 0.9046 (tttt) cc_final: 0.8787 (mmtm) REVERT: H 78 LYS cc_start: 0.9199 (tptt) cc_final: 0.8831 (tppt) REVERT: H 112 MET cc_start: 0.7916 (tpp) cc_final: 0.7714 (tpp) REVERT: H 115 ASP cc_start: 0.8424 (p0) cc_final: 0.8190 (p0) REVERT: H 116 GLU cc_start: 0.8480 (mp0) cc_final: 0.8272 (mp0) REVERT: H 119 ASN cc_start: 0.8661 (t0) cc_final: 0.8295 (m110) REVERT: H 132 ASN cc_start: 0.8973 (t0) cc_final: 0.8466 (t0) REVERT: H 135 TYR cc_start: 0.7738 (m-80) cc_final: 0.6926 (m-80) REVERT: H 143 LYS cc_start: 0.9229 (tppt) cc_final: 0.8801 (tppt) outliers start: 35 outliers final: 22 residues processed: 276 average time/residue: 0.1037 time to fit residues: 42.0185 Evaluate side-chains 262 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 98 THR Chi-restraints excluded: chain H residue 55 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 71 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 162 optimal weight: 40.0000 chunk 69 optimal weight: 40.0000 chunk 135 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.0050 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 297 GLN B 311 HIS C 73 GLN C 80 HIS E 43 HIS ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS G 86 ASN ** 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 = 0.4025 r_free = 0.4025 target = 0.159919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099430 restraints weight = 19520.628| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.87 r_work: 0.3027 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13798 Z= 0.122 Angle : 0.537 10.620 18638 Z= 0.279 Chirality : 0.044 0.157 1916 Planarity : 0.003 0.057 2510 Dihedral : 4.126 51.711 1790 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.90 % Allowed : 18.60 % Favored : 78.49 % 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 aren not related in a simple way. whole: 0.34 (0.21), residues: 1650 helix: 1.59 (0.23), residues: 506 sheet: 0.53 (0.29), residues: 356 loop : -0.82 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 81 TYR 0.023 0.001 TYR C 138 PHE 0.023 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 covalent geometry : bond 0.00277 (13794) covalent geometry : angle 0.53531 (18630) SS BOND : bond 0.00184 ( 4) SS BOND : angle 2.25275 ( 8) hydrogen bonds : bond 0.03210 ( 606) hydrogen bonds : angle 4.01315 ( 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 304 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.517 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: A 118 ILE cc_start: 0.9226 (mm) cc_final: 0.8873 (mm) REVERT: A 218 ASN cc_start: 0.6890 (t0) cc_final: 0.6355 (p0) REVERT: A 224 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7799 (tptt) REVERT: A 225 ASN cc_start: 0.8193 (t0) cc_final: 0.7946 (t0) REVERT: A 306 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: A 335 PHE cc_start: 0.9099 (t80) cc_final: 0.8882 (t80) REVERT: A 336 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8174 (mm-30) REVERT: A 349 ASN cc_start: 0.8382 (t0) cc_final: 0.8105 (t0) REVERT: B 77 SER cc_start: 0.9080 (m) cc_final: 0.8745 (t) REVERT: B 223 ASP cc_start: 0.8161 (t0) cc_final: 0.7794 (t0) REVERT: B 224 LYS cc_start: 0.8280 (mtmt) cc_final: 0.7459 (tptt) REVERT: B 347 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7845 (tm-30) REVERT: B 350 ARG cc_start: 0.7391 (ttp80) cc_final: 0.7180 (ttp80) REVERT: B 352 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8024 (tt) REVERT: C 86 ASN cc_start: 0.9035 (m-40) cc_final: 0.8487 (m-40) REVERT: C 94 SER cc_start: 0.8924 (t) cc_final: 0.8577 (p) REVERT: C 132 ASN cc_start: 0.9077 (t0) cc_final: 0.8616 (t0) REVERT: D 53 MET cc_start: 0.9131 (mmm) cc_final: 0.8829 (mmp) REVERT: D 79 MET cc_start: 0.8144 (tmm) cc_final: 0.7492 (ppp) REVERT: D 80 HIS cc_start: 0.8040 (m90) cc_final: 0.7353 (m90) REVERT: D 119 ASN cc_start: 0.8038 (m-40) cc_final: 0.7563 (m110) REVERT: D 126 ARG cc_start: 0.8668 (ptp-110) cc_final: 0.8172 (ptp-110) REVERT: D 132 ASN cc_start: 0.8435 (t0) cc_final: 0.7839 (t0) REVERT: E 171 ASN cc_start: 0.9025 (m110) cc_final: 0.8534 (t0) REVERT: F 258 ASP cc_start: 0.8201 (m-30) cc_final: 0.7957 (m-30) REVERT: G 47 HIS cc_start: 0.9239 (m-70) cc_final: 0.8727 (m-70) REVERT: G 67 MET cc_start: 0.8248 (mpp) cc_final: 0.7850 (pmm) REVERT: G 73 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8151 (pp30) REVERT: G 74 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8558 (mm) REVERT: G 75 HIS cc_start: 0.9113 (OUTLIER) cc_final: 0.8685 (t-90) REVERT: G 92 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6760 (mt-10) REVERT: G 127 ASP cc_start: 0.8500 (m-30) cc_final: 0.8213 (m-30) REVERT: G 128 ASP cc_start: 0.8477 (m-30) cc_final: 0.7938 (m-30) REVERT: G 140 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7865 (mt-10) REVERT: H 78 LYS cc_start: 0.9178 (tptt) cc_final: 0.8781 (tppt) REVERT: H 112 MET cc_start: 0.7892 (tpp) cc_final: 0.7657 (tpp) REVERT: H 115 ASP cc_start: 0.8396 (p0) cc_final: 0.8082 (p0) REVERT: H 116 GLU cc_start: 0.8583 (mp0) cc_final: 0.8205 (mp0) REVERT: H 119 ASN cc_start: 0.8682 (t0) cc_final: 0.8336 (m110) REVERT: H 132 ASN cc_start: 0.8963 (t0) cc_final: 0.8443 (t0) REVERT: H 135 TYR cc_start: 0.7746 (m-80) cc_final: 0.6910 (m-80) REVERT: H 143 LYS cc_start: 0.9245 (tppt) cc_final: 0.8811 (tppt) outliers start: 42 outliers final: 23 residues processed: 295 average time/residue: 0.1061 time to fit residues: 46.4419 Evaluate side-chains 274 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 191 GLN 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 B residue 352 LEU 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 42 ASP Chi-restraints excluded: chain G residue 59 VAL 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 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: 8.9990 chunk 9 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN E 43 HIS F 191 GLN F 235 ASN F 359 GLN G 49 GLN G 61 ASN ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN H 55 HIS H 101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.155509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100240 restraints weight = 19789.453| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.07 r_work: 0.2936 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13798 Z= 0.263 Angle : 0.623 9.141 18638 Z= 0.331 Chirality : 0.048 0.163 1916 Planarity : 0.004 0.063 2510 Dihedral : 4.550 53.102 1790 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.60 % Allowed : 18.88 % Favored : 77.52 % 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 aren not related in a simple way. whole: 0.10 (0.21), residues: 1650 helix: 1.49 (0.23), residues: 506 sheet: 0.25 (0.29), residues: 356 loop : -0.96 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 192 TYR 0.018 0.002 TYR D 76 PHE 0.031 0.002 PHE B 296 TRP 0.012 0.002 TRP A 67 HIS 0.010 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00615 (13794) covalent geometry : angle 0.62048 (18630) SS BOND : bond 0.00264 ( 4) SS BOND : angle 2.89104 ( 8) hydrogen bonds : bond 0.03897 ( 606) hydrogen bonds : angle 4.39389 ( 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 300 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 0.648 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: 0.8414 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: A 218 ASN cc_start: 0.7048 (t0) cc_final: 0.6430 (p0) REVERT: A 224 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7972 (tttp) REVERT: A 258 ASP cc_start: 0.8653 (m-30) cc_final: 0.8195 (m-30) REVERT: A 295 HIS cc_start: 0.9351 (t70) cc_final: 0.9089 (t70) REVERT: A 323 PHE cc_start: 0.6720 (t80) cc_final: 0.6487 (t80) REVERT: A 349 ASN cc_start: 0.8404 (t0) cc_final: 0.8094 (t0) REVERT: B 77 SER cc_start: 0.9208 (m) cc_final: 0.8945 (t) REVERT: B 223 ASP cc_start: 0.8262 (t0) cc_final: 0.7892 (t0) REVERT: B 224 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7374 (tptt) REVERT: B 347 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 350 ARG cc_start: 0.7364 (ttp80) cc_final: 0.6852 (mtm110) REVERT: C 132 ASN cc_start: 0.9173 (t0) cc_final: 0.8667 (t0) REVERT: D 53 MET cc_start: 0.9156 (mmm) cc_final: 0.8805 (mmp) REVERT: D 61 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.8059 (p0) REVERT: D 67 MET cc_start: 0.7448 (tmm) cc_final: 0.6907 (pmm) REVERT: D 79 MET cc_start: 0.8146 (tmm) cc_final: 0.7707 (ppp) REVERT: D 80 HIS cc_start: 0.8229 (m90) cc_final: 0.7899 (m-70) REVERT: D 119 ASN cc_start: 0.8157 (m-40) cc_final: 0.7659 (m110) REVERT: D 126 ARG cc_start: 0.8705 (ptp-110) cc_final: 0.8162 (ptp-110) REVERT: D 132 ASN cc_start: 0.8619 (t0) cc_final: 0.8130 (t0) REVERT: D 143 LYS cc_start: 0.8661 (pttt) cc_final: 0.8435 (pttt) REVERT: E 171 ASN cc_start: 0.9076 (m110) cc_final: 0.8434 (t0) REVERT: E 344 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7849 (mm-30) REVERT: F 289 TYR cc_start: 0.8898 (m-80) cc_final: 0.8633 (m-10) REVERT: G 47 HIS cc_start: 0.9329 (m-70) cc_final: 0.8500 (m-70) REVERT: G 49 GLN cc_start: 0.8866 (tp40) cc_final: 0.8200 (tp-100) REVERT: G 67 MET cc_start: 0.8286 (mpp) cc_final: 0.7566 (ttm) REVERT: G 75 HIS cc_start: 0.9168 (OUTLIER) cc_final: 0.8811 (t-90) REVERT: G 140 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7769 (mt-10) REVERT: H 55 HIS cc_start: 0.9100 (OUTLIER) cc_final: 0.8807 (m-70) REVERT: H 62 LYS cc_start: 0.9124 (tttt) cc_final: 0.8809 (mmtm) REVERT: H 78 LYS cc_start: 0.9117 (tptt) cc_final: 0.8721 (tppt) REVERT: H 112 MET cc_start: 0.7924 (tpp) cc_final: 0.7622 (tpp) REVERT: H 115 ASP cc_start: 0.8255 (p0) cc_final: 0.8055 (p0) REVERT: H 119 ASN cc_start: 0.8646 (t0) cc_final: 0.8359 (m110) REVERT: H 132 ASN cc_start: 0.8928 (t0) cc_final: 0.8454 (t0) outliers start: 52 outliers final: 29 residues processed: 292 average time/residue: 0.1104 time to fit residues: 47.6402 Evaluate side-chains 274 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 352 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 190 CYS 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 72 LEU Chi-restraints excluded: chain C residue 80 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 79 GLN 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 118 ILE 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 H residue 55 HIS 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: 9.9990 chunk 110 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 126 optimal weight: 0.7980 chunk 152 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 162 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 297 GLN C 49 GLN C 86 ASN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS E 131 GLN E 308 GLN G 73 GLN G 80 HIS G 86 ASN H 55 HIS ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.159130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098255 restraints weight = 19777.179| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.94 r_work: 0.2976 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13798 Z= 0.114 Angle : 0.578 12.999 18638 Z= 0.298 Chirality : 0.044 0.191 1916 Planarity : 0.003 0.049 2510 Dihedral : 4.252 51.282 1790 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.28 % Allowed : 20.40 % 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 aren not related in a simple way. whole: 0.19 (0.21), residues: 1650 helix: 1.52 (0.24), residues: 500 sheet: 0.44 (0.29), residues: 356 loop : -0.94 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 340 TYR 0.020 0.001 TYR A 362 PHE 0.024 0.001 PHE B 296 TRP 0.013 0.001 TRP B 126 HIS 0.013 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00256 (13794) covalent geometry : angle 0.57656 (18630) SS BOND : bond 0.00164 ( 4) SS BOND : angle 2.20497 ( 8) hydrogen bonds : bond 0.03283 ( 606) hydrogen bonds : angle 4.05449 ( 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: 33 poor density : 251 time to evaluate : 0.556 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: A 209 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: A 218 ASN cc_start: 0.6766 (t0) cc_final: 0.6195 (p0) REVERT: A 226 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: A 258 ASP cc_start: 0.8467 (m-30) cc_final: 0.8095 (m-30) REVERT: A 336 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8207 (mm-30) REVERT: A 349 ASN cc_start: 0.8416 (t0) cc_final: 0.8130 (t0) REVERT: B 77 SER cc_start: 0.9121 (m) cc_final: 0.8805 (t) REVERT: B 223 ASP cc_start: 0.8241 (t0) cc_final: 0.7801 (t0) REVERT: B 224 LYS cc_start: 0.8287 (mtmt) cc_final: 0.7256 (tptt) REVERT: B 347 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7767 (tm-30) REVERT: B 350 ARG cc_start: 0.7368 (ttp80) cc_final: 0.6880 (mtm110) REVERT: C 94 SER cc_start: 0.8890 (t) cc_final: 0.8347 (p) REVERT: C 132 ASN cc_start: 0.9029 (t0) cc_final: 0.8420 (t0) REVERT: D 53 MET cc_start: 0.9151 (mmm) cc_final: 0.8871 (mmp) REVERT: D 79 MET cc_start: 0.7961 (tmm) cc_final: 0.7299 (ppp) REVERT: D 80 HIS cc_start: 0.8006 (m90) cc_final: 0.7526 (m170) REVERT: D 119 ASN cc_start: 0.8192 (m-40) cc_final: 0.7682 (m110) REVERT: D 126 ARG cc_start: 0.8695 (ptp-110) cc_final: 0.8155 (ptp-110) REVERT: D 132 ASN cc_start: 0.8614 (t0) cc_final: 0.8104 (t0) REVERT: E 171 ASN cc_start: 0.9068 (m110) cc_final: 0.8424 (t0) REVERT: E 344 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7957 (mm-30) REVERT: F 258 ASP cc_start: 0.8302 (m-30) cc_final: 0.8049 (m-30) REVERT: F 289 TYR cc_start: 0.8925 (m-80) cc_final: 0.8639 (m-10) REVERT: G 47 HIS cc_start: 0.9080 (m-70) cc_final: 0.8572 (m-70) REVERT: G 49 GLN cc_start: 0.8992 (tp40) cc_final: 0.8387 (tp-100) REVERT: H 53 MET cc_start: 0.9200 (mmm) cc_final: 0.8958 (mmm) REVERT: H 78 LYS cc_start: 0.9079 (tptt) cc_final: 0.8587 (tppt) REVERT: H 86 ASN cc_start: 0.8956 (m-40) cc_final: 0.8700 (m-40) REVERT: H 112 MET cc_start: 0.7786 (tpp) cc_final: 0.7519 (tpp) REVERT: H 116 GLU cc_start: 0.8375 (mp0) cc_final: 0.7971 (mp0) REVERT: H 132 ASN cc_start: 0.8974 (t0) cc_final: 0.8469 (t0) outliers start: 33 outliers final: 22 residues processed: 276 average time/residue: 0.1164 time to fit residues: 47.4723 Evaluate side-chains 258 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 226 ASP 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 C residue 60 ILE Chi-restraints excluded: chain C residue 80 HIS 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 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 98 THR 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: 7.9990 chunk 100 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 139 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS E 131 GLN E 308 GLN ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN F 175 HIS G 73 GLN ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** 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 = 0.3983 r_free = 0.3983 target = 0.156404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097194 restraints weight = 19809.963| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.07 r_work: 0.2908 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13798 Z= 0.225 Angle : 0.648 14.290 18638 Z= 0.335 Chirality : 0.048 0.322 1916 Planarity : 0.004 0.051 2510 Dihedral : 4.494 52.144 1790 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.04 % Allowed : 19.71 % Favored : 77.25 % 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 aren not related in a simple way. whole: 0.11 (0.21), residues: 1650 helix: 1.65 (0.24), residues: 468 sheet: 0.21 (0.29), residues: 356 loop : -0.92 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 111 TYR 0.017 0.002 TYR G 138 PHE 0.027 0.002 PHE B 293 TRP 0.009 0.002 TRP E 67 HIS 0.014 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00528 (13794) covalent geometry : angle 0.64548 (18630) SS BOND : bond 0.00341 ( 4) SS BOND : angle 2.58931 ( 8) hydrogen bonds : bond 0.03735 ( 606) hydrogen bonds : angle 4.33159 ( 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 283 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 0.578 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 79 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: A 209 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: A 218 ASN cc_start: 0.6908 (t0) cc_final: 0.6305 (p0) REVERT: A 226 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7748 (m-30) REVERT: A 258 ASP cc_start: 0.8615 (m-30) cc_final: 0.8142 (m-30) REVERT: A 349 ASN cc_start: 0.8365 (t0) cc_final: 0.8052 (t0) REVERT: B 223 ASP cc_start: 0.8288 (t0) cc_final: 0.7900 (t0) REVERT: B 224 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7258 (tptt) REVERT: B 347 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7869 (tm-30) REVERT: C 94 SER cc_start: 0.8902 (t) cc_final: 0.8316 (p) REVERT: C 132 ASN cc_start: 0.9170 (t0) cc_final: 0.8665 (t0) REVERT: C 140 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7379 (mt-10) REVERT: D 67 MET cc_start: 0.7364 (tmm) cc_final: 0.7009 (pmm) REVERT: D 79 MET cc_start: 0.8078 (tmm) cc_final: 0.7412 (ppp) REVERT: D 80 HIS cc_start: 0.8129 (m90) cc_final: 0.7524 (m-70) REVERT: D 119 ASN cc_start: 0.8193 (m-40) cc_final: 0.7712 (m110) REVERT: D 126 ARG cc_start: 0.8706 (ptp-110) cc_final: 0.8243 (ptp-110) REVERT: D 132 ASN cc_start: 0.8668 (t0) cc_final: 0.8182 (t0) REVERT: E 171 ASN cc_start: 0.9050 (m110) cc_final: 0.8384 (t0) REVERT: E 344 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7967 (mm-30) REVERT: E 354 MET cc_start: 0.8146 (tpp) cc_final: 0.7835 (tmm) REVERT: F 289 TYR cc_start: 0.8945 (m-80) cc_final: 0.8703 (m-10) REVERT: G 47 HIS cc_start: 0.9105 (m-70) cc_final: 0.8520 (m-70) REVERT: G 49 GLN cc_start: 0.8811 (tp40) cc_final: 0.8467 (tp-100) REVERT: G 73 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8060 (pp30) REVERT: G 132 ASN cc_start: 0.8348 (t0) cc_final: 0.7906 (t0) REVERT: H 53 MET cc_start: 0.9188 (mmm) cc_final: 0.8979 (mmm) REVERT: H 67 MET cc_start: 0.6616 (mmp) cc_final: 0.5167 (ttm) REVERT: H 78 LYS cc_start: 0.9063 (tptt) cc_final: 0.8490 (tppt) REVERT: H 86 ASN cc_start: 0.8965 (m-40) cc_final: 0.8697 (m-40) REVERT: H 101 HIS cc_start: 0.7925 (t70) cc_final: 0.7366 (t70) REVERT: H 112 MET cc_start: 0.7807 (tpp) cc_final: 0.7553 (tpp) REVERT: H 119 ASN cc_start: 0.8802 (t0) cc_final: 0.8326 (m110) REVERT: H 132 ASN cc_start: 0.8943 (t0) cc_final: 0.8472 (t0) outliers start: 44 outliers final: 34 residues processed: 270 average time/residue: 0.1158 time to fit residues: 46.0357 Evaluate side-chains 270 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN 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 226 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 218 ASN 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 79 MET Chi-restraints excluded: chain C residue 80 HIS 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 79 GLN 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 311 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS F 342 HIS G 73 GLN ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.157544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096885 restraints weight = 19386.368| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.85 r_work: 0.2976 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13798 Z= 0.163 Angle : 0.635 16.410 18638 Z= 0.323 Chirality : 0.046 0.250 1916 Planarity : 0.004 0.051 2510 Dihedral : 4.410 51.073 1790 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.77 % Allowed : 20.54 % Favored : 76.69 % 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 aren not related in a simple way. whole: 0.13 (0.21), residues: 1650 helix: 1.62 (0.24), residues: 468 sheet: 0.27 (0.28), residues: 358 loop : -0.90 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 340 TYR 0.017 0.002 TYR B 176 PHE 0.027 0.002 PHE B 293 TRP 0.010 0.001 TRP F 126 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00379 (13794) covalent geometry : angle 0.63323 (18630) SS BOND : bond 0.00215 ( 4) SS BOND : angle 2.42016 ( 8) hydrogen bonds : bond 0.03592 ( 606) hydrogen bonds : angle 4.19857 ( 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 287 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 0.609 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 78 ASP cc_start: 0.8455 (t0) cc_final: 0.8220 (t0) REVERT: A 79 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: A 209 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: A 218 ASN cc_start: 0.6955 (t0) cc_final: 0.6371 (p0) REVERT: A 226 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: A 258 ASP cc_start: 0.8523 (m-30) cc_final: 0.8035 (m-30) REVERT: A 349 ASN cc_start: 0.8375 (t0) cc_final: 0.8073 (t0) REVERT: B 77 SER cc_start: 0.9157 (m) cc_final: 0.8903 (t) REVERT: B 223 ASP cc_start: 0.8255 (t0) cc_final: 0.7908 (t0) REVERT: B 224 LYS cc_start: 0.8299 (mtmt) cc_final: 0.7329 (tptt) REVERT: B 347 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7836 (tm-30) REVERT: B 350 ARG cc_start: 0.7418 (ttp80) cc_final: 0.7196 (ttp80) REVERT: C 94 SER cc_start: 0.8956 (t) cc_final: 0.8372 (p) REVERT: C 132 ASN cc_start: 0.9123 (t0) cc_final: 0.8594 (t0) REVERT: D 53 MET cc_start: 0.9121 (mmm) cc_final: 0.8919 (mmp) REVERT: D 67 MET cc_start: 0.7223 (tmm) cc_final: 0.6977 (pmm) REVERT: D 79 MET cc_start: 0.8028 (tmm) cc_final: 0.7342 (ppp) REVERT: D 80 HIS cc_start: 0.8091 (m90) cc_final: 0.7521 (m-70) REVERT: D 119 ASN cc_start: 0.8176 (m-40) cc_final: 0.7673 (m110) REVERT: D 126 ARG cc_start: 0.8689 (ptp-110) cc_final: 0.8230 (ptp-110) REVERT: D 132 ASN cc_start: 0.8618 (t0) cc_final: 0.8158 (t0) REVERT: E 171 ASN cc_start: 0.9012 (m110) cc_final: 0.8378 (t0) REVERT: E 354 MET cc_start: 0.8206 (tpp) cc_final: 0.7841 (tmm) REVERT: F 61 ASP cc_start: 0.8591 (t0) cc_final: 0.8370 (t0) REVERT: F 258 ASP cc_start: 0.8245 (m-30) cc_final: 0.8003 (m-30) REVERT: F 289 TYR cc_start: 0.8909 (m-80) cc_final: 0.8701 (m-10) REVERT: G 47 HIS cc_start: 0.9047 (m-70) cc_final: 0.8370 (m-70) REVERT: G 49 GLN cc_start: 0.8697 (tp40) cc_final: 0.8360 (tp-100) REVERT: G 73 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8381 (pp30) REVERT: G 132 ASN cc_start: 0.8329 (t0) cc_final: 0.7892 (t0) REVERT: G 140 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7643 (mt-10) REVERT: H 53 MET cc_start: 0.9139 (mmm) cc_final: 0.8858 (mmm) REVERT: H 62 LYS cc_start: 0.9201 (tttt) cc_final: 0.8861 (mmtm) REVERT: H 78 LYS cc_start: 0.9037 (tptt) cc_final: 0.8474 (tppt) REVERT: H 86 ASN cc_start: 0.8969 (m-40) cc_final: 0.8685 (m-40) REVERT: H 101 HIS cc_start: 0.7929 (t70) cc_final: 0.7379 (t70) REVERT: H 116 GLU cc_start: 0.8439 (mp0) cc_final: 0.8149 (mp0) REVERT: H 132 ASN cc_start: 0.8883 (t0) cc_final: 0.8445 (t0) outliers start: 40 outliers final: 33 residues processed: 276 average time/residue: 0.1103 time to fit residues: 45.2565 Evaluate side-chains 276 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN 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 226 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 80 HIS 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 63 THR 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 311 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 80 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 52 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS F 342 HIS G 73 GLN G 80 HIS G 99 HIS H 70 GLN H 80 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103957 restraints weight = 19658.972| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.69 r_work: 0.2941 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13798 Z= 0.146 Angle : 0.648 16.657 18638 Z= 0.329 Chirality : 0.046 0.255 1916 Planarity : 0.003 0.050 2510 Dihedral : 4.393 49.708 1790 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.56 % Allowed : 21.37 % Favored : 76.07 % 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 aren not related in a simple way. whole: 0.17 (0.21), residues: 1650 helix: 1.66 (0.24), residues: 466 sheet: 0.24 (0.29), residues: 358 loop : -0.85 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 340 TYR 0.023 0.001 TYR A 362 PHE 0.026 0.001 PHE B 293 TRP 0.010 0.001 TRP F 126 HIS 0.005 0.001 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00336 (13794) covalent geometry : angle 0.64684 (18630) SS BOND : bond 0.00260 ( 4) SS BOND : angle 2.24426 ( 8) hydrogen bonds : bond 0.03449 ( 606) hydrogen bonds : angle 4.12817 ( 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 278 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.580 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: A 78 ASP cc_start: 0.8537 (t0) cc_final: 0.8289 (t0) REVERT: A 79 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8290 (pt0) REVERT: A 209 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: A 218 ASN cc_start: 0.6927 (t0) cc_final: 0.6314 (p0) REVERT: A 226 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7737 (m-30) REVERT: A 258 ASP cc_start: 0.8555 (m-30) cc_final: 0.8109 (m-30) REVERT: A 349 ASN cc_start: 0.8380 (t0) cc_final: 0.8094 (t0) REVERT: B 223 ASP cc_start: 0.8339 (t0) cc_final: 0.7929 (t0) REVERT: B 224 LYS cc_start: 0.8325 (mtmt) cc_final: 0.7252 (tptt) REVERT: B 347 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 350 ARG cc_start: 0.7412 (ttp80) cc_final: 0.7191 (ttp80) REVERT: C 94 SER cc_start: 0.8974 (t) cc_final: 0.8426 (p) REVERT: C 132 ASN cc_start: 0.9059 (t0) cc_final: 0.8504 (t0) REVERT: D 53 MET cc_start: 0.9194 (mmm) cc_final: 0.8987 (mmp) REVERT: D 79 MET cc_start: 0.8032 (tmm) cc_final: 0.7325 (tmm) REVERT: D 80 HIS cc_start: 0.8057 (m90) cc_final: 0.7508 (m-70) REVERT: D 119 ASN cc_start: 0.8174 (m-40) cc_final: 0.7638 (m110) REVERT: D 126 ARG cc_start: 0.8711 (ptp-110) cc_final: 0.8236 (ptp-110) REVERT: D 132 ASN cc_start: 0.8655 (t0) cc_final: 0.8171 (t0) REVERT: E 79 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: E 171 ASN cc_start: 0.9083 (m110) cc_final: 0.8391 (t0) REVERT: E 354 MET cc_start: 0.8202 (tpp) cc_final: 0.7823 (tmm) REVERT: F 61 ASP cc_start: 0.8711 (t0) cc_final: 0.8465 (t0) REVERT: F 258 ASP cc_start: 0.8368 (m-30) cc_final: 0.8124 (m-30) REVERT: F 289 TYR cc_start: 0.8977 (m-80) cc_final: 0.8722 (m-10) REVERT: G 47 HIS cc_start: 0.9030 (m-70) cc_final: 0.8355 (m-70) REVERT: G 49 GLN cc_start: 0.8744 (tp40) cc_final: 0.8106 (tp-100) REVERT: G 73 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8415 (pp30) REVERT: G 86 ASN cc_start: 0.8397 (m-40) cc_final: 0.8171 (t0) REVERT: G 132 ASN cc_start: 0.8366 (t0) cc_final: 0.7910 (t0) REVERT: G 140 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7953 (mt-10) REVERT: H 53 MET cc_start: 0.9184 (mmm) cc_final: 0.8942 (mmm) REVERT: H 78 LYS cc_start: 0.9017 (tptt) cc_final: 0.8453 (tppt) REVERT: H 79 MET cc_start: 0.9345 (ppp) cc_final: 0.9143 (ppp) REVERT: H 86 ASN cc_start: 0.8964 (m-40) cc_final: 0.8709 (m-40) REVERT: H 101 HIS cc_start: 0.8070 (t70) cc_final: 0.7585 (t70) REVERT: H 132 ASN cc_start: 0.8930 (t0) cc_final: 0.8471 (t0) outliers start: 37 outliers final: 31 residues processed: 267 average time/residue: 0.1102 time to fit residues: 43.3574 Evaluate side-chains 268 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN 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 226 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 218 ASN 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 79 MET Chi-restraints excluded: chain C residue 80 HIS 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 63 THR Chi-restraints excluded: chain E residue 79 GLN 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 311 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 127 optimal weight: 0.0770 chunk 25 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS F 191 GLN G 73 GLN ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.156444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102021 restraints weight = 19767.233| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.61 r_work: 0.2928 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13798 Z= 0.217 Angle : 0.683 16.242 18638 Z= 0.351 Chirality : 0.048 0.255 1916 Planarity : 0.004 0.053 2510 Dihedral : 4.525 49.900 1790 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.77 % Allowed : 21.44 % Favored : 75.80 % 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 aren not related in a simple way. whole: 0.01 (0.21), residues: 1650 helix: 1.48 (0.24), residues: 480 sheet: 0.14 (0.29), residues: 358 loop : -0.95 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 111 TYR 0.019 0.002 TYR G 138 PHE 0.026 0.002 PHE B 293 TRP 0.009 0.001 TRP F 126 HIS 0.018 0.001 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00510 (13794) covalent geometry : angle 0.68170 (18630) SS BOND : bond 0.00241 ( 4) SS BOND : angle 2.45704 ( 8) hydrogen bonds : bond 0.03751 ( 606) hydrogen bonds : angle 4.31410 ( 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 277 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.535 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: A 79 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8282 (pt0) REVERT: A 209 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: A 218 ASN cc_start: 0.6913 (t0) cc_final: 0.6308 (p0) REVERT: A 258 ASP cc_start: 0.8609 (m-30) cc_final: 0.8056 (m-30) REVERT: A 349 ASN cc_start: 0.8374 (t0) cc_final: 0.8077 (t0) REVERT: B 223 ASP cc_start: 0.8345 (t0) cc_final: 0.7960 (t0) REVERT: B 224 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7303 (tptt) REVERT: B 347 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 350 ARG cc_start: 0.7359 (ttp80) cc_final: 0.7023 (ptt-90) REVERT: C 94 SER cc_start: 0.8971 (t) cc_final: 0.8397 (p) REVERT: C 130 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8750 (mtmt) REVERT: C 132 ASN cc_start: 0.9176 (t0) cc_final: 0.8662 (t0) REVERT: D 53 MET cc_start: 0.9186 (mmm) cc_final: 0.8973 (mmp) REVERT: D 75 HIS cc_start: 0.9523 (OUTLIER) cc_final: 0.9244 (t-90) REVERT: D 79 MET cc_start: 0.8001 (tmm) cc_final: 0.7276 (tmm) REVERT: D 80 HIS cc_start: 0.8058 (m90) cc_final: 0.7507 (m-70) REVERT: D 119 ASN cc_start: 0.8145 (m-40) cc_final: 0.7600 (m110) REVERT: D 126 ARG cc_start: 0.8738 (ptp-110) cc_final: 0.8266 (ptp-110) REVERT: D 132 ASN cc_start: 0.8667 (t0) cc_final: 0.8234 (t0) REVERT: E 171 ASN cc_start: 0.9058 (m110) cc_final: 0.8369 (t0) REVERT: E 344 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7884 (mm-30) REVERT: E 354 MET cc_start: 0.8207 (tpp) cc_final: 0.7836 (tmm) REVERT: F 61 ASP cc_start: 0.8678 (t0) cc_final: 0.8434 (t0) REVERT: F 289 TYR cc_start: 0.8970 (m-80) cc_final: 0.8739 (m-10) REVERT: G 47 HIS cc_start: 0.8981 (m-70) cc_final: 0.8289 (m-70) REVERT: G 49 GLN cc_start: 0.8621 (tp40) cc_final: 0.8217 (tp-100) REVERT: G 86 ASN cc_start: 0.8500 (m-40) cc_final: 0.8265 (t0) REVERT: G 132 ASN cc_start: 0.8397 (t0) cc_final: 0.7998 (t0) REVERT: G 140 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7972 (mt-10) REVERT: H 53 MET cc_start: 0.9162 (mmm) cc_final: 0.8933 (mmm) REVERT: H 78 LYS cc_start: 0.9073 (tptt) cc_final: 0.8535 (tppt) REVERT: H 79 MET cc_start: 0.9376 (ppp) cc_final: 0.9168 (ppp) REVERT: H 86 ASN cc_start: 0.9014 (m-40) cc_final: 0.8707 (m-40) REVERT: H 101 HIS cc_start: 0.7990 (t70) cc_final: 0.7414 (t-90) REVERT: H 132 ASN cc_start: 0.8898 (t0) cc_final: 0.8479 (t0) outliers start: 40 outliers final: 31 residues processed: 266 average time/residue: 0.1122 time to fit residues: 44.1271 Evaluate side-chains 265 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN 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 298 GLN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 190 CYS 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 79 MET Chi-restraints excluded: chain C residue 80 HIS 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 63 THR Chi-restraints excluded: chain E residue 79 GLN 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 311 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 20 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 chunk 164 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 43 HIS E 131 GLN E 308 GLN ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.157864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098582 restraints weight = 20456.878| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.83 r_work: 0.3023 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13798 Z= 0.123 Angle : 0.649 16.612 18638 Z= 0.329 Chirality : 0.045 0.256 1916 Planarity : 0.003 0.049 2510 Dihedral : 4.295 48.067 1790 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.14 % Allowed : 21.99 % Favored : 75.86 % 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 aren not related in a simple way. whole: 0.13 (0.21), residues: 1650 helix: 1.56 (0.24), residues: 478 sheet: 0.28 (0.28), residues: 358 loop : -0.90 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 340 TYR 0.015 0.001 TYR B 48 PHE 0.021 0.001 PHE B 293 TRP 0.016 0.001 TRP F 126 HIS 0.010 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00275 (13794) covalent geometry : angle 0.64768 (18630) SS BOND : bond 0.00207 ( 4) SS BOND : angle 2.14316 ( 8) hydrogen bonds : bond 0.03356 ( 606) hydrogen bonds : angle 4.06422 ( 1866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3387.87 seconds wall clock time: 58 minutes 40.97 seconds (3520.97 seconds total)