Starting phenix.real_space_refine on Thu Jul 31 08:23:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp8_36471/07_2025/8jp8_36471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp8_36471/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jp8_36471/07_2025/8jp8_36471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp8_36471/07_2025/8jp8_36471.map" model { file = "/net/cci-nas-00/data/ceres_data/8jp8_36471/07_2025/8jp8_36471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp8_36471/07_2025/8jp8_36471.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.82, per 1000 atoms: 0.65 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: 3.17 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.56 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: 4.12 Time building geometry restraints manager: 3.80 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: 0.05 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.490 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.600 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP A 126 HIS 0.007 0.001 HIS H 55 PHE 0.013 0.001 PHE E 52 TYR 0.012 0.001 TYR D 76 ARG 0.005 0.000 ARG E 360 Details of bonding type rmsd hydrogen bonds : bond 0.11199 ( 606) hydrogen bonds : angle 5.04473 ( 1866) SS BOND : bond 0.00144 ( 4) SS BOND : angle 1.86326 ( 8) covalent geometry : bond 0.00220 (13794) covalent geometry : angle 0.51602 (18630) *********************** 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 : 1.570 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 118 ILE cc_start: 0.9165 (mm) cc_final: 0.8945 (mm) REVERT: A 218 ASN cc_start: 0.6771 (t0) cc_final: 0.6429 (p0) REVERT: A 226 ASP cc_start: 0.7509 (t70) cc_final: 0.7238 (t0) REVERT: A 297 GLN cc_start: 0.9236 (mt0) cc_final: 0.8875 (mt0) REVERT: A 349 ASN cc_start: 0.8430 (t0) cc_final: 0.8094 (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: 0.8254 (pt0) REVERT: C 70 GLN cc_start: 0.8977 (pp30) cc_final: 0.8066 (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: 0.7898 (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: 0.7143 (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: 0.8460 (t80) REVERT: F 223 ASP cc_start: 0.7926 (t0) cc_final: 0.7655 (t0) REVERT: G 49 GLN cc_start: 0.8565 (tp-100) cc_final: 0.8347 (tp-100) REVERT: H 78 LYS cc_start: 0.9294 (tptt) cc_final: 0.9046 (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: 0.7136 (m-80) outliers start: 1 outliers final: 1 residues processed: 398 average time/residue: 0.2743 time to fit residues: 153.4574 Evaluate side-chains 255 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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 140 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 40.0000 chunk 96 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 257 HIS A 351 GLN B 241 GLN B 311 HIS B 333 GLN B 342 HIS B 359 GLN C 70 GLN C 75 HIS C 80 HIS C 86 ASN D 55 HIS D 80 HIS D 101 HIS E 43 HIS E 59 GLN E 79 GLN E 257 HIS E 342 HIS E 351 GLN F 191 GLN F 235 ASN F 241 GLN F 333 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.162972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106447 restraints weight = 19938.513| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.68 r_work: 0.3183 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13798 Z= 0.177 Angle : 0.575 11.538 18638 Z= 0.305 Chirality : 0.046 0.204 1916 Planarity : 0.004 0.066 2510 Dihedral : 4.282 57.844 1790 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.42 % Allowed : 17.08 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1650 helix: 1.68 (0.23), residues: 506 sheet: 0.50 (0.29), residues: 360 loop : -0.99 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 126 HIS 0.012 0.001 HIS C 80 PHE 0.023 0.002 PHE E 323 TYR 0.024 0.002 TYR D 76 ARG 0.007 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 606) hydrogen bonds : angle 4.23218 ( 1866) SS BOND : bond 0.00209 ( 4) SS BOND : angle 1.79611 ( 8) covalent geometry : bond 0.00412 (13794) covalent geometry : angle 0.57409 (18630) *********************** 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 301 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 1.429 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: A 118 ILE cc_start: 0.9266 (mm) cc_final: 0.9010 (mm) REVERT: A 218 ASN cc_start: 0.6933 (t0) cc_final: 0.6505 (p0) REVERT: A 226 ASP cc_start: 0.7927 (t70) cc_final: 0.7642 (t0) REVERT: A 349 ASN cc_start: 0.8544 (t0) cc_final: 0.8209 (t0) REVERT: B 77 SER cc_start: 0.8987 (m) cc_final: 0.8775 (t) REVERT: B 224 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7720 (tptt) REVERT: C 70 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8164 (pp30) REVERT: C 73 GLN cc_start: 0.8548 (pt0) cc_final: 0.8256 (pp30) REVERT: C 94 SER cc_start: 0.8999 (t) cc_final: 0.8478 (p) REVERT: C 132 ASN cc_start: 0.8900 (t0) cc_final: 0.8407 (t0) REVERT: C 138 TYR cc_start: 0.8659 (t80) cc_final: 0.8171 (t80) REVERT: D 49 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8580 (tp-100) REVERT: D 77 PHE cc_start: 0.8360 (t80) cc_final: 0.8072 (t80) REVERT: D 113 SER cc_start: 0.8782 (t) cc_final: 0.8518 (t) REVERT: D 119 ASN cc_start: 0.8236 (m-40) cc_final: 0.7932 (m110) REVERT: D 132 ASN cc_start: 0.8219 (t0) cc_final: 0.7700 (t0) REVERT: E 171 ASN cc_start: 0.8771 (m110) cc_final: 0.8502 (t0) REVERT: E 258 ASP cc_start: 0.7973 (m-30) cc_final: 0.7763 (m-30) REVERT: F 289 TYR cc_start: 0.8811 (m-80) cc_final: 0.8518 (m-10) REVERT: F 340 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7485 (ttm-80) REVERT: G 47 HIS cc_start: 0.9144 (m-70) cc_final: 0.8571 (m-70) REVERT: G 75 HIS cc_start: 0.9036 (OUTLIER) cc_final: 0.8626 (t-90) REVERT: G 86 ASN cc_start: 0.8285 (m-40) cc_final: 0.8040 (m-40) REVERT: G 92 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6857 (mt-10) REVERT: H 75 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.8382 (t70) REVERT: H 78 LYS cc_start: 0.9242 (tptt) cc_final: 0.8931 (tppt) REVERT: H 112 MET cc_start: 0.7935 (tpp) cc_final: 0.7641 (tpp) REVERT: H 132 ASN cc_start: 0.8688 (t0) cc_final: 0.8267 (t0) REVERT: H 135 TYR cc_start: 0.7641 (m-80) cc_final: 0.6891 (m-80) outliers start: 35 outliers final: 21 residues processed: 290 average time/residue: 0.2507 time to fit residues: 104.3542 Evaluate side-chains 261 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 206 THR 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 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 E residue 352 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 75 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 117 optimal weight: 4.9990 chunk 75 optimal weight: 40.0000 chunk 39 optimal weight: 0.0470 chunk 122 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS B 191 GLN B 297 GLN B 311 HIS C 75 HIS C 80 HIS C 86 ASN D 55 HIS F 359 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3975 r_free = 0.3975 target = 0.154113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099930 restraints weight = 20050.037| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.23 r_work: 0.2916 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3350 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= 0.251 Angle : 0.616 12.836 18638 Z= 0.325 Chirality : 0.048 0.205 1916 Planarity : 0.004 0.085 2510 Dihedral : 4.502 53.418 1790 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.87 % Allowed : 17.08 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1650 helix: 1.62 (0.23), residues: 498 sheet: 0.27 (0.29), residues: 356 loop : -1.02 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 126 HIS 0.013 0.001 HIS D 55 PHE 0.023 0.002 PHE F 52 TYR 0.019 0.002 TYR D 76 ARG 0.004 0.000 ARG F 340 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 606) hydrogen bonds : angle 4.34295 ( 1866) SS BOND : bond 0.00224 ( 4) SS BOND : angle 2.62558 ( 8) covalent geometry : bond 0.00586 (13794) covalent geometry : angle 0.61382 (18630) *********************** 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 310 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 254 time to evaluate : 1.649 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: A 218 ASN cc_start: 0.7170 (t0) cc_final: 0.6489 (p0) REVERT: A 224 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7876 (tptt) REVERT: A 323 PHE cc_start: 0.6662 (t80) cc_final: 0.6439 (t80) REVERT: A 349 ASN cc_start: 0.8509 (t0) cc_final: 0.8123 (t0) REVERT: B 77 SER cc_start: 0.9183 (m) cc_final: 0.8940 (t) REVERT: B 223 ASP cc_start: 0.8289 (t0) cc_final: 0.8069 (t0) REVERT: B 224 LYS cc_start: 0.8349 (mtmt) cc_final: 0.7532 (tptt) REVERT: B 347 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 350 ARG cc_start: 0.7196 (ptp-170) cc_final: 0.6865 (mtm110) REVERT: C 94 SER cc_start: 0.9022 (t) cc_final: 0.8500 (p) REVERT: C 132 ASN cc_start: 0.9140 (t0) cc_final: 0.8644 (t0) REVERT: D 43 LYS cc_start: 0.9266 (mmtm) cc_final: 0.9060 (mmtm) REVERT: D 49 GLN cc_start: 0.9344 (tp-100) cc_final: 0.9091 (tp-100) REVERT: D 55 HIS cc_start: 0.9147 (OUTLIER) cc_final: 0.8725 (m-70) REVERT: D 113 SER cc_start: 0.9022 (t) cc_final: 0.8790 (t) REVERT: D 126 ARG cc_start: 0.8674 (ptp-110) cc_final: 0.8070 (ptp-110) REVERT: D 132 ASN cc_start: 0.8552 (t0) cc_final: 0.8035 (t0) REVERT: E 171 ASN cc_start: 0.9043 (m110) cc_final: 0.8516 (t0) REVERT: E 258 ASP cc_start: 0.8306 (m-30) cc_final: 0.7842 (m-30) REVERT: E 344 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7844 (mm-30) REVERT: F 340 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7767 (ttp-110) REVERT: G 47 HIS cc_start: 0.9259 (m-70) cc_final: 0.8702 (m-70) REVERT: G 54 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8824 (tt0) REVERT: G 75 HIS cc_start: 0.9110 (OUTLIER) cc_final: 0.8732 (t-90) REVERT: G 112 MET cc_start: 0.8079 (ttm) cc_final: 0.7879 (ttt) REVERT: G 130 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8629 (mtpt) REVERT: G 132 ASN cc_start: 0.8216 (t0) cc_final: 0.7873 (t0) REVERT: G 140 GLU cc_start: 0.8124 (mt-10) cc_final: 0.6773 (mt-10) REVERT: H 53 MET cc_start: 0.9401 (mmm) cc_final: 0.9175 (mmp) REVERT: H 54 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8511 (pp20) REVERT: H 55 HIS cc_start: 0.8883 (OUTLIER) cc_final: 0.8584 (m-70) REVERT: H 78 LYS cc_start: 0.9214 (tptt) cc_final: 0.8873 (tppt) REVERT: H 112 MET cc_start: 0.7933 (tpp) cc_final: 0.7729 (tpp) REVERT: H 116 GLU cc_start: 0.8504 (mp0) cc_final: 0.8194 (mp0) REVERT: H 132 ASN cc_start: 0.8866 (t0) cc_final: 0.8409 (t0) REVERT: H 135 TYR cc_start: 0.7745 (m-80) cc_final: 0.6863 (m-80) REVERT: H 143 LYS cc_start: 0.9245 (tppt) cc_final: 0.8819 (tppt) outliers start: 56 outliers final: 33 residues processed: 294 average time/residue: 0.2827 time to fit residues: 120.8359 Evaluate side-chains 275 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 2.170 ------------------------------------------------------------------------------- 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 B residue 50 TYR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 190 CYS 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 C residue 68 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 136 optimal weight: 0.9990 chunk 55 optimal weight: 50.0000 chunk 143 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 311 HIS C 73 GLN C 75 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN E 43 HIS G 49 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.159344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106866 restraints weight = 19303.095| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.50 r_work: 0.2978 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3514 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= 0.116 Angle : 0.563 13.302 18638 Z= 0.294 Chirality : 0.045 0.216 1916 Planarity : 0.003 0.061 2510 Dihedral : 4.230 45.782 1790 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.25 % Allowed : 19.36 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1650 helix: 1.70 (0.24), residues: 488 sheet: 0.41 (0.29), residues: 356 loop : -0.98 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 126 HIS 0.013 0.001 HIS H 55 PHE 0.023 0.001 PHE B 293 TYR 0.031 0.001 TYR C 138 ARG 0.006 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 606) hydrogen bonds : angle 4.06672 ( 1866) SS BOND : bond 0.00267 ( 4) SS BOND : angle 2.42350 ( 8) covalent geometry : bond 0.00258 (13794) covalent geometry : angle 0.56074 (18630) *********************** 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 296 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 249 time to evaluate : 1.417 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: A 209 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7831 (mp10) REVERT: A 218 ASN cc_start: 0.6857 (t0) cc_final: 0.6285 (p0) REVERT: A 224 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7994 (tttp) REVERT: A 258 ASP cc_start: 0.8472 (m-30) cc_final: 0.8055 (m-30) REVERT: A 336 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8249 (mm-30) REVERT: A 349 ASN cc_start: 0.8494 (t0) cc_final: 0.8181 (t0) REVERT: B 77 SER cc_start: 0.9141 (m) cc_final: 0.8857 (t) REVERT: B 223 ASP cc_start: 0.8167 (t0) cc_final: 0.7805 (t0) REVERT: B 224 LYS cc_start: 0.8327 (mtmt) cc_final: 0.7405 (tptt) REVERT: B 347 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7857 (tm-30) REVERT: C 73 GLN cc_start: 0.8682 (pt0) cc_final: 0.8367 (pp30) REVERT: C 94 SER cc_start: 0.8948 (t) cc_final: 0.8485 (p) REVERT: C 132 ASN cc_start: 0.9109 (t0) cc_final: 0.8566 (t0) REVERT: D 49 GLN cc_start: 0.9355 (tp-100) cc_final: 0.9153 (tp-100) REVERT: D 112 MET cc_start: 0.7926 (tmm) cc_final: 0.7522 (tmm) REVERT: D 113 SER cc_start: 0.8783 (t) cc_final: 0.8578 (t) REVERT: D 119 ASN cc_start: 0.8075 (m-40) cc_final: 0.7617 (m110) REVERT: D 126 ARG cc_start: 0.8687 (ptp-110) cc_final: 0.8145 (ptp-110) REVERT: D 132 ASN cc_start: 0.8546 (t0) cc_final: 0.8041 (t0) REVERT: E 171 ASN cc_start: 0.9089 (m110) cc_final: 0.8495 (t0) REVERT: E 258 ASP cc_start: 0.8251 (m-30) cc_final: 0.7922 (m-30) REVERT: G 47 HIS cc_start: 0.9244 (m-70) cc_final: 0.8706 (m-70) REVERT: G 49 GLN cc_start: 0.8688 (tp40) cc_final: 0.8163 (tp-100) REVERT: G 53 MET cc_start: 0.9121 (ptt) cc_final: 0.8332 (ptt) REVERT: G 54 GLU cc_start: 0.9121 (tp30) cc_final: 0.8857 (tt0) REVERT: G 73 GLN cc_start: 0.8420 (pt0) cc_final: 0.7840 (pp30) REVERT: G 74 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8699 (mm) REVERT: G 75 HIS cc_start: 0.9154 (OUTLIER) cc_final: 0.8681 (t-90) REVERT: G 132 ASN cc_start: 0.8278 (t0) cc_final: 0.7850 (t0) REVERT: G 140 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7461 (mt-10) REVERT: H 53 MET cc_start: 0.9397 (mmm) cc_final: 0.9193 (mmm) REVERT: H 54 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8654 (pp20) REVERT: H 55 HIS cc_start: 0.9101 (OUTLIER) cc_final: 0.8700 (m170) REVERT: H 78 LYS cc_start: 0.9143 (tptt) cc_final: 0.8771 (tppt) REVERT: H 112 MET cc_start: 0.7910 (tpp) cc_final: 0.7707 (tpp) REVERT: H 132 ASN cc_start: 0.8896 (t0) cc_final: 0.8391 (t0) REVERT: H 143 LYS cc_start: 0.9236 (tppt) cc_final: 0.8783 (tppt) outliers start: 47 outliers final: 27 residues processed: 283 average time/residue: 0.3040 time to fit residues: 123.8138 Evaluate side-chains 266 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 82 VAL 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 80 HIS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 63 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 42 ASP Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 50 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN A 311 HIS A 342 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 311 HIS C 49 GLN C 75 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS F 235 ASN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.156599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102466 restraints weight = 19367.869| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.07 r_work: 0.2950 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13798 Z= 0.181 Angle : 0.598 12.759 18638 Z= 0.312 Chirality : 0.046 0.226 1916 Planarity : 0.004 0.061 2510 Dihedral : 4.327 44.722 1790 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.67 % Allowed : 19.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1650 helix: 1.55 (0.24), residues: 486 sheet: 0.29 (0.29), residues: 356 loop : -0.99 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 126 HIS 0.011 0.001 HIS G 80 PHE 0.033 0.002 PHE B 296 TYR 0.029 0.002 TYR C 138 ARG 0.002 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 606) hydrogen bonds : angle 4.18505 ( 1866) SS BOND : bond 0.00214 ( 4) SS BOND : angle 2.55776 ( 8) covalent geometry : bond 0.00422 (13794) covalent geometry : angle 0.59531 (18630) *********************** 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 292 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 239 time to evaluate : 1.550 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: A 79 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8667 (pt0) REVERT: A 209 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: A 218 ASN cc_start: 0.7025 (t0) cc_final: 0.6381 (p0) REVERT: A 224 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7985 (tttp) REVERT: A 349 ASN cc_start: 0.8436 (t0) cc_final: 0.8109 (t0) REVERT: B 77 SER cc_start: 0.9191 (m) cc_final: 0.8925 (t) REVERT: B 223 ASP cc_start: 0.8244 (t0) cc_final: 0.7882 (t0) REVERT: B 224 LYS cc_start: 0.8290 (mtmt) cc_final: 0.7343 (tptt) REVERT: B 347 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7855 (tm-30) REVERT: B 350 ARG cc_start: 0.7426 (ttp80) cc_final: 0.7190 (ptt-90) REVERT: C 94 SER cc_start: 0.8942 (t) cc_final: 0.8622 (p) REVERT: C 132 ASN cc_start: 0.9136 (t0) cc_final: 0.8572 (t0) REVERT: D 49 GLN cc_start: 0.9384 (tp-100) cc_final: 0.9019 (tp-100) REVERT: D 67 MET cc_start: 0.7400 (tmm) cc_final: 0.6838 (pmm) REVERT: D 112 MET cc_start: 0.7964 (tmm) cc_final: 0.7497 (tmm) REVERT: D 119 ASN cc_start: 0.8157 (m-40) cc_final: 0.7688 (m110) REVERT: D 126 ARG cc_start: 0.8704 (ptp-110) cc_final: 0.8252 (ptp-110) REVERT: D 132 ASN cc_start: 0.8615 (t0) cc_final: 0.8110 (t0) REVERT: E 171 ASN cc_start: 0.9047 (m110) cc_final: 0.8401 (t0) REVERT: F 289 TYR cc_start: 0.8878 (m-80) cc_final: 0.8590 (m-10) REVERT: G 47 HIS cc_start: 0.9305 (m-70) cc_final: 0.8763 (m-70) REVERT: G 49 GLN cc_start: 0.8620 (tp40) cc_final: 0.8391 (tp-100) REVERT: G 54 GLU cc_start: 0.9129 (tp30) cc_final: 0.8701 (tm-30) REVERT: G 73 GLN cc_start: 0.8459 (pt0) cc_final: 0.7867 (pp30) REVERT: G 74 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8712 (mm) REVERT: G 75 HIS cc_start: 0.9147 (OUTLIER) cc_final: 0.8773 (t-90) REVERT: G 132 ASN cc_start: 0.8281 (t0) cc_final: 0.7840 (t0) REVERT: G 140 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7684 (mt-10) REVERT: H 53 MET cc_start: 0.9390 (mmm) cc_final: 0.9189 (mmm) REVERT: H 54 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8581 (pp20) REVERT: H 78 LYS cc_start: 0.9109 (tptt) cc_final: 0.8716 (tppt) REVERT: H 112 MET cc_start: 0.7878 (tpp) cc_final: 0.7610 (tpp) REVERT: H 116 GLU cc_start: 0.8217 (mp0) cc_final: 0.7935 (mp0) REVERT: H 132 ASN cc_start: 0.8896 (t0) cc_final: 0.8422 (t0) outliers start: 53 outliers final: 35 residues processed: 279 average time/residue: 0.2913 time to fit residues: 117.3179 Evaluate side-chains 272 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN 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 216 ILE 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 191 GLN 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 B residue 311 HIS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 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 306 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 74 LEU 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 G residue 113 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 58 optimal weight: 30.0000 chunk 25 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 152 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 298 GLN A 351 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.156698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.094821 restraints weight = 19922.053| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.93 r_work: 0.2945 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13798 Z= 0.208 Angle : 0.610 14.284 18638 Z= 0.319 Chirality : 0.047 0.246 1916 Planarity : 0.004 0.058 2510 Dihedral : 4.429 44.653 1790 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.97 % Allowed : 19.43 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1650 helix: 1.76 (0.24), residues: 462 sheet: 0.27 (0.29), residues: 346 loop : -1.00 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 126 HIS 0.011 0.001 HIS G 80 PHE 0.023 0.002 PHE B 296 TYR 0.020 0.002 TYR D 76 ARG 0.002 0.000 ARG F 340 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 606) hydrogen bonds : angle 4.25076 ( 1866) SS BOND : bond 0.00229 ( 4) SS BOND : angle 2.59134 ( 8) covalent geometry : bond 0.00488 (13794) covalent geometry : angle 0.60731 (18630) *********************** 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 281 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 1.446 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: A 79 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: A 209 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: A 218 ASN cc_start: 0.6918 (t0) cc_final: 0.6352 (p0) REVERT: A 224 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7970 (tttp) REVERT: A 258 ASP cc_start: 0.8554 (m-30) cc_final: 0.8094 (m-30) REVERT: A 349 ASN cc_start: 0.8443 (t0) cc_final: 0.8090 (t0) REVERT: B 223 ASP cc_start: 0.8259 (t0) cc_final: 0.7865 (t0) REVERT: B 224 LYS cc_start: 0.8302 (mtmt) cc_final: 0.7279 (tptt) REVERT: B 347 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7780 (tm-30) REVERT: C 56 LEU cc_start: 0.9315 (tp) cc_final: 0.9030 (mt) REVERT: C 89 ASP cc_start: 0.7895 (p0) cc_final: 0.7499 (p0) REVERT: C 132 ASN cc_start: 0.9141 (t0) cc_final: 0.8577 (t0) REVERT: D 49 GLN cc_start: 0.9335 (tp-100) cc_final: 0.8406 (tp-100) REVERT: D 53 MET cc_start: 0.9267 (mmt) cc_final: 0.8678 (mmp) REVERT: D 112 MET cc_start: 0.7822 (tmm) cc_final: 0.7355 (tmm) REVERT: D 119 ASN cc_start: 0.8195 (m-40) cc_final: 0.7643 (m110) REVERT: D 126 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8251 (ptp-110) REVERT: D 132 ASN cc_start: 0.8717 (t0) cc_final: 0.8249 (t0) REVERT: E 171 ASN cc_start: 0.9007 (m110) cc_final: 0.8369 (t0) REVERT: E 344 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7834 (mm-30) REVERT: F 289 TYR cc_start: 0.8925 (m-80) cc_final: 0.8638 (m-10) REVERT: G 47 HIS cc_start: 0.9305 (m-70) cc_final: 0.8485 (m-70) REVERT: G 54 GLU cc_start: 0.9102 (tp30) cc_final: 0.8668 (tm-30) REVERT: G 73 GLN cc_start: 0.8507 (pt0) cc_final: 0.7878 (pp30) REVERT: G 74 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8723 (mm) REVERT: G 75 HIS cc_start: 0.9144 (OUTLIER) cc_final: 0.8736 (t-90) REVERT: G 132 ASN cc_start: 0.8251 (t0) cc_final: 0.7887 (t0) REVERT: G 140 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7673 (mt-10) REVERT: H 78 LYS cc_start: 0.9124 (tptt) cc_final: 0.8722 (tppt) REVERT: H 112 MET cc_start: 0.7942 (tpp) cc_final: 0.7573 (tpp) REVERT: H 116 GLU cc_start: 0.8307 (mp0) cc_final: 0.7980 (mp0) REVERT: H 132 ASN cc_start: 0.8909 (t0) cc_final: 0.8467 (t0) outliers start: 43 outliers final: 29 residues processed: 272 average time/residue: 0.2514 time to fit residues: 99.4457 Evaluate side-chains 257 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 1.583 ------------------------------------------------------------------------------- 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 213 THR Chi-restraints excluded: chain A residue 216 ILE 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 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 126 ARG 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 306 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 74 LEU Chi-restraints excluded: chain G residue 75 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 34 optimal weight: 0.0870 chunk 21 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- 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** C 75 HIS E 43 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN H 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.159279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101805 restraints weight = 19642.539| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.31 r_work: 0.2985 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4052 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= 0.113 Angle : 0.599 14.982 18638 Z= 0.310 Chirality : 0.045 0.272 1916 Planarity : 0.003 0.051 2510 Dihedral : 4.244 42.617 1790 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.77 % Allowed : 20.06 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1650 helix: 1.69 (0.24), residues: 464 sheet: 0.41 (0.29), residues: 346 loop : -0.92 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 126 HIS 0.010 0.001 HIS H 80 PHE 0.023 0.001 PHE B 293 TYR 0.018 0.001 TYR B 289 ARG 0.004 0.000 ARG F 340 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 606) hydrogen bonds : angle 3.99488 ( 1866) SS BOND : bond 0.00162 ( 4) SS BOND : angle 2.25284 ( 8) covalent geometry : bond 0.00247 (13794) covalent geometry : angle 0.59737 (18630) *********************** 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 294 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 1.522 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: A 79 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8328 (pt0) REVERT: A 209 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: A 218 ASN cc_start: 0.6867 (t0) cc_final: 0.6274 (p0) REVERT: A 224 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7930 (tttp) REVERT: A 258 ASP cc_start: 0.8445 (m-30) cc_final: 0.8089 (m-30) REVERT: A 297 GLN cc_start: 0.9178 (mt0) cc_final: 0.8851 (mt0) REVERT: A 349 ASN cc_start: 0.8391 (t0) cc_final: 0.8068 (t0) REVERT: B 223 ASP cc_start: 0.8250 (t0) cc_final: 0.7882 (t0) REVERT: B 224 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7248 (tptt) REVERT: B 347 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 350 ARG cc_start: 0.7436 (ttp80) cc_final: 0.6829 (ptt-90) REVERT: C 56 LEU cc_start: 0.9345 (tp) cc_final: 0.9096 (mt) REVERT: C 78 LYS cc_start: 0.8919 (tptp) cc_final: 0.8618 (tppt) REVERT: C 132 ASN cc_start: 0.9011 (t0) cc_final: 0.8413 (t0) REVERT: C 140 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7040 (mt-10) REVERT: D 49 GLN cc_start: 0.9371 (tp-100) cc_final: 0.8304 (tp-100) REVERT: D 52 ILE cc_start: 0.9536 (pt) cc_final: 0.9169 (pt) REVERT: D 53 MET cc_start: 0.9288 (mmt) cc_final: 0.8760 (mmp) REVERT: D 67 MET cc_start: 0.7221 (tmm) cc_final: 0.6983 (pmm) REVERT: D 80 HIS cc_start: 0.8374 (m90) cc_final: 0.7633 (m90) REVERT: D 112 MET cc_start: 0.7680 (tmm) cc_final: 0.7313 (tmm) REVERT: D 126 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8252 (ptp-110) REVERT: D 132 ASN cc_start: 0.8655 (t0) cc_final: 0.8175 (t0) REVERT: E 171 ASN cc_start: 0.9045 (m110) cc_final: 0.8388 (t0) REVERT: E 258 ASP cc_start: 0.8134 (m-30) cc_final: 0.7843 (m-30) REVERT: F 61 ASP cc_start: 0.8660 (t0) cc_final: 0.8421 (t0) REVERT: F 234 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7778 (pp20) REVERT: F 235 ASN cc_start: 0.8713 (m110) cc_final: 0.8129 (m110) REVERT: F 289 TYR cc_start: 0.8954 (m-80) cc_final: 0.8691 (m-10) REVERT: G 47 HIS cc_start: 0.8995 (m-70) cc_final: 0.8435 (m-70) REVERT: G 54 GLU cc_start: 0.9126 (tp30) cc_final: 0.8687 (tm-30) REVERT: G 73 GLN cc_start: 0.8510 (pt0) cc_final: 0.7917 (pp30) REVERT: G 75 HIS cc_start: 0.9120 (OUTLIER) cc_final: 0.8810 (t70) REVERT: G 127 ASP cc_start: 0.8480 (m-30) cc_final: 0.8138 (m-30) REVERT: G 128 ASP cc_start: 0.8595 (m-30) cc_final: 0.8200 (m-30) REVERT: G 132 ASN cc_start: 0.8266 (t0) cc_final: 0.7819 (t0) REVERT: G 138 TYR cc_start: 0.8378 (t80) cc_final: 0.7850 (t80) REVERT: G 140 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7358 (mt-10) REVERT: H 54 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8363 (pp20) REVERT: H 55 HIS cc_start: 0.8962 (OUTLIER) cc_final: 0.8463 (m170) REVERT: H 70 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7674 (pp30) REVERT: H 78 LYS cc_start: 0.9052 (tptt) cc_final: 0.8480 (tppt) REVERT: H 86 ASN cc_start: 0.9020 (m-40) cc_final: 0.8719 (m-40) REVERT: H 112 MET cc_start: 0.7957 (tpp) cc_final: 0.7658 (tpp) REVERT: H 116 GLU cc_start: 0.8435 (mp0) cc_final: 0.8117 (mp0) REVERT: H 132 ASN cc_start: 0.8871 (t0) cc_final: 0.8372 (t0) outliers start: 40 outliers final: 28 residues processed: 283 average time/residue: 0.2638 time to fit residues: 107.4649 Evaluate side-chains 275 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 230 CYS Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 74 LEU 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 126 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 190 CYS 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 306 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 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 Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 72 LEU 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 33 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 73 optimal weight: 40.0000 chunk 91 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 50.0000 chunk 115 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** A 311 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN C 86 ASN ** D 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.154317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.092254 restraints weight = 19894.672| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.16 r_work: 0.2847 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 13798 Z= 0.360 Angle : 0.739 13.450 18638 Z= 0.392 Chirality : 0.052 0.276 1916 Planarity : 0.005 0.070 2510 Dihedral : 4.816 44.240 1790 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.11 % Allowed : 20.54 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1650 helix: 1.20 (0.24), residues: 490 sheet: 0.11 (0.29), residues: 344 loop : -1.21 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 67 HIS 0.008 0.001 HIS F 342 PHE 0.032 0.003 PHE E 52 TYR 0.027 0.002 TYR B 289 ARG 0.004 0.001 ARG E 340 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 606) hydrogen bonds : angle 4.63404 ( 1866) SS BOND : bond 0.00364 ( 4) SS BOND : angle 3.10267 ( 8) covalent geometry : bond 0.00849 (13794) covalent geometry : angle 0.73591 (18630) *********************** 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 278 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: A 218 ASN cc_start: 0.7203 (t0) cc_final: 0.6437 (p0) REVERT: A 224 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7951 (tttp) REVERT: A 258 ASP cc_start: 0.8651 (m-30) cc_final: 0.8302 (m-30) REVERT: A 297 GLN cc_start: 0.9249 (mt0) cc_final: 0.8977 (mt0) REVERT: A 330 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7845 (pt0) REVERT: A 349 ASN cc_start: 0.8372 (t0) cc_final: 0.8042 (t0) REVERT: B 223 ASP cc_start: 0.8367 (t0) cc_final: 0.7969 (t0) REVERT: B 224 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7178 (tptt) REVERT: B 347 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7870 (tm-30) REVERT: B 350 ARG cc_start: 0.7457 (ttp80) cc_final: 0.7147 (ptt-90) REVERT: C 78 LYS cc_start: 0.8994 (tptp) cc_final: 0.8745 (tppt) REVERT: C 132 ASN cc_start: 0.9267 (t0) cc_final: 0.8705 (t0) REVERT: D 49 GLN cc_start: 0.9402 (tp-100) cc_final: 0.8196 (tp-100) REVERT: D 53 MET cc_start: 0.9420 (mmt) cc_final: 0.8788 (mmt) REVERT: D 67 MET cc_start: 0.7473 (tmm) cc_final: 0.6891 (mpp) REVERT: D 77 PHE cc_start: 0.8096 (t80) cc_final: 0.7793 (t80) REVERT: D 112 MET cc_start: 0.7660 (tmm) cc_final: 0.7278 (tmm) REVERT: D 116 GLU cc_start: 0.8499 (pm20) cc_final: 0.8276 (pm20) REVERT: D 119 ASN cc_start: 0.8184 (m-40) cc_final: 0.7655 (m110) REVERT: D 126 ARG cc_start: 0.8763 (ptp-110) cc_final: 0.8269 (ptp-110) REVERT: D 132 ASN cc_start: 0.8790 (t0) cc_final: 0.8374 (t0) REVERT: E 43 HIS cc_start: 0.7113 (t-90) cc_final: 0.6807 (t-90) REVERT: E 171 ASN cc_start: 0.9089 (m110) cc_final: 0.8419 (t0) REVERT: E 344 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8019 (mm-30) REVERT: E 354 MET cc_start: 0.8084 (tpp) cc_final: 0.7838 (tmm) REVERT: G 50 GLU cc_start: 0.9268 (tp30) cc_final: 0.8969 (tm-30) REVERT: G 75 HIS cc_start: 0.9215 (OUTLIER) cc_final: 0.8947 (t70) REVERT: G 112 MET cc_start: 0.7890 (tmm) cc_final: 0.7620 (tmm) REVERT: G 114 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8311 (mm-30) REVERT: G 132 ASN cc_start: 0.8322 (t0) cc_final: 0.7685 (t0) REVERT: G 138 TYR cc_start: 0.8605 (t80) cc_final: 0.8312 (t80) REVERT: G 140 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7709 (mt-10) REVERT: H 70 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7749 (pp30) REVERT: H 78 LYS cc_start: 0.9068 (tptt) cc_final: 0.8582 (tppt) REVERT: H 112 MET cc_start: 0.7933 (tpp) cc_final: 0.7631 (tpp) REVERT: H 116 GLU cc_start: 0.8312 (mp0) cc_final: 0.8040 (mp0) REVERT: H 132 ASN cc_start: 0.8933 (t0) cc_final: 0.8538 (t0) outliers start: 45 outliers final: 34 residues processed: 266 average time/residue: 0.2602 time to fit residues: 99.9417 Evaluate side-chains 265 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL 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 C residue 74 LEU 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 E residue 63 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 190 CYS 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 E residue 352 LEU 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 75 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 70 GLN 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 130 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 D 51 HIS F 191 GLN ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.156252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101797 restraints weight = 19251.321| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.58 r_work: 0.2918 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13798 Z= 0.155 Angle : 0.655 16.645 18638 Z= 0.342 Chirality : 0.048 0.341 1916 Planarity : 0.004 0.051 2510 Dihedral : 4.494 41.611 1790 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.35 % Allowed : 21.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1650 helix: 1.49 (0.24), residues: 466 sheet: 0.14 (0.29), residues: 356 loop : -0.98 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 126 HIS 0.010 0.001 HIS H 80 PHE 0.024 0.002 PHE B 293 TYR 0.030 0.002 TYR B 289 ARG 0.004 0.000 ARG F 340 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 606) hydrogen bonds : angle 4.24828 ( 1866) SS BOND : bond 0.00481 ( 4) SS BOND : angle 2.34538 ( 8) covalent geometry : bond 0.00357 (13794) covalent geometry : angle 0.65340 (18630) *********************** 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 275 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 1.865 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: A 224 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7865 (tttp) REVERT: A 258 ASP cc_start: 0.8568 (m-30) cc_final: 0.8361 (m-30) REVERT: A 297 GLN cc_start: 0.9197 (mt0) cc_final: 0.8855 (mt0) REVERT: A 349 ASN cc_start: 0.8447 (t0) cc_final: 0.8055 (t0) REVERT: A 353 ASP cc_start: 0.9043 (m-30) cc_final: 0.8779 (m-30) REVERT: B 223 ASP cc_start: 0.8359 (t0) cc_final: 0.7979 (t0) REVERT: B 224 LYS cc_start: 0.8374 (mtmt) cc_final: 0.7331 (tptt) REVERT: B 347 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7946 (tm-30) REVERT: B 350 ARG cc_start: 0.7355 (ttp80) cc_final: 0.7036 (ptt-90) REVERT: C 78 LYS cc_start: 0.9026 (tptp) cc_final: 0.8736 (tppt) REVERT: C 94 SER cc_start: 0.9027 (t) cc_final: 0.8475 (p) REVERT: C 119 ASN cc_start: 0.8932 (m-40) cc_final: 0.8719 (m-40) REVERT: C 132 ASN cc_start: 0.9191 (t0) cc_final: 0.8675 (t0) REVERT: D 49 GLN cc_start: 0.9337 (tp-100) cc_final: 0.8025 (tp-100) REVERT: D 53 MET cc_start: 0.9375 (mmt) cc_final: 0.8753 (mmt) REVERT: D 80 HIS cc_start: 0.8482 (m90) cc_final: 0.7709 (m90) REVERT: D 112 MET cc_start: 0.7669 (tmm) cc_final: 0.7319 (tmm) REVERT: D 119 ASN cc_start: 0.8215 (m-40) cc_final: 0.7676 (m110) REVERT: D 126 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8252 (ptp-110) REVERT: D 132 ASN cc_start: 0.8690 (t0) cc_final: 0.8283 (t0) REVERT: E 171 ASN cc_start: 0.9053 (m110) cc_final: 0.8383 (t0) REVERT: E 344 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7914 (mm-30) REVERT: E 354 MET cc_start: 0.8212 (tpp) cc_final: 0.7913 (tmm) REVERT: F 61 ASP cc_start: 0.8695 (t0) cc_final: 0.8459 (t0) REVERT: G 50 GLU cc_start: 0.9178 (tp30) cc_final: 0.8762 (tm-30) REVERT: G 73 GLN cc_start: 0.8450 (pt0) cc_final: 0.8126 (pp30) REVERT: G 75 HIS cc_start: 0.9120 (OUTLIER) cc_final: 0.8806 (t70) REVERT: G 112 MET cc_start: 0.7867 (tmm) cc_final: 0.7651 (tmm) REVERT: G 126 ARG cc_start: 0.8246 (tmm-80) cc_final: 0.8004 (tmm-80) REVERT: G 130 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8369 (ptpt) REVERT: G 132 ASN cc_start: 0.8316 (t0) cc_final: 0.8003 (t0) REVERT: G 140 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7793 (mt-10) REVERT: H 49 GLN cc_start: 0.8974 (tp40) cc_final: 0.8658 (tp40) REVERT: H 70 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7778 (pp30) REVERT: H 78 LYS cc_start: 0.9042 (tptt) cc_final: 0.8564 (tppt) REVERT: H 86 ASN cc_start: 0.9010 (m-40) cc_final: 0.8692 (m-40) REVERT: H 112 MET cc_start: 0.8058 (tpp) cc_final: 0.7652 (tpp) REVERT: H 116 GLU cc_start: 0.8451 (mp0) cc_final: 0.8179 (mp0) REVERT: H 132 ASN cc_start: 0.8845 (t0) cc_final: 0.8435 (t0) outliers start: 34 outliers final: 27 residues processed: 265 average time/residue: 0.3164 time to fit residues: 121.4848 Evaluate side-chains 261 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 190 CYS 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 E residue 343 LEU 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 75 HIS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLN 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 147 optimal weight: 0.0770 chunk 118 optimal weight: 0.4980 chunk 96 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 159 optimal weight: 0.0270 chunk 5 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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** D 49 GLN E 43 HIS F 342 HIS ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 HIS H 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.157864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103330 restraints weight = 19938.331| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.15 r_work: 0.3036 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4486 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= 0.115 Angle : 0.638 15.409 18638 Z= 0.330 Chirality : 0.047 0.351 1916 Planarity : 0.003 0.049 2510 Dihedral : 4.139 25.288 1788 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.59 % Allowed : 23.03 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1650 helix: 1.59 (0.25), residues: 464 sheet: 0.64 (0.29), residues: 324 loop : -0.99 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 126 HIS 0.009 0.001 HIS H 80 PHE 0.023 0.001 PHE B 293 TYR 0.030 0.001 TYR B 289 ARG 0.004 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 606) hydrogen bonds : angle 4.01295 ( 1866) SS BOND : bond 0.00164 ( 4) SS BOND : angle 2.44794 ( 8) covalent geometry : bond 0.00253 (13794) covalent geometry : angle 0.63599 (18630) ********************** 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 268 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 1.476 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: A 79 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8293 (pt0) REVERT: A 218 ASN cc_start: 0.6957 (t0) cc_final: 0.6307 (p0) REVERT: A 258 ASP cc_start: 0.8389 (m-30) cc_final: 0.8139 (m-30) REVERT: A 349 ASN cc_start: 0.8436 (t0) cc_final: 0.8038 (t0) REVERT: A 353 ASP cc_start: 0.8950 (m-30) cc_final: 0.8678 (m-30) REVERT: B 223 ASP cc_start: 0.8273 (t0) cc_final: 0.7956 (t0) REVERT: B 224 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7410 (tptt) REVERT: B 347 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7997 (tm-30) REVERT: B 350 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7091 (ptt-90) REVERT: C 74 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7925 (tp) REVERT: C 78 LYS cc_start: 0.8934 (tptp) cc_final: 0.8726 (tppt) REVERT: C 112 MET cc_start: 0.7892 (ttm) cc_final: 0.7048 (ttm) REVERT: C 132 ASN cc_start: 0.8997 (t0) cc_final: 0.8466 (t0) REVERT: D 53 MET cc_start: 0.9303 (mmt) cc_final: 0.8789 (ptp) REVERT: D 67 MET cc_start: 0.6266 (pmm) cc_final: 0.5869 (tpt) REVERT: D 80 HIS cc_start: 0.8327 (m90) cc_final: 0.7646 (m170) REVERT: D 112 MET cc_start: 0.7670 (tmm) cc_final: 0.7354 (tmm) REVERT: D 116 GLU cc_start: 0.8505 (pm20) cc_final: 0.8270 (pm20) REVERT: D 119 ASN cc_start: 0.8247 (m-40) cc_final: 0.7723 (m110) REVERT: D 126 ARG cc_start: 0.8720 (ptp-110) cc_final: 0.8266 (ptp-110) REVERT: D 132 ASN cc_start: 0.8601 (t0) cc_final: 0.8209 (t0) REVERT: E 171 ASN cc_start: 0.8916 (m110) cc_final: 0.8319 (t0) REVERT: E 354 MET cc_start: 0.8210 (tpp) cc_final: 0.7903 (tmm) REVERT: F 289 TYR cc_start: 0.8920 (m-80) cc_final: 0.8663 (m-10) REVERT: G 73 GLN cc_start: 0.8432 (pt0) cc_final: 0.8143 (pp30) REVERT: G 112 MET cc_start: 0.7885 (tmm) cc_final: 0.7527 (tmm) REVERT: G 126 ARG cc_start: 0.8264 (tmm-80) cc_final: 0.8005 (tmm-80) REVERT: G 132 ASN cc_start: 0.8341 (t0) cc_final: 0.7982 (t0) REVERT: G 140 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7698 (mt-10) REVERT: H 49 GLN cc_start: 0.9013 (tp40) cc_final: 0.8681 (tp40) REVERT: H 78 LYS cc_start: 0.9077 (tptt) cc_final: 0.8525 (tppt) REVERT: H 86 ASN cc_start: 0.8988 (m-40) cc_final: 0.8722 (m-40) REVERT: H 112 MET cc_start: 0.7998 (tpp) cc_final: 0.7725 (tpp) REVERT: H 116 GLU cc_start: 0.8486 (mp0) cc_final: 0.8162 (mp0) REVERT: H 132 ASN cc_start: 0.8750 (t0) cc_final: 0.8331 (t0) outliers start: 23 outliers final: 17 residues processed: 261 average time/residue: 0.3281 time to fit residues: 123.3591 Evaluate side-chains 258 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain E residue 190 CYS 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 118 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 55 HIS 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 54 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 41 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** E 43 HIS F 175 HIS ** H 51 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.158675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.103175 restraints weight = 20339.964| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.41 r_work: 0.3012 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13798 Z= 0.121 Angle : 0.656 15.907 18638 Z= 0.338 Chirality : 0.047 0.347 1916 Planarity : 0.003 0.049 2510 Dihedral : 4.076 24.083 1788 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.31 % Allowed : 23.51 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1650 helix: 1.48 (0.24), residues: 462 sheet: 0.62 (0.29), residues: 334 loop : -0.97 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 126 HIS 0.011 0.001 HIS H 80 PHE 0.021 0.001 PHE B 293 TYR 0.041 0.002 TYR B 289 ARG 0.004 0.000 ARG F 340 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 606) hydrogen bonds : angle 4.00420 ( 1866) SS BOND : bond 0.00177 ( 4) SS BOND : angle 2.37366 ( 8) covalent geometry : bond 0.00272 (13794) covalent geometry : angle 0.65443 (18630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7849.63 seconds wall clock time: 141 minutes 28.82 seconds (8488.82 seconds total)