Starting phenix.real_space_refine on Thu May 15 15:05:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp8_36471/05_2025/8jp8_36471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp8_36471/05_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_36471/05_2025/8jp8_36471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp8_36471/05_2025/8jp8_36471.map" model { file = "/net/cci-nas-00/data/ceres_data/8jp8_36471/05_2025/8jp8_36471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp8_36471/05_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-5687/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: 7.75, per 1000 atoms: 0.57 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: 2.99 Conformation dependent library (CDL) restraints added in 1.6 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: 3.55 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: 0.610 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 30.740 Find NCS groups from input model: 0.700 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.730 ------------------------------------------------------------------------------- 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 : 1.471 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: 0.2681 time to fit residues: 149.5166 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 : 1.624 ------------------------------------------------------------------------------- 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 = 56)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106441 restraints weight = 19938.513| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.68 r_work: 0.3186 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 1.587 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: 0.9265 (mm) cc_final: 0.9011 (mm) REVERT: A 218 ASN cc_start: 0.6930 (t0) cc_final: 0.6502 (p0) REVERT: A 226 ASP cc_start: 0.7926 (t70) cc_final: 0.7641 (t0) REVERT: A 349 ASN cc_start: 0.8543 (t0) cc_final: 0.8210 (t0) REVERT: B 77 SER cc_start: 0.8982 (m) cc_final: 0.8772 (t) REVERT: B 224 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7720 (tptt) REVERT: C 70 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8163 (pp30) REVERT: C 73 GLN cc_start: 0.8548 (pt0) cc_final: 0.8259 (pp30) REVERT: C 94 SER cc_start: 0.9003 (t) cc_final: 0.8484 (p) REVERT: C 132 ASN cc_start: 0.8894 (t0) cc_final: 0.8411 (t0) REVERT: C 138 TYR cc_start: 0.8659 (t80) cc_final: 0.8180 (t80) REVERT: D 49 GLN cc_start: 0.9159 (tp-100) cc_final: 0.8588 (tp-100) REVERT: D 77 PHE cc_start: 0.8359 (t80) cc_final: 0.8069 (t80) REVERT: D 113 SER cc_start: 0.8747 (t) cc_final: 0.8505 (t) REVERT: D 119 ASN cc_start: 0.8226 (m-40) cc_final: 0.7924 (m110) REVERT: D 132 ASN cc_start: 0.8179 (t0) cc_final: 0.7675 (t0) REVERT: E 171 ASN cc_start: 0.8779 (m110) cc_final: 0.8506 (t0) REVERT: E 258 ASP cc_start: 0.7978 (m-30) cc_final: 0.7770 (m-30) REVERT: F 289 TYR cc_start: 0.8819 (m-80) cc_final: 0.8525 (m-10) REVERT: F 340 ARG cc_start: 0.7809 (mtp85) cc_final: 0.7490 (ttm-80) REVERT: G 47 HIS cc_start: 0.9142 (m-70) cc_final: 0.8568 (m-70) REVERT: G 75 HIS cc_start: 0.9027 (OUTLIER) cc_final: 0.8620 (t-90) REVERT: G 86 ASN cc_start: 0.8284 (m-40) cc_final: 0.8041 (m-40) REVERT: G 92 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6869 (mt-10) REVERT: H 78 LYS cc_start: 0.9234 (tptt) cc_final: 0.8927 (tppt) REVERT: H 112 MET cc_start: 0.7928 (tpp) cc_final: 0.7642 (tpp) REVERT: H 132 ASN cc_start: 0.8657 (t0) cc_final: 0.8237 (t0) REVERT: H 135 TYR cc_start: 0.7646 (m-80) cc_final: 0.6900 (m-80) outliers start: 35 outliers final: 21 residues processed: 290 average time/residue: 0.2550 time to fit residues: 106.9227 Evaluate side-chains 260 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 117 optimal weight: 5.9990 chunk 75 optimal weight: 40.0000 chunk 39 optimal weight: 3.9990 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: 20.0000 chunk 134 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS C 75 HIS C 80 HIS C 86 ASN D 55 HIS D 70 GLN D 101 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.152876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098167 restraints weight = 20032.318| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.20 r_work: 0.2891 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 13798 Z= 0.318 Angle : 0.661 12.973 18638 Z= 0.351 Chirality : 0.050 0.209 1916 Planarity : 0.005 0.088 2510 Dihedral : 4.690 53.701 1790 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.15 % Allowed : 17.08 % Favored : 78.77 % 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: -0.00 (0.20), residues: 1650 helix: 1.49 (0.23), residues: 498 sheet: 0.26 (0.29), residues: 350 loop : -1.10 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 67 HIS 0.014 0.001 HIS D 55 PHE 0.028 0.003 PHE E 52 TYR 0.019 0.002 TYR C 138 ARG 0.004 0.001 ARG F 340 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 606) hydrogen bonds : angle 4.52254 ( 1866) SS BOND : bond 0.00303 ( 4) SS BOND : angle 2.80067 ( 8) covalent geometry : bond 0.00745 (13794) covalent geometry : angle 0.65862 (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 302 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: A 258 ASP cc_start: 0.8623 (m-30) cc_final: 0.8326 (m-30) REVERT: A 349 ASN cc_start: 0.8500 (t0) cc_final: 0.8105 (t0) REVERT: B 223 ASP cc_start: 0.8333 (t0) cc_final: 0.8125 (t0) REVERT: B 224 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7576 (tptt) REVERT: B 350 ARG cc_start: 0.7224 (ptp-170) cc_final: 0.6905 (mtm110) REVERT: C 94 SER cc_start: 0.9005 (t) cc_final: 0.8430 (p) REVERT: C 132 ASN cc_start: 0.9216 (t0) cc_final: 0.8705 (t0) REVERT: D 49 GLN cc_start: 0.9346 (tp-100) cc_final: 0.9107 (tp-100) REVERT: D 55 HIS cc_start: 0.9144 (OUTLIER) cc_final: 0.8731 (m-70) REVERT: D 113 SER cc_start: 0.9043 (t) cc_final: 0.8791 (t) REVERT: D 126 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8075 (ptp-110) REVERT: D 132 ASN cc_start: 0.8585 (t0) cc_final: 0.8090 (t0) REVERT: E 171 ASN cc_start: 0.9043 (m110) cc_final: 0.8500 (t0) REVERT: E 258 ASP cc_start: 0.8308 (m-30) cc_final: 0.7847 (m-30) REVERT: E 344 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7905 (mm-30) REVERT: F 340 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7822 (ttp-110) REVERT: G 47 HIS cc_start: 0.9258 (m-70) cc_final: 0.8700 (m-70) REVERT: G 54 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8822 (tt0) REVERT: G 75 HIS cc_start: 0.9131 (OUTLIER) cc_final: 0.8750 (t-90) REVERT: G 114 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8393 (mm-30) REVERT: G 130 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8688 (mtpt) REVERT: G 132 ASN cc_start: 0.8245 (t0) cc_final: 0.7927 (t0) REVERT: G 140 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7591 (mt-10) REVERT: H 53 MET cc_start: 0.9433 (mmm) cc_final: 0.9156 (mmm) REVERT: H 54 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8432 (pp20) REVERT: H 55 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8659 (m-70) REVERT: H 78 LYS cc_start: 0.9218 (tptt) cc_final: 0.8877 (tppt) REVERT: H 101 HIS cc_start: 0.7639 (t-90) cc_final: 0.7177 (t-90) REVERT: H 112 MET cc_start: 0.7932 (tpp) cc_final: 0.7651 (tpp) REVERT: H 116 GLU cc_start: 0.8542 (mp0) cc_final: 0.8103 (mp0) REVERT: H 132 ASN cc_start: 0.8838 (t0) cc_final: 0.8399 (t0) REVERT: H 135 TYR cc_start: 0.7775 (m-80) cc_final: 0.6839 (m-80) REVERT: H 143 LYS cc_start: 0.9248 (tppt) cc_final: 0.8822 (tppt) outliers start: 60 outliers final: 37 residues processed: 288 average time/residue: 0.2441 time to fit residues: 101.6152 Evaluate side-chains 272 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS 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 B residue 290 GLN 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 70 GLN 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 123 LEU 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: 4.9990 chunk 55 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 F 191 GLN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.157629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103854 restraints weight = 19342.501| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.88 r_work: 0.2999 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13798 Z= 0.117 Angle : 0.558 13.251 18638 Z= 0.293 Chirality : 0.045 0.218 1916 Planarity : 0.003 0.062 2510 Dihedral : 4.259 44.334 1790 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.32 % Allowed : 19.36 % 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: 0.13 (0.21), residues: 1650 helix: 1.70 (0.24), residues: 488 sheet: 0.30 (0.29), residues: 356 loop : -1.04 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 126 HIS 0.012 0.001 HIS H 55 PHE 0.023 0.001 PHE B 293 TYR 0.030 0.001 TYR C 138 ARG 0.003 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 606) hydrogen bonds : angle 4.11985 ( 1866) SS BOND : bond 0.00135 ( 4) SS BOND : angle 2.49068 ( 8) covalent geometry : bond 0.00257 (13794) covalent geometry : angle 0.55580 (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 293 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 1.575 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: 0.8376 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: A 218 ASN cc_start: 0.6992 (t0) cc_final: 0.6355 (p0) REVERT: A 224 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7959 (tttp) REVERT: A 258 ASP cc_start: 0.8361 (m-30) cc_final: 0.8027 (m-30) REVERT: A 349 ASN cc_start: 0.8458 (t0) cc_final: 0.8126 (t0) REVERT: B 223 ASP cc_start: 0.8138 (t0) cc_final: 0.7793 (t0) REVERT: B 224 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7411 (tptt) REVERT: B 350 ARG cc_start: 0.7143 (ptp-170) cc_final: 0.6863 (mtm110) REVERT: C 70 GLN cc_start: 0.9212 (pm20) cc_final: 0.8977 (pm20) REVERT: C 73 GLN cc_start: 0.8662 (pt0) cc_final: 0.8310 (pp30) REVERT: C 94 SER cc_start: 0.8935 (t) cc_final: 0.8466 (p) REVERT: C 132 ASN cc_start: 0.9091 (t0) cc_final: 0.8570 (t0) REVERT: D 132 ASN cc_start: 0.8605 (t0) cc_final: 0.8125 (t0) REVERT: E 171 ASN cc_start: 0.9061 (m110) cc_final: 0.8463 (t0) REVERT: E 344 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7829 (mm-30) REVERT: G 47 HIS cc_start: 0.9238 (m-70) cc_final: 0.8702 (m-70) REVERT: G 49 GLN cc_start: 0.8644 (tp40) cc_final: 0.8095 (tp-100) REVERT: G 53 MET cc_start: 0.9080 (ptt) cc_final: 0.8266 (ptt) REVERT: G 54 GLU cc_start: 0.9112 (tp30) cc_final: 0.8849 (tt0) REVERT: G 73 GLN cc_start: 0.8455 (pt0) cc_final: 0.7879 (pp30) REVERT: G 74 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8774 (mm) REVERT: G 75 HIS cc_start: 0.9145 (OUTLIER) cc_final: 0.8668 (t-90) REVERT: G 126 ARG cc_start: 0.8257 (tmm-80) cc_final: 0.8000 (tmm-80) REVERT: G 127 ASP cc_start: 0.8491 (m-30) cc_final: 0.7775 (m-30) REVERT: G 128 ASP cc_start: 0.8617 (m-30) cc_final: 0.8248 (m-30) REVERT: G 130 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8479 (mtpt) REVERT: G 132 ASN cc_start: 0.8277 (t0) cc_final: 0.7873 (t0) REVERT: G 137 ASP cc_start: 0.8800 (m-30) cc_final: 0.8595 (p0) REVERT: G 140 GLU cc_start: 0.8095 (mt-10) cc_final: 0.6899 (mt-10) REVERT: H 53 MET cc_start: 0.9406 (mmm) cc_final: 0.9191 (mmm) REVERT: H 54 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8548 (pp20) REVERT: H 55 HIS cc_start: 0.9078 (OUTLIER) cc_final: 0.8650 (m170) REVERT: H 78 LYS cc_start: 0.9168 (tptt) cc_final: 0.8814 (tppt) REVERT: H 112 MET cc_start: 0.7904 (tpp) cc_final: 0.7601 (tpp) REVERT: H 116 GLU cc_start: 0.8429 (mp0) cc_final: 0.8106 (mp0) REVERT: H 132 ASN cc_start: 0.8882 (t0) cc_final: 0.8405 (t0) outliers start: 48 outliers final: 25 residues processed: 278 average time/residue: 0.2557 time to fit residues: 102.4684 Evaluate side-chains 267 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS 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 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 89 ASP 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: 5.9990 chunk 117 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 A 351 GLN ** 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 86 ASN ** 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 = 0.4004 r_free = 0.4004 target = 0.157926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096442 restraints weight = 19707.211| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.90 r_work: 0.2976 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13798 Z= 0.145 Angle : 0.591 12.801 18638 Z= 0.307 Chirality : 0.045 0.235 1916 Planarity : 0.004 0.057 2510 Dihedral : 4.286 43.516 1790 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.32 % Allowed : 19.78 % Favored : 76.90 % 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 (0.21), residues: 1650 helix: 1.58 (0.24), residues: 486 sheet: 0.30 (0.29), residues: 356 loop : -1.00 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 126 HIS 0.013 0.001 HIS G 80 PHE 0.034 0.002 PHE B 296 TYR 0.018 0.002 TYR D 76 ARG 0.006 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 606) hydrogen bonds : angle 4.11884 ( 1866) SS BOND : bond 0.00188 ( 4) SS BOND : angle 2.39089 ( 8) covalent geometry : bond 0.00337 (13794) covalent geometry : angle 0.58949 (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 290 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 1.642 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: 0.9097 (OUTLIER) cc_final: 0.8612 (pt0) REVERT: A 209 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: A 218 ASN cc_start: 0.6982 (t0) cc_final: 0.6314 (p0) REVERT: A 224 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7949 (tttp) REVERT: A 349 ASN cc_start: 0.8374 (t0) cc_final: 0.8048 (t0) REVERT: B 223 ASP cc_start: 0.8245 (t0) cc_final: 0.7863 (t0) REVERT: B 224 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7312 (tptt) REVERT: B 350 ARG cc_start: 0.7177 (ptp-170) cc_final: 0.6895 (mtm110) REVERT: C 94 SER cc_start: 0.8911 (t) cc_final: 0.8592 (p) REVERT: C 132 ASN cc_start: 0.9110 (t0) cc_final: 0.8608 (t0) REVERT: D 41 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5895 (mp) REVERT: D 52 ILE cc_start: 0.9558 (pt) cc_final: 0.9343 (pt) REVERT: D 67 MET cc_start: 0.7408 (tmm) cc_final: 0.6935 (pmm) REVERT: D 126 ARG cc_start: 0.8969 (mtm110) cc_final: 0.8747 (mtm110) REVERT: D 132 ASN cc_start: 0.8655 (t0) cc_final: 0.8199 (t0) REVERT: E 171 ASN cc_start: 0.9039 (m110) cc_final: 0.8343 (t0) REVERT: E 344 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7889 (mm-30) REVERT: F 289 TYR cc_start: 0.8886 (m-80) cc_final: 0.8623 (m-10) REVERT: G 47 HIS cc_start: 0.9332 (m-70) cc_final: 0.8796 (m-70) REVERT: G 49 GLN cc_start: 0.8643 (tp40) cc_final: 0.8388 (tp-100) REVERT: G 54 GLU cc_start: 0.9169 (tp30) cc_final: 0.8735 (tm-30) REVERT: G 73 GLN cc_start: 0.8459 (pt0) cc_final: 0.7867 (pp30) REVERT: G 75 HIS cc_start: 0.9155 (OUTLIER) cc_final: 0.8766 (t-90) REVERT: G 126 ARG cc_start: 0.8275 (tmm-80) cc_final: 0.7964 (tmm-80) REVERT: G 127 ASP cc_start: 0.8495 (m-30) cc_final: 0.7679 (m-30) REVERT: G 128 ASP cc_start: 0.8561 (m-30) cc_final: 0.8159 (m-30) REVERT: G 130 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8504 (mtpt) REVERT: G 132 ASN cc_start: 0.8276 (t0) cc_final: 0.7825 (t0) REVERT: G 137 ASP cc_start: 0.8845 (m-30) cc_final: 0.8567 (p0) REVERT: G 140 GLU cc_start: 0.8090 (mt-10) cc_final: 0.6868 (mt-10) REVERT: H 53 MET cc_start: 0.9407 (mmm) cc_final: 0.9191 (mmm) REVERT: H 54 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8511 (pp20) REVERT: H 78 LYS cc_start: 0.9107 (tptt) cc_final: 0.8717 (tppt) REVERT: H 112 MET cc_start: 0.7932 (tpp) cc_final: 0.7528 (tpp) REVERT: H 116 GLU cc_start: 0.8380 (mp0) cc_final: 0.7847 (mp0) REVERT: H 132 ASN cc_start: 0.8903 (t0) cc_final: 0.8409 (t0) outliers start: 48 outliers final: 28 residues processed: 279 average time/residue: 0.2474 time to fit residues: 99.6525 Evaluate side-chains 267 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 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 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 41 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 99 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 152 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS F 173 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 GLN G 80 HIS G 86 ASN ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.160036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.106721 restraints weight = 19504.954| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.07 r_work: 0.2984 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13798 Z= 0.129 Angle : 0.589 14.543 18638 Z= 0.304 Chirality : 0.045 0.247 1916 Planarity : 0.003 0.050 2510 Dihedral : 4.215 42.443 1790 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.90 % Allowed : 19.78 % 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: 0.23 (0.20), residues: 1650 helix: 1.83 (0.24), residues: 460 sheet: 0.41 (0.29), residues: 346 loop : -0.93 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 126 HIS 0.007 0.001 HIS B 311 PHE 0.024 0.001 PHE B 296 TYR 0.018 0.001 TYR B 289 ARG 0.005 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 606) hydrogen bonds : angle 4.02164 ( 1866) SS BOND : bond 0.00239 ( 4) SS BOND : angle 2.27934 ( 8) covalent geometry : bond 0.00294 (13794) covalent geometry : angle 0.58765 (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 291 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 249 time to evaluate : 1.637 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: 0.9109 (OUTLIER) cc_final: 0.8629 (pt0) REVERT: A 209 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: A 218 ASN cc_start: 0.6903 (t0) cc_final: 0.6313 (p0) REVERT: A 226 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7616 (m-30) REVERT: A 349 ASN cc_start: 0.8415 (t0) cc_final: 0.8063 (t0) REVERT: B 223 ASP cc_start: 0.8216 (t0) cc_final: 0.7823 (t0) REVERT: B 224 LYS cc_start: 0.8282 (mtmt) cc_final: 0.7261 (tptt) REVERT: B 350 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6969 (mtm110) REVERT: C 56 LEU cc_start: 0.9322 (tp) cc_final: 0.9093 (mt) REVERT: C 89 ASP cc_start: 0.7851 (p0) cc_final: 0.7574 (p0) REVERT: C 94 SER cc_start: 0.8963 (t) cc_final: 0.8663 (p) REVERT: C 132 ASN cc_start: 0.9092 (t0) cc_final: 0.8646 (t0) REVERT: D 41 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5866 (mp) REVERT: D 53 MET cc_start: 0.8983 (mmp) cc_final: 0.8745 (mmm) REVERT: D 80 HIS cc_start: 0.8391 (m90) cc_final: 0.7646 (m90) REVERT: D 126 ARG cc_start: 0.8972 (mtm110) cc_final: 0.8509 (ptp-110) REVERT: D 132 ASN cc_start: 0.8658 (t0) cc_final: 0.8167 (t0) REVERT: E 171 ASN cc_start: 0.9033 (m110) cc_final: 0.8351 (t0) REVERT: E 344 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7880 (mm-30) REVERT: F 90 ARG cc_start: 0.8610 (mtm110) cc_final: 0.8342 (mtm-85) REVERT: F 289 TYR cc_start: 0.8901 (m-80) cc_final: 0.8564 (m-10) REVERT: G 47 HIS cc_start: 0.9315 (m-70) cc_final: 0.8513 (m-70) REVERT: G 54 GLU cc_start: 0.9079 (tp30) cc_final: 0.8609 (tm-30) REVERT: G 70 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8479 (pp30) REVERT: G 71 GLU cc_start: 0.8557 (pt0) cc_final: 0.8330 (pt0) REVERT: G 75 HIS cc_start: 0.9159 (OUTLIER) cc_final: 0.8728 (t-90) REVERT: G 126 ARG cc_start: 0.8344 (tmm-80) cc_final: 0.8066 (tmm-80) REVERT: G 127 ASP cc_start: 0.8508 (m-30) cc_final: 0.7624 (m-30) REVERT: G 128 ASP cc_start: 0.8592 (m-30) cc_final: 0.8082 (m-30) REVERT: G 130 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8538 (mtpt) REVERT: G 132 ASN cc_start: 0.8273 (t0) cc_final: 0.7811 (t0) REVERT: G 137 ASP cc_start: 0.8838 (m-30) cc_final: 0.8532 (p0) REVERT: G 140 GLU cc_start: 0.8067 (mt-10) cc_final: 0.6846 (mt-10) REVERT: H 78 LYS cc_start: 0.9087 (tptt) cc_final: 0.8630 (tppt) REVERT: H 86 ASN cc_start: 0.8948 (m-40) cc_final: 0.8722 (m-40) REVERT: H 112 MET cc_start: 0.7974 (tpp) cc_final: 0.7732 (tpp) REVERT: H 116 GLU cc_start: 0.8460 (mp0) cc_final: 0.8182 (mp0) REVERT: H 132 ASN cc_start: 0.8870 (t0) cc_final: 0.8371 (t0) outliers start: 42 outliers final: 28 residues processed: 281 average time/residue: 0.2545 time to fit residues: 103.6272 Evaluate side-chains 267 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 41 LEU 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 311 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 34 optimal weight: 0.0170 chunk 21 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- 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 ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS E 43 HIS G 49 GLN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.159094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097395 restraints weight = 19788.546| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.95 r_work: 0.2990 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13798 Z= 0.133 Angle : 0.617 14.761 18638 Z= 0.318 Chirality : 0.046 0.295 1916 Planarity : 0.003 0.051 2510 Dihedral : 4.219 41.332 1790 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.32 % Allowed : 19.92 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.21), residues: 1650 helix: 1.42 (0.24), residues: 488 sheet: 0.42 (0.29), residues: 346 loop : -1.01 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 126 HIS 0.013 0.001 HIS G 80 PHE 0.022 0.001 PHE D 77 TYR 0.018 0.001 TYR B 289 ARG 0.004 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 606) hydrogen bonds : angle 4.01916 ( 1866) SS BOND : bond 0.00151 ( 4) SS BOND : angle 2.24211 ( 8) covalent geometry : bond 0.00305 (13794) covalent geometry : angle 0.61502 (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 293 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 1.536 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: A 79 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8752 (pt0) REVERT: A 209 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: A 218 ASN cc_start: 0.6836 (t0) cc_final: 0.6291 (p0) REVERT: A 226 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: A 349 ASN cc_start: 0.8366 (t0) cc_final: 0.7966 (t0) REVERT: A 353 ASP cc_start: 0.8970 (m-30) cc_final: 0.8722 (m-30) REVERT: B 223 ASP cc_start: 0.8231 (t0) cc_final: 0.7883 (t0) REVERT: B 224 LYS cc_start: 0.8290 (mtmt) cc_final: 0.7256 (tptt) REVERT: B 350 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6966 (mtm110) REVERT: C 56 LEU cc_start: 0.9334 (tp) cc_final: 0.9128 (mt) REVERT: C 89 ASP cc_start: 0.7925 (p0) cc_final: 0.7678 (p0) REVERT: C 94 SER cc_start: 0.8947 (t) cc_final: 0.8662 (p) REVERT: C 132 ASN cc_start: 0.9107 (t0) cc_final: 0.8529 (t0) REVERT: D 41 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.5932 (mp) REVERT: D 53 MET cc_start: 0.9071 (mmp) cc_final: 0.8829 (mmp) REVERT: D 67 MET cc_start: 0.7224 (tmm) cc_final: 0.6951 (pmm) REVERT: D 80 HIS cc_start: 0.8346 (m90) cc_final: 0.7690 (m170) REVERT: D 119 ASN cc_start: 0.8242 (m-40) cc_final: 0.7763 (m110) REVERT: D 126 ARG cc_start: 0.8980 (mtm110) cc_final: 0.8516 (ptp-110) REVERT: D 132 ASN cc_start: 0.8676 (t0) cc_final: 0.8197 (t0) REVERT: E 171 ASN cc_start: 0.9067 (m110) cc_final: 0.8355 (t0) REVERT: E 344 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7925 (mm-30) REVERT: F 61 ASP cc_start: 0.8596 (t0) cc_final: 0.8384 (t0) REVERT: F 234 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7792 (pp20) REVERT: F 235 ASN cc_start: 0.8706 (m110) cc_final: 0.8119 (m110) REVERT: F 289 TYR cc_start: 0.8940 (m-80) cc_final: 0.8625 (m-10) REVERT: G 47 HIS cc_start: 0.9049 (m-70) cc_final: 0.8496 (m-70) REVERT: G 73 GLN cc_start: 0.8472 (pt0) cc_final: 0.8102 (pp30) REVERT: G 74 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8691 (mm) REVERT: G 75 HIS cc_start: 0.9146 (OUTLIER) cc_final: 0.8664 (t-90) REVERT: G 130 LYS cc_start: 0.8929 (mtmt) cc_final: 0.8524 (mtpt) REVERT: G 132 ASN cc_start: 0.8267 (t0) cc_final: 0.7807 (t0) REVERT: G 137 ASP cc_start: 0.8799 (m-30) cc_final: 0.8547 (p0) REVERT: G 138 TYR cc_start: 0.8519 (t80) cc_final: 0.7540 (t80) REVERT: G 140 GLU cc_start: 0.8010 (mt-10) cc_final: 0.6701 (mt-10) REVERT: H 55 HIS cc_start: 0.8948 (OUTLIER) cc_final: 0.8596 (m170) REVERT: H 70 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7571 (pp30) REVERT: H 78 LYS cc_start: 0.9059 (tptt) cc_final: 0.8491 (tppt) REVERT: H 86 ASN cc_start: 0.8985 (m-40) cc_final: 0.8693 (m-40) REVERT: H 112 MET cc_start: 0.7995 (tpp) cc_final: 0.7682 (tpp) REVERT: H 116 GLU cc_start: 0.8462 (mp0) cc_final: 0.8051 (mp0) REVERT: H 132 ASN cc_start: 0.8851 (t0) cc_final: 0.8387 (t0) outliers start: 48 outliers final: 35 residues processed: 278 average time/residue: 0.2436 time to fit residues: 98.2984 Evaluate side-chains 282 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 221 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 350 ARG 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 C residue 130 LYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 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 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 49 GLN 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 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: 4.9990 chunk 159 optimal weight: 9.9990 chunk 158 optimal weight: 0.4980 chunk 73 optimal weight: 40.0000 chunk 91 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- 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** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS D 101 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN H 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.156418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.094268 restraints weight = 19773.429| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.93 r_work: 0.2940 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13798 Z= 0.217 Angle : 0.646 13.817 18638 Z= 0.339 Chirality : 0.048 0.263 1916 Planarity : 0.004 0.056 2510 Dihedral : 4.437 41.339 1790 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.04 % Allowed : 20.40 % Favored : 76.56 % 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: -0.08 (0.20), residues: 1650 helix: 1.34 (0.24), residues: 486 sheet: 0.23 (0.29), residues: 346 loop : -1.05 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 67 HIS 0.006 0.001 HIS G 80 PHE 0.024 0.002 PHE B 293 TYR 0.019 0.002 TYR D 76 ARG 0.003 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 606) hydrogen bonds : angle 4.26790 ( 1866) SS BOND : bond 0.00215 ( 4) SS BOND : angle 2.48878 ( 8) covalent geometry : bond 0.00510 (13794) covalent geometry : angle 0.64440 (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 283 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8288 (pt0) REVERT: A 209 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: A 218 ASN cc_start: 0.6996 (t0) cc_final: 0.6361 (p0) REVERT: A 226 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: A 258 ASP cc_start: 0.8566 (m-30) cc_final: 0.8263 (m-30) REVERT: A 349 ASN cc_start: 0.8382 (t0) cc_final: 0.7973 (t0) REVERT: A 353 ASP cc_start: 0.8993 (m-30) cc_final: 0.8748 (m-30) REVERT: B 223 ASP cc_start: 0.8319 (t0) cc_final: 0.7959 (t0) REVERT: B 224 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7267 (tptt) REVERT: B 350 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6981 (mtm110) REVERT: C 56 LEU cc_start: 0.9389 (tp) cc_final: 0.9185 (mt) REVERT: C 132 ASN cc_start: 0.9167 (t0) cc_final: 0.8600 (t0) REVERT: D 67 MET cc_start: 0.7227 (tmm) cc_final: 0.7026 (pmm) REVERT: D 80 HIS cc_start: 0.8438 (m90) cc_final: 0.7641 (m90) REVERT: D 119 ASN cc_start: 0.8279 (m-40) cc_final: 0.7726 (m110) REVERT: D 126 ARG cc_start: 0.9008 (mtm110) cc_final: 0.8559 (ptp-110) REVERT: D 132 ASN cc_start: 0.8729 (t0) cc_final: 0.8275 (t0) REVERT: E 171 ASN cc_start: 0.9064 (m110) cc_final: 0.8375 (t0) REVERT: E 344 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7923 (mm-30) REVERT: E 354 MET cc_start: 0.8176 (tpp) cc_final: 0.7895 (tmm) REVERT: F 61 ASP cc_start: 0.8622 (t0) cc_final: 0.8393 (t0) REVERT: F 289 TYR cc_start: 0.8939 (m-80) cc_final: 0.8662 (m-10) REVERT: G 47 HIS cc_start: 0.9049 (m-70) cc_final: 0.8474 (m-70) REVERT: G 75 HIS cc_start: 0.9101 (OUTLIER) cc_final: 0.8849 (t70) REVERT: G 114 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8333 (mm-30) REVERT: G 126 ARG cc_start: 0.8277 (tmm-80) cc_final: 0.8021 (tmm-80) REVERT: G 130 LYS cc_start: 0.8999 (mtmt) cc_final: 0.8707 (mtpt) REVERT: G 132 ASN cc_start: 0.8252 (t0) cc_final: 0.7922 (t0) REVERT: G 140 GLU cc_start: 0.8051 (mt-10) cc_final: 0.6636 (mt-10) REVERT: H 70 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7581 (pp30) REVERT: H 78 LYS cc_start: 0.9112 (tptt) cc_final: 0.8615 (tppt) REVERT: H 112 MET cc_start: 0.7969 (tpp) cc_final: 0.7547 (tpp) REVERT: H 116 GLU cc_start: 0.8506 (mp0) cc_final: 0.8051 (mp0) REVERT: H 132 ASN cc_start: 0.8870 (t0) cc_final: 0.8420 (t0) outliers start: 44 outliers final: 33 residues processed: 268 average time/residue: 0.2621 time to fit residues: 100.8730 Evaluate side-chains 270 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 79 MET 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 113 SER 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 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: 0.0570 chunk 75 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 67 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- 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 A 351 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS E 43 HIS G 70 GLN ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.159343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105383 restraints weight = 19110.285| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.54 r_work: 0.2977 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4263 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= 0.114 Angle : 0.626 16.711 18638 Z= 0.323 Chirality : 0.046 0.294 1916 Planarity : 0.003 0.051 2510 Dihedral : 4.113 24.793 1788 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.70 % Allowed : 21.37 % Favored : 75.93 % 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: 0.22 (0.21), residues: 1650 helix: 1.66 (0.25), residues: 462 sheet: 0.69 (0.29), residues: 334 loop : -0.95 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 126 HIS 0.005 0.001 HIS C 80 PHE 0.024 0.001 PHE B 293 TYR 0.026 0.001 TYR B 289 ARG 0.007 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 606) hydrogen bonds : angle 3.98004 ( 1866) SS BOND : bond 0.00132 ( 4) SS BOND : angle 2.12018 ( 8) covalent geometry : bond 0.00252 (13794) covalent geometry : angle 0.62417 (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 284 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 1.579 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 79 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8744 (pt0) REVERT: A 218 ASN cc_start: 0.6857 (t0) cc_final: 0.6303 (p0) REVERT: A 349 ASN cc_start: 0.8356 (t0) cc_final: 0.7970 (t0) REVERT: A 353 ASP cc_start: 0.9000 (m-30) cc_final: 0.8736 (m-30) REVERT: B 223 ASP cc_start: 0.8296 (t0) cc_final: 0.7901 (t0) REVERT: B 224 LYS cc_start: 0.8327 (mtmt) cc_final: 0.7251 (tptt) REVERT: B 347 GLN cc_start: 0.8431 (tm-30) cc_final: 0.7917 (tm-30) REVERT: C 132 ASN cc_start: 0.9012 (t0) cc_final: 0.8405 (t0) REVERT: D 41 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6038 (mp) REVERT: D 80 HIS cc_start: 0.8270 (m90) cc_final: 0.7572 (m170) REVERT: D 119 ASN cc_start: 0.8300 (m-40) cc_final: 0.7726 (m110) REVERT: D 126 ARG cc_start: 0.8990 (mtm110) cc_final: 0.8507 (ptp-110) REVERT: D 132 ASN cc_start: 0.8692 (t0) cc_final: 0.8219 (t0) REVERT: E 171 ASN cc_start: 0.9076 (m110) cc_final: 0.8402 (t0) REVERT: E 258 ASP cc_start: 0.8090 (m-30) cc_final: 0.7858 (m-30) REVERT: E 354 MET cc_start: 0.8210 (tpp) cc_final: 0.7894 (tmm) REVERT: F 61 ASP cc_start: 0.8679 (t0) cc_final: 0.8434 (t0) REVERT: F 289 TYR cc_start: 0.9031 (m-80) cc_final: 0.8705 (m-10) REVERT: G 54 GLU cc_start: 0.9042 (tp30) cc_final: 0.8510 (tm-30) REVERT: G 70 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8341 (pp30) REVERT: G 73 GLN cc_start: 0.8363 (pt0) cc_final: 0.8034 (pp30) REVERT: G 75 HIS cc_start: 0.9112 (OUTLIER) cc_final: 0.8852 (t70) REVERT: G 122 ASP cc_start: 0.8243 (t70) cc_final: 0.7990 (m-30) REVERT: G 126 ARG cc_start: 0.8322 (tmm-80) cc_final: 0.8049 (tmm-80) REVERT: G 132 ASN cc_start: 0.8312 (t0) cc_final: 0.7896 (t0) REVERT: G 140 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7793 (mt-10) REVERT: H 55 HIS cc_start: 0.9004 (OUTLIER) cc_final: 0.8699 (m170) REVERT: H 70 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7589 (pp30) REVERT: H 78 LYS cc_start: 0.9096 (tptt) cc_final: 0.8560 (tppt) REVERT: H 79 MET cc_start: 0.9371 (ppp) cc_final: 0.9123 (ppp) REVERT: H 86 ASN cc_start: 0.8992 (m-40) cc_final: 0.8701 (m-40) REVERT: H 112 MET cc_start: 0.8045 (tpp) cc_final: 0.7628 (tpp) REVERT: H 116 GLU cc_start: 0.8619 (mp0) cc_final: 0.8256 (mp0) REVERT: H 132 ASN cc_start: 0.8867 (t0) cc_final: 0.8394 (t0) outliers start: 39 outliers final: 29 residues processed: 270 average time/residue: 0.2718 time to fit residues: 109.2370 Evaluate side-chains 270 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 230 CYS Chi-restraints excluded: chain A residue 298 GLN 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 41 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 113 SER 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 F residue 118 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 55 HIS 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: 9.9990 chunk 118 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 159 optimal weight: 0.0570 chunk 5 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 overall best weight: 1.7504 ------------------------------------------------------------------------------- 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** E 43 HIS ** G 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 = 0.3997 r_free = 0.3997 target = 0.157256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104520 restraints weight = 19236.636| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.35 r_work: 0.2951 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13798 Z= 0.167 Angle : 0.657 15.260 18638 Z= 0.344 Chirality : 0.048 0.343 1916 Planarity : 0.004 0.050 2510 Dihedral : 4.181 25.248 1788 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.28 % Allowed : 22.54 % 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: 0.08 (0.21), residues: 1650 helix: 1.44 (0.25), residues: 468 sheet: 0.50 (0.29), residues: 340 loop : -0.96 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 126 HIS 0.010 0.001 HIS C 75 PHE 0.023 0.002 PHE B 293 TYR 0.031 0.002 TYR B 289 ARG 0.006 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 606) hydrogen bonds : angle 4.15830 ( 1866) SS BOND : bond 0.00209 ( 4) SS BOND : angle 2.38417 ( 8) covalent geometry : bond 0.00388 (13794) covalent geometry : angle 0.65510 (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: 33 poor density : 235 time to evaluate : 1.640 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: 0.9110 (OUTLIER) cc_final: 0.8623 (pt0) REVERT: A 218 ASN cc_start: 0.6888 (t0) cc_final: 0.6317 (p0) REVERT: A 349 ASN cc_start: 0.8382 (t0) cc_final: 0.7971 (t0) REVERT: A 353 ASP cc_start: 0.8959 (m-30) cc_final: 0.8694 (m-30) REVERT: B 223 ASP cc_start: 0.8303 (t0) cc_final: 0.7928 (t0) REVERT: B 224 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7262 (tptt) REVERT: B 354 MET cc_start: 0.8771 (tpp) cc_final: 0.8566 (tpp) REVERT: C 74 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7881 (tp) REVERT: C 132 ASN cc_start: 0.9044 (t0) cc_final: 0.8434 (t0) REVERT: D 67 MET cc_start: 0.6367 (pmm) cc_final: 0.5718 (tmm) REVERT: D 80 HIS cc_start: 0.8256 (m90) cc_final: 0.7677 (m90) REVERT: D 119 ASN cc_start: 0.8278 (m-40) cc_final: 0.7718 (m110) REVERT: D 126 ARG cc_start: 0.9005 (mtm110) cc_final: 0.8517 (ptp-110) REVERT: D 132 ASN cc_start: 0.8700 (t0) cc_final: 0.8263 (t0) REVERT: E 171 ASN cc_start: 0.9100 (m110) cc_final: 0.8389 (t0) REVERT: E 354 MET cc_start: 0.8183 (tpp) cc_final: 0.7877 (tmm) REVERT: F 61 ASP cc_start: 0.8693 (t0) cc_final: 0.8452 (t0) REVERT: F 289 TYR cc_start: 0.8976 (m-80) cc_final: 0.8644 (m-10) REVERT: G 73 GLN cc_start: 0.8432 (pt0) cc_final: 0.8071 (pp30) REVERT: G 86 ASN cc_start: 0.8586 (m-40) cc_final: 0.8316 (t0) REVERT: G 112 MET cc_start: 0.8045 (ttm) cc_final: 0.7801 (ttt) REVERT: G 122 ASP cc_start: 0.8302 (t70) cc_final: 0.8071 (m-30) REVERT: G 126 ARG cc_start: 0.8297 (tmm-80) cc_final: 0.8023 (tmm-80) REVERT: G 132 ASN cc_start: 0.8362 (t0) cc_final: 0.7987 (t0) REVERT: G 140 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7594 (mt-10) REVERT: H 70 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7548 (pp30) REVERT: H 78 LYS cc_start: 0.9099 (tptt) cc_final: 0.8565 (tppt) REVERT: H 79 MET cc_start: 0.9385 (ppp) cc_final: 0.9184 (ppp) REVERT: H 86 ASN cc_start: 0.9038 (m-40) cc_final: 0.8692 (m-40) REVERT: H 112 MET cc_start: 0.8010 (tpp) cc_final: 0.7661 (tpp) REVERT: H 116 GLU cc_start: 0.8638 (mp0) cc_final: 0.8240 (mp0) REVERT: H 132 ASN cc_start: 0.8842 (t0) cc_final: 0.8394 (t0) outliers start: 33 outliers final: 28 residues processed: 260 average time/residue: 0.2455 time to fit residues: 92.9148 Evaluate side-chains 259 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 213 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 74 LEU 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 113 SER 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 F residue 118 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 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 54 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 118 optimal weight: 0.0370 chunk 77 optimal weight: 4.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 298 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS G 49 GLN G 70 GLN ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.158542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102157 restraints weight = 19286.298| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.21 r_work: 0.2988 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13798 Z= 0.142 Angle : 0.664 16.084 18638 Z= 0.347 Chirality : 0.047 0.338 1916 Planarity : 0.004 0.050 2510 Dihedral : 4.133 24.509 1788 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.42 % Allowed : 22.68 % Favored : 74.90 % 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: 0.06 (0.21), residues: 1650 helix: 1.43 (0.25), residues: 464 sheet: 0.51 (0.29), residues: 328 loop : -0.95 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 126 HIS 0.008 0.001 HIS H 80 PHE 0.022 0.001 PHE B 293 TYR 0.042 0.002 TYR B 289 ARG 0.008 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 606) hydrogen bonds : angle 4.16436 ( 1866) SS BOND : bond 0.00164 ( 4) SS BOND : angle 2.20701 ( 8) covalent geometry : bond 0.00328 (13794) covalent geometry : angle 0.66278 (18630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6944.96 seconds wall clock time: 120 minutes 40.42 seconds (7240.42 seconds total)