Starting phenix.real_space_refine on Fri Jul 3 23:47:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qh2_13960/07_2026/7qh2_13960.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qh2_13960/07_2026/7qh2_13960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qh2_13960/07_2026/7qh2_13960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qh2_13960/07_2026/7qh2_13960.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7qh2_13960/07_2026/7qh2_13960.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qh2_13960/07_2026/7qh2_13960.cif" model { file = "/net/cci-nas-00/data/ceres_data/7qh2_13960/07_2026/7qh2_13960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qh2_13960/07_2026/7qh2_13960.cif" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Fe 2 7.16 5 P 12 5.49 5 S 98 5.16 5 C 10676 2.51 5 N 2755 2.21 5 O 3265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16808 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2604 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 320} Chain: "B" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2041 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 250} Chain: "C" Number of atoms: 3603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 467, 3593 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 18, 'TRANS': 448} Conformer: "B" Number of residues, atoms: 467, 3593 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 18, 'TRANS': 448} bond proxies already assigned to first conformer: 3643 Chain: "D" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2604 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 320} Chain: "E" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2041 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 250} Chain: "F" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3593 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 18, 'TRANS': 448} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' FE': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' FE': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS C 42 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 42 " occ=0.50 Time building chain proxies: 3.90, per 1000 atoms: 0.23 Number of scatterers: 16808 At special positions: 0 Unit cell: (162.75, 78.12, 115.32, 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) Fe 2 26.01 S 98 16.00 P 12 15.00 O 3265 8.00 N 2755 7.00 C 10676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 731.3 milliseconds 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3934 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 22 sheets defined 39.1% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 87 through 104 removed outlier: 3.678A pdb=" N GLU A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 143 through 159 Processing helix chain 'A' and resid 170 through 183 removed outlier: 3.520A pdb=" N ALA A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Proline residue: A 176 - end of helix removed outlier: 3.546A pdb=" N ARG A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 292 through 301 removed outlier: 3.514A pdb=" N ILE A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.705A pdb=" N GLN A 324 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 380 through 398 Proline residue: A 386 - end of helix removed outlier: 3.525A pdb=" N GLU A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Proline residue: A 395 - end of helix Processing helix chain 'B' and resid 36 through 54 removed outlier: 3.726A pdb=" N PHE B 41 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 42 " --> pdb=" O TYR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 78 removed outlier: 3.778A pdb=" N LEU B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.711A pdb=" N GLY B 91 " --> pdb=" O ARG B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 128 through 138 removed outlier: 3.556A pdb=" N GLU B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 4.069A pdb=" N ALA B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 253 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 18 removed outlier: 3.655A pdb=" N LEU C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 21 No H-bonds generated for 'chain 'C' and resid 19 through 21' Processing helix chain 'C' and resid 27 through 29 No H-bonds generated for 'chain 'C' and resid 27 through 29' Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.518A pdb=" N PHE C 33 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS C 35 " --> pdb=" O ASP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 118 through 129 removed outlier: 3.530A pdb=" N LYS C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 129 " --> pdb=" O PHE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.691A pdb=" N ALA C 157 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL C 158 " --> pdb=" O MET C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 158' Processing helix chain 'C' and resid 162 through 165 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 232 through 239 removed outlier: 3.681A pdb=" N ILE C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.755A pdb=" N PHE C 263 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 306 removed outlier: 3.590A pdb=" N THR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 330 removed outlier: 3.747A pdb=" N SER C 326 " --> pdb=" O ASP C 322 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 353 through 369 Processing helix chain 'C' and resid 393 through 415 Processing helix chain 'C' and resid 429 through 437 Processing helix chain 'C' and resid 438 through 453 Processing helix chain 'D' and resid 87 through 104 removed outlier: 3.679A pdb=" N GLU D 91 " --> pdb=" O PRO D 87 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 101 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 143 through 159 Processing helix chain 'D' and resid 170 through 183 removed outlier: 3.519A pdb=" N ALA D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Proline residue: D 176 - end of helix removed outlier: 3.546A pdb=" N ARG D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 292 through 301 removed outlier: 3.513A pdb=" N ILE D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 316 Processing helix chain 'D' and resid 320 through 324 removed outlier: 3.706A pdb=" N GLN D 324 " --> pdb=" O ALA D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 380 through 398 Proline residue: D 386 - end of helix removed outlier: 3.525A pdb=" N GLU D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Proline residue: D 395 - end of helix Processing helix chain 'E' and resid 36 through 54 removed outlier: 3.726A pdb=" N PHE E 41 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 67 through 78 removed outlier: 3.777A pdb=" N LEU E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.712A pdb=" N GLY E 91 " --> pdb=" O ARG E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 109 Processing helix chain 'E' and resid 128 through 138 removed outlier: 3.556A pdb=" N GLU E 135 " --> pdb=" O PRO E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 195 Processing helix chain 'E' and resid 247 through 261 removed outlier: 4.069A pdb=" N ALA E 251 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 18 removed outlier: 3.704A pdb=" N LEU F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 30 through 35 removed outlier: 3.934A pdb=" N HIS F 35 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 68 Processing helix chain 'F' and resid 118 through 129 removed outlier: 3.726A pdb=" N ASN F 129 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 151 Processing helix chain 'F' and resid 154 through 158 removed outlier: 3.710A pdb=" N ALA F 157 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL F 158 " --> pdb=" O MET F 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 154 through 158' Processing helix chain 'F' and resid 162 through 165 Processing helix chain 'F' and resid 195 through 200 Processing helix chain 'F' and resid 232 through 239 removed outlier: 3.661A pdb=" N ILE F 239 " --> pdb=" O ASP F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 245 Processing helix chain 'F' and resid 258 through 269 removed outlier: 3.663A pdb=" N PHE F 263 " --> pdb=" O GLN F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 305 Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 317 through 330 removed outlier: 4.531A pdb=" N ALA F 327 " --> pdb=" O SER F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 339 removed outlier: 3.634A pdb=" N THR F 339 " --> pdb=" O ILE F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 353 through 369 Processing helix chain 'F' and resid 393 through 415 Processing helix chain 'F' and resid 429 through 437 Processing helix chain 'F' and resid 438 through 453 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 7.007A pdb=" N PHE A 225 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA A 188 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR A 227 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR A 75 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLY A 166 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N TYR A 77 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 107 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N PHE A 132 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA A 109 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR A 134 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU A 111 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 131 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.564A pdb=" N GLN A 84 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 195 removed outlier: 5.385A pdb=" N LEU A 201 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR A 218 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET A 213 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE B 231 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN A 215 " --> pdb=" O GLU B 229 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 217 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 227 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 267 removed outlier: 6.067A pdb=" N VAL A 262 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG B 170 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 264 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR B 157 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B 147 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 161 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 145 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 176 " --> pdb=" O HIS B 141 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR B 143 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N THR B 178 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 115 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL B 179 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N CYS B 117 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS B 3 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE B 116 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 5 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE B 4 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 60 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 6 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY B 82 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 309 removed outlier: 7.010A pdb=" N THR A 279 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ALA A 308 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 281 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A 280 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU A 340 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 282 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 358 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET A 377 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 360 " --> pdb=" O MET A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 19 removed outlier: 4.191A pdb=" N GLU B 18 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.192A pdb=" N THR C 171 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA C 212 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY C 169 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 214 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 167 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 315 removed outlier: 3.630A pdb=" N ALA C 279 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 252 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY C 376 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU C 257 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N SER C 374 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 186 through 190 removed outlier: 6.949A pdb=" N PHE D 225 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA D 188 " --> pdb=" O PHE D 225 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR D 227 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE D 163 " --> pdb=" O CYS D 226 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL D 228 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL D 165 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR D 75 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N GLY D 166 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N TYR D 77 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D 107 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N PHE D 132 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA D 109 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR D 134 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU D 111 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL D 131 " --> pdb=" O GLU D 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.564A pdb=" N GLN D 84 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 192 through 195 removed outlier: 5.383A pdb=" N LEU D 201 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR D 218 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET D 213 " --> pdb=" O ILE E 231 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE E 231 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN D 215 " --> pdb=" O GLU E 229 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D 217 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN E 227 " --> pdb=" O VAL D 217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 261 through 267 removed outlier: 5.862A pdb=" N VAL D 262 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG E 170 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 264 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR E 157 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS E 147 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN E 161 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL E 145 " --> pdb=" O ASN E 161 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU E 176 " --> pdb=" O HIS E 141 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR E 143 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR E 178 " --> pdb=" O THR E 143 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE E 115 " --> pdb=" O ILE E 177 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL E 179 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N CYS E 117 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS E 3 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE E 116 " --> pdb=" O LYS E 3 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU E 5 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE E 4 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU E 60 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL E 6 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY E 82 " --> pdb=" O LYS E 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 306 through 309 removed outlier: 7.012A pdb=" N THR D 279 " --> pdb=" O THR D 306 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA D 308 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL D 281 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE D 280 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU D 340 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA D 282 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE D 358 " --> pdb=" O CYS D 375 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET D 377 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA D 360 " --> pdb=" O MET D 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AB9, first strand: chain 'E' and resid 18 through 19 removed outlier: 3.988A pdb=" N GLU E 18 " --> pdb=" O ILE E 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 23 through 25 Processing sheet with id=AC2, first strand: chain 'F' and resid 101 through 105 removed outlier: 6.185A pdb=" N THR F 171 " --> pdb=" O THR F 210 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA F 212 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY F 169 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU F 214 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL F 167 " --> pdb=" O LEU F 214 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC4, first strand: chain 'F' and resid 313 through 315 removed outlier: 3.630A pdb=" N ALA F 279 " --> pdb=" O PHE F 230 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 252 " --> pdb=" O THR F 284 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY F 376 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLU F 257 " --> pdb=" O SER F 374 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N SER F 374 " --> pdb=" O GLU F 257 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1782 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: 2.98 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2887 1.28 - 1.42: 3865 1.42 - 1.55: 10159 1.55 - 1.68: 38 1.68 - 1.82: 165 Bond restraints: 17114 Sorted by residual: bond pdb=" N PRO E 201 " pdb=" CA PRO E 201 " ideal model delta sigma weight residual 1.469 1.699 -0.230 1.28e-02 6.10e+03 3.23e+02 bond pdb=" N PRO F 460 " pdb=" CA PRO F 460 " ideal model delta sigma weight residual 1.467 1.674 -0.207 1.21e-02 6.83e+03 2.92e+02 bond pdb=" C ASN F 459 " pdb=" N PRO F 460 " ideal model delta sigma weight residual 1.332 1.435 -0.103 1.30e-02 5.92e+03 6.30e+01 bond pdb=" C2 FAD C 501 " pdb=" N3 FAD C 501 " ideal model delta sigma weight residual 1.399 1.259 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C2 FAD F 501 " pdb=" N3 FAD F 501 " ideal model delta sigma weight residual 1.399 1.260 0.139 2.00e-02 2.50e+03 4.82e+01 ... (remaining 17109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 23052 4.29 - 8.59: 145 8.59 - 12.88: 13 12.88 - 17.17: 5 17.17 - 21.47: 1 Bond angle restraints: 23216 Sorted by residual: angle pdb=" C ASN E 200 " pdb=" N PRO E 201 " pdb=" CA PRO E 201 " ideal model delta sigma weight residual 119.84 141.31 -21.47 1.25e+00 6.40e-01 2.95e+02 angle pdb=" C ASN F 459 " pdb=" N PRO F 460 " pdb=" CA PRO F 460 " ideal model delta sigma weight residual 119.76 136.90 -17.14 1.03e+00 9.43e-01 2.77e+02 angle pdb=" O CYS C 464 " pdb=" C CYS C 464 " pdb=" N GLN C 465 " ideal model delta sigma weight residual 121.89 105.44 16.45 1.55e+00 4.16e-01 1.13e+02 angle pdb=" CA PRO E 201 " pdb=" N PRO E 201 " pdb=" CD PRO E 201 " ideal model delta sigma weight residual 112.00 97.90 14.10 1.40e+00 5.10e-01 1.01e+02 angle pdb=" N SER E 198 " pdb=" CA SER E 198 " pdb=" C SER E 198 " ideal model delta sigma weight residual 113.18 102.12 11.06 1.33e+00 5.65e-01 6.92e+01 ... (remaining 23211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.70: 9939 31.70 - 63.40: 297 63.40 - 95.10: 22 95.10 - 126.80: 0 126.80 - 158.50: 4 Dihedral angle restraints: 10262 sinusoidal: 4126 harmonic: 6136 Sorted by residual: dihedral pdb=" CA ILE E 197 " pdb=" C ILE E 197 " pdb=" N SER E 198 " pdb=" CA SER E 198 " ideal model delta harmonic sigma weight residual 180.00 145.48 34.52 0 5.00e+00 4.00e-02 4.77e+01 dihedral pdb=" CA SER E 198 " pdb=" C SER E 198 " pdb=" N LYS E 199 " pdb=" CA LYS E 199 " ideal model delta harmonic sigma weight residual 180.00 148.92 31.08 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA GLU E 22 " pdb=" C GLU E 22 " pdb=" N THR E 23 " pdb=" CA THR E 23 " ideal model delta harmonic sigma weight residual 180.00 154.54 25.46 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 10259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2283 0.081 - 0.163: 375 0.163 - 0.244: 22 0.244 - 0.326: 4 0.326 - 0.407: 1 Chirality restraints: 2685 Sorted by residual: chirality pdb=" CA PRO F 460 " pdb=" N PRO F 460 " pdb=" C PRO F 460 " pdb=" CB PRO F 460 " both_signs ideal model delta sigma weight residual False 2.72 3.13 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA ILE E 27 " pdb=" N ILE E 27 " pdb=" C ILE E 27 " pdb=" CB ILE E 27 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA ARG C 351 " pdb=" N ARG C 351 " pdb=" C ARG C 351 " pdb=" CB ARG C 351 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2682 not shown) Planarity restraints: 2921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 464 " -0.083 2.00e-02 2.50e+03 1.52e-01 2.31e+02 pdb=" C CYS C 464 " 0.263 2.00e-02 2.50e+03 pdb=" O CYS C 464 " -0.094 2.00e-02 2.50e+03 pdb=" N GLN C 465 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD C 501 " 0.010 2.00e-02 2.50e+03 2.06e-02 2.02e+01 pdb=" C10 FAD C 501 " -0.011 2.00e-02 2.50e+03 pdb=" C2 FAD C 501 " 0.028 2.00e-02 2.50e+03 pdb=" C4 FAD C 501 " -0.013 2.00e-02 2.50e+03 pdb=" C4X FAD C 501 " -0.009 2.00e-02 2.50e+03 pdb=" C5X FAD C 501 " -0.003 2.00e-02 2.50e+03 pdb=" C6 FAD C 501 " -0.001 2.00e-02 2.50e+03 pdb=" C7 FAD C 501 " 0.027 2.00e-02 2.50e+03 pdb=" C7M FAD C 501 " 0.038 2.00e-02 2.50e+03 pdb=" C8 FAD C 501 " -0.012 2.00e-02 2.50e+03 pdb=" C8M FAD C 501 " 0.011 2.00e-02 2.50e+03 pdb=" C9 FAD C 501 " -0.019 2.00e-02 2.50e+03 pdb=" C9A FAD C 501 " -0.021 2.00e-02 2.50e+03 pdb=" N1 FAD C 501 " -0.002 2.00e-02 2.50e+03 pdb=" N10 FAD C 501 " -0.034 2.00e-02 2.50e+03 pdb=" N3 FAD C 501 " 0.003 2.00e-02 2.50e+03 pdb=" N5 FAD C 501 " -0.024 2.00e-02 2.50e+03 pdb=" O2 FAD C 501 " 0.041 2.00e-02 2.50e+03 pdb=" O4 FAD C 501 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD F 501 " -0.010 2.00e-02 2.50e+03 2.06e-02 2.02e+01 pdb=" C10 FAD F 501 " 0.011 2.00e-02 2.50e+03 pdb=" C2 FAD F 501 " -0.029 2.00e-02 2.50e+03 pdb=" C4 FAD F 501 " 0.013 2.00e-02 2.50e+03 pdb=" C4X FAD F 501 " 0.009 2.00e-02 2.50e+03 pdb=" C5X FAD F 501 " 0.003 2.00e-02 2.50e+03 pdb=" C6 FAD F 501 " 0.001 2.00e-02 2.50e+03 pdb=" C7 FAD F 501 " -0.027 2.00e-02 2.50e+03 pdb=" C7M FAD F 501 " -0.038 2.00e-02 2.50e+03 pdb=" C8 FAD F 501 " 0.012 2.00e-02 2.50e+03 pdb=" C8M FAD F 501 " -0.011 2.00e-02 2.50e+03 pdb=" C9 FAD F 501 " 0.019 2.00e-02 2.50e+03 pdb=" C9A FAD F 501 " 0.022 2.00e-02 2.50e+03 pdb=" N1 FAD F 501 " 0.002 2.00e-02 2.50e+03 pdb=" N10 FAD F 501 " 0.035 2.00e-02 2.50e+03 pdb=" N3 FAD F 501 " -0.003 2.00e-02 2.50e+03 pdb=" N5 FAD F 501 " 0.024 2.00e-02 2.50e+03 pdb=" O2 FAD F 501 " -0.041 2.00e-02 2.50e+03 pdb=" O4 FAD F 501 " 0.007 2.00e-02 2.50e+03 ... (remaining 2918 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 29 2.32 - 2.96: 7337 2.96 - 3.61: 23840 3.61 - 4.25: 42552 4.25 - 4.90: 68561 Nonbonded interactions: 142319 Sorted by model distance: nonbonded pdb=" OE2 GLU C 422 " pdb="FE FE C 502 " model vdw 1.674 2.260 nonbonded pdb=" OE2 GLU F 422 " pdb="FE FE F 502 " model vdw 1.704 2.260 nonbonded pdb=" NE2 HIS C 377 " pdb="FE FE C 502 " model vdw 1.730 2.340 nonbonded pdb="FE FE C 502 " pdb=" O HOH C 601 " model vdw 1.775 2.260 nonbonded pdb="FE FE F 502 " pdb=" O HOH F 601 " model vdw 1.866 2.260 ... (remaining 142314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 1 through 41 or resid 43 through 502)) selection = (chain 'F' and (resid 1 through 41 or resid 43 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.450 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.008 0.230 17114 Z= 0.441 Angle : 1.008 21.466 23216 Z= 0.599 Chirality : 0.057 0.407 2685 Planarity : 0.008 0.152 2921 Dihedral : 15.057 158.496 6328 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.34 % Favored : 96.43 % Rotamer: Outliers : 2.88 % Allowed : 4.27 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.14), residues: 2129 helix: -4.40 (0.07), residues: 694 sheet: -1.53 (0.21), residues: 430 loop : -1.91 (0.16), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 322 TYR 0.029 0.001 TYR C 297 PHE 0.016 0.002 PHE C 272 TRP 0.009 0.002 TRP F 397 HIS 0.007 0.001 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.44 (17114) covalent geometry : angle 1.00837 / 0.60 (23216) hydrogen bonds : bond 0.28337 / 18.81 ( 635) hydrogen bonds : angle 9.94344 / 6.72 ( 1782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 0.599 Fit side-chains REVERT: A 84 GLN cc_start: 0.8436 (tp-100) cc_final: 0.8224 (pp30) REVERT: A 126 TYR cc_start: 0.8935 (m-80) cc_final: 0.8407 (m-80) REVERT: A 199 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7991 (m) REVERT: A 226 CYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7500 (t) REVERT: B 3 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7533 (mmmt) REVERT: B 199 LYS cc_start: 0.4114 (OUTLIER) cc_final: 0.3104 (mmmt) REVERT: C 292 GLN cc_start: 0.8717 (tt0) cc_final: 0.8388 (tt0) REVERT: C 322 ASP cc_start: 0.7703 (m-30) cc_final: 0.7413 (m-30) REVERT: C 366 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8686 (mtmt) REVERT: D 126 TYR cc_start: 0.8964 (m-80) cc_final: 0.8535 (m-80) REVERT: D 226 CYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7791 (t) REVERT: E 3 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7300 (mmmt) REVERT: E 202 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6342 (pp20) REVERT: E 216 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: F 266 ASP cc_start: 0.8179 (t70) cc_final: 0.7866 (t0) REVERT: F 322 ASP cc_start: 0.7930 (m-30) cc_final: 0.7639 (m-30) REVERT: F 366 LYS cc_start: 0.8726 (mttp) cc_final: 0.8425 (mttt) outliers start: 52 outliers final: 17 residues processed: 231 average time/residue: 0.6323 time to fit residues: 160.2267 Evaluate side-chains 154 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 248 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN A 353 GLN A 354 ASN B 16 ASN B 200 ASN C 382 ASN D 115 ASN D 324 GLN D 354 ASN F 292 GLN F 382 ASN F 394 GLN F 423 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.096389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.063823 restraints weight = 36808.978| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.75 r_work: 0.2695 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17114 Z= 0.127 Angle : 0.579 8.394 23216 Z= 0.305 Chirality : 0.046 0.271 2685 Planarity : 0.006 0.073 2921 Dihedral : 10.820 179.587 2358 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.07 % Favored : 97.74 % Rotamer: Outliers : 1.88 % Allowed : 8.64 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.16), residues: 2129 helix: -1.67 (0.16), residues: 720 sheet: -1.16 (0.22), residues: 436 loop : -1.21 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 238 TYR 0.022 0.001 TYR C 297 PHE 0.011 0.001 PHE C 272 TRP 0.009 0.001 TRP C 325 HIS 0.007 0.001 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (17114) covalent geometry : angle 0.57874 / 0.30 (23216) hydrogen bonds : bond 0.04222 / 2.79 ( 635) hydrogen bonds : angle 5.48031 / 3.73 ( 1782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.592 Fit side-chains REVERT: B 108 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8485 (tpt90) REVERT: B 227 GLN cc_start: 0.8788 (pm20) cc_final: 0.8509 (pm20) REVERT: B 248 LYS cc_start: 0.8709 (pptt) cc_final: 0.8225 (ptpt) REVERT: C 1 MET cc_start: 0.6295 (ptp) cc_final: 0.6059 (ptp) REVERT: C 292 GLN cc_start: 0.8312 (tt0) cc_final: 0.8051 (tt0) REVERT: C 322 ASP cc_start: 0.8367 (m-30) cc_final: 0.8088 (m-30) REVERT: C 342 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8990 (ptm) REVERT: D 126 TYR cc_start: 0.8732 (m-80) cc_final: 0.8246 (m-80) REVERT: D 242 PRO cc_start: 0.8941 (Cg_endo) cc_final: 0.8722 (Cg_exo) REVERT: E 1 MET cc_start: 0.6702 (ttp) cc_final: 0.6315 (ttm) REVERT: E 202 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6799 (tm-30) REVERT: E 248 LYS cc_start: 0.8638 (pptt) cc_final: 0.8221 (ptpt) REVERT: F 181 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8522 (mp0) REVERT: F 256 MET cc_start: 0.9383 (ptm) cc_final: 0.9115 (ptp) REVERT: F 322 ASP cc_start: 0.8422 (m-30) cc_final: 0.8212 (t70) REVERT: F 342 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.8911 (ptm) REVERT: F 369 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8645 (t0) REVERT: F 450 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8326 (tt0) outliers start: 34 outliers final: 14 residues processed: 164 average time/residue: 0.5850 time to fit residues: 106.3187 Evaluate side-chains 149 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 42 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN B 141 HIS D 115 ASN D 353 GLN ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.061194 restraints weight = 40981.355| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.76 r_work: 0.2628 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17114 Z= 0.187 Angle : 0.579 8.244 23216 Z= 0.300 Chirality : 0.047 0.200 2685 Planarity : 0.005 0.075 2921 Dihedral : 9.234 179.667 2314 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.65 % Rotamer: Outliers : 1.55 % Allowed : 9.97 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.17), residues: 2129 helix: -0.24 (0.18), residues: 722 sheet: -0.83 (0.23), residues: 436 loop : -0.89 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 238 TYR 0.023 0.001 TYR F 297 PHE 0.020 0.001 PHE C 272 TRP 0.010 0.001 TRP C 325 HIS 0.007 0.001 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (17114) covalent geometry : angle 0.57949 / 0.30 (23216) hydrogen bonds : bond 0.04308 / 2.85 ( 635) hydrogen bonds : angle 5.04921 / 3.44 ( 1782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.652 Fit side-chains REVERT: A 126 TYR cc_start: 0.8692 (m-80) cc_final: 0.8218 (m-80) REVERT: B 1 MET cc_start: 0.7209 (ttt) cc_final: 0.6864 (ttm) REVERT: B 62 MET cc_start: 0.8868 (ttp) cc_final: 0.8562 (ttp) REVERT: B 248 LYS cc_start: 0.8762 (pptt) cc_final: 0.8297 (ptpt) REVERT: C 222 MET cc_start: 0.8673 (mtp) cc_final: 0.8375 (ptp) REVERT: C 292 GLN cc_start: 0.8337 (tt0) cc_final: 0.8050 (tt0) REVERT: C 322 ASP cc_start: 0.8526 (m-30) cc_final: 0.8289 (m-30) REVERT: D 84 GLN cc_start: 0.8346 (tp40) cc_final: 0.8110 (mm-40) REVERT: D 126 TYR cc_start: 0.8762 (m-80) cc_final: 0.8266 (m-80) REVERT: E 202 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6692 (pp20) REVERT: E 227 GLN cc_start: 0.8809 (pm20) cc_final: 0.8176 (pm20) REVERT: E 248 LYS cc_start: 0.8741 (pptt) cc_final: 0.8281 (ptpt) REVERT: F 1 MET cc_start: 0.5937 (ppp) cc_final: 0.5699 (ppp) REVERT: F 181 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: F 256 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.9198 (ptp) REVERT: F 322 ASP cc_start: 0.8365 (m-30) cc_final: 0.8157 (t70) REVERT: F 369 ASP cc_start: 0.9099 (OUTLIER) cc_final: 0.8728 (t0) REVERT: F 450 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8278 (tt0) outliers start: 28 outliers final: 12 residues processed: 149 average time/residue: 0.6237 time to fit residues: 102.1728 Evaluate side-chains 141 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 130 optimal weight: 0.0870 chunk 135 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 188 optimal weight: 0.4980 chunk 189 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN A 353 GLN D 353 GLN E 16 ASN E 141 HIS F 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.096264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.063922 restraints weight = 36734.990| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.73 r_work: 0.2694 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17114 Z= 0.107 Angle : 0.513 7.909 23216 Z= 0.265 Chirality : 0.045 0.180 2685 Planarity : 0.004 0.074 2921 Dihedral : 8.661 176.682 2310 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.16 % Favored : 97.70 % Rotamer: Outliers : 1.77 % Allowed : 10.36 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2129 helix: 0.59 (0.19), residues: 720 sheet: -0.67 (0.23), residues: 446 loop : -0.65 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 108 TYR 0.016 0.001 TYR C 297 PHE 0.011 0.001 PHE F 255 TRP 0.009 0.001 TRP F 325 HIS 0.004 0.001 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (17114) covalent geometry : angle 0.51278 / 0.26 (23216) hydrogen bonds : bond 0.03199 / 2.13 ( 635) hydrogen bonds : angle 4.71765 / 3.21 ( 1782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.624 Fit side-chains REVERT: A 126 TYR cc_start: 0.8624 (m-80) cc_final: 0.8156 (m-80) REVERT: B 1 MET cc_start: 0.7171 (ttt) cc_final: 0.6848 (ttm) REVERT: B 26 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7415 (mt) REVERT: B 227 GLN cc_start: 0.8754 (pm20) cc_final: 0.8194 (pm20) REVERT: B 248 LYS cc_start: 0.8775 (pptt) cc_final: 0.8383 (ptmt) REVERT: C 222 MET cc_start: 0.8622 (mtp) cc_final: 0.8356 (ptp) REVERT: C 292 GLN cc_start: 0.8243 (tt0) cc_final: 0.7982 (tt0) REVERT: C 322 ASP cc_start: 0.8458 (m-30) cc_final: 0.8223 (m-30) REVERT: D 84 GLN cc_start: 0.8377 (tp40) cc_final: 0.8128 (mm-40) REVERT: D 126 TYR cc_start: 0.8695 (m-80) cc_final: 0.8199 (m-80) REVERT: E 108 ARG cc_start: 0.8666 (tpt90) cc_final: 0.8175 (tpp-160) REVERT: E 202 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6693 (pp20) REVERT: E 209 LYS cc_start: 0.8943 (mmpt) cc_final: 0.8650 (mmmt) REVERT: E 227 GLN cc_start: 0.8749 (pm20) cc_final: 0.8145 (pm20) REVERT: E 248 LYS cc_start: 0.8766 (pptt) cc_final: 0.8347 (ptpt) REVERT: F 1 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.5433 (ppp) REVERT: F 181 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8471 (mp0) REVERT: F 256 MET cc_start: 0.9385 (ptm) cc_final: 0.9151 (ptp) REVERT: F 292 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7897 (pt0) REVERT: F 342 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.8818 (ptm) REVERT: F 369 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8686 (t0) REVERT: F 450 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8142 (tt0) outliers start: 32 outliers final: 9 residues processed: 156 average time/residue: 0.6193 time to fit residues: 106.3241 Evaluate side-chains 143 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 76 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN D 353 GLN E 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.093429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.060883 restraints weight = 33196.783| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.58 r_work: 0.2632 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 17114 Z= 0.215 Angle : 0.574 9.234 23216 Z= 0.295 Chirality : 0.048 0.172 2685 Planarity : 0.005 0.075 2921 Dihedral : 8.770 176.367 2304 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.35 % Favored : 97.51 % Rotamer: Outliers : 1.99 % Allowed : 10.75 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 2129 helix: 0.83 (0.19), residues: 722 sheet: -0.63 (0.23), residues: 442 loop : -0.59 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 108 TYR 0.022 0.002 TYR F 297 PHE 0.017 0.001 PHE C 272 TRP 0.010 0.002 TRP F 325 HIS 0.007 0.001 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.21 (17114) covalent geometry : angle 0.57377 / 0.29 (23216) hydrogen bonds : bond 0.04067 / 2.68 ( 635) hydrogen bonds : angle 4.83571 / 3.29 ( 1782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.531 Fit side-chains REVERT: A 126 TYR cc_start: 0.8678 (m-80) cc_final: 0.8220 (m-80) REVERT: A 396 GLU cc_start: 0.4461 (OUTLIER) cc_final: 0.4225 (mt-10) REVERT: B 1 MET cc_start: 0.6966 (ttt) cc_final: 0.6662 (ttm) REVERT: B 26 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7380 (mt) REVERT: B 81 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: B 248 LYS cc_start: 0.8776 (pptt) cc_final: 0.8387 (ptmt) REVERT: B 252 LYS cc_start: 0.8939 (ttmm) cc_final: 0.8712 (pptt) REVERT: C 181 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: C 222 MET cc_start: 0.8558 (mtp) cc_final: 0.8265 (ptp) REVERT: C 292 GLN cc_start: 0.8283 (tt0) cc_final: 0.8020 (tt0) REVERT: C 322 ASP cc_start: 0.8477 (m-30) cc_final: 0.8166 (t70) REVERT: C 450 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: D 126 TYR cc_start: 0.8733 (m-80) cc_final: 0.8205 (m-80) REVERT: E 202 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6825 (pp20) REVERT: E 248 LYS cc_start: 0.8791 (pptt) cc_final: 0.8344 (ptpt) REVERT: E 252 LYS cc_start: 0.8893 (ttmm) cc_final: 0.8636 (pptt) REVERT: F 1 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.5463 (ppp) REVERT: F 94 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8686 (tm-30) REVERT: F 181 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8545 (mp0) REVERT: F 256 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.9173 (ptp) REVERT: F 369 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8780 (t0) REVERT: F 450 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8371 (tt0) outliers start: 36 outliers final: 12 residues processed: 152 average time/residue: 0.6077 time to fit residues: 101.5428 Evaluate side-chains 143 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 197 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 122 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN D 353 GLN E 66 GLN F 292 GLN F 394 GLN F 456 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.061638 restraints weight = 37245.393| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.76 r_work: 0.2643 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17114 Z= 0.139 Angle : 0.528 9.655 23216 Z= 0.272 Chirality : 0.046 0.170 2685 Planarity : 0.004 0.075 2921 Dihedral : 8.640 175.069 2304 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.26 % Favored : 97.60 % Rotamer: Outliers : 1.66 % Allowed : 11.25 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2129 helix: 1.05 (0.20), residues: 724 sheet: -0.52 (0.24), residues: 442 loop : -0.47 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 108 TYR 0.018 0.001 TYR F 297 PHE 0.010 0.001 PHE F 255 TRP 0.011 0.001 TRP F 325 HIS 0.005 0.001 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (17114) covalent geometry : angle 0.52812 / 0.27 (23216) hydrogen bonds : bond 0.03469 / 2.30 ( 635) hydrogen bonds : angle 4.69259 / 3.19 ( 1782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.543 Fit side-chains REVERT: A 126 TYR cc_start: 0.8634 (m-80) cc_final: 0.8153 (m-80) REVERT: B 1 MET cc_start: 0.6795 (ttt) cc_final: 0.6565 (ttm) REVERT: B 26 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7365 (mt) REVERT: B 81 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: B 227 GLN cc_start: 0.8705 (pm20) cc_final: 0.8147 (pm20) REVERT: B 248 LYS cc_start: 0.8764 (pptt) cc_final: 0.8374 (ptmt) REVERT: B 252 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8676 (pptt) REVERT: C 222 MET cc_start: 0.8581 (mtp) cc_final: 0.8260 (ptp) REVERT: C 292 GLN cc_start: 0.8159 (tt0) cc_final: 0.7904 (tt0) REVERT: C 322 ASP cc_start: 0.8391 (m-30) cc_final: 0.8097 (t70) REVERT: C 342 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.8672 (ptm) REVERT: C 450 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: E 202 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6835 (pp20) REVERT: E 209 LYS cc_start: 0.8916 (mmpt) cc_final: 0.8625 (mmmt) REVERT: E 248 LYS cc_start: 0.8775 (pptt) cc_final: 0.8335 (ptmt) REVERT: E 252 LYS cc_start: 0.8890 (ttmm) cc_final: 0.8658 (pptt) REVERT: F 1 MET cc_start: 0.5939 (OUTLIER) cc_final: 0.5536 (ppp) REVERT: F 181 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: F 342 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.8649 (ptm) REVERT: F 369 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8732 (t0) REVERT: F 450 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8185 (tt0) outliers start: 30 outliers final: 11 residues processed: 150 average time/residue: 0.5935 time to fit residues: 97.9183 Evaluate side-chains 146 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 52 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN D 211 ASN D 353 GLN E 66 GLN F 292 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.095748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.063523 restraints weight = 30532.649| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.50 r_work: 0.2693 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17114 Z= 0.112 Angle : 0.507 9.081 23216 Z= 0.260 Chirality : 0.045 0.172 2685 Planarity : 0.004 0.075 2921 Dihedral : 8.457 174.124 2304 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.78 % Favored : 97.08 % Rotamer: Outliers : 1.55 % Allowed : 11.91 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.19), residues: 2129 helix: 1.26 (0.20), residues: 724 sheet: -0.40 (0.24), residues: 448 loop : -0.39 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 108 TYR 0.015 0.001 TYR C 297 PHE 0.011 0.001 PHE F 255 TRP 0.010 0.001 TRP C 325 HIS 0.004 0.001 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (17114) covalent geometry : angle 0.50669 / 0.26 (23216) hydrogen bonds : bond 0.03156 / 2.09 ( 635) hydrogen bonds : angle 4.56912 / 3.10 ( 1782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8585 (m-80) cc_final: 0.8084 (m-80) REVERT: B 1 MET cc_start: 0.6612 (ttt) cc_final: 0.6401 (ttm) REVERT: B 26 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7373 (mt) REVERT: B 108 ARG cc_start: 0.8582 (tpt90) cc_final: 0.8139 (tpp-160) REVERT: B 152 ASP cc_start: 0.8178 (t0) cc_final: 0.7832 (t70) REVERT: B 162 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6679 (mpp) REVERT: B 227 GLN cc_start: 0.8681 (pm20) cc_final: 0.8150 (pm20) REVERT: B 248 LYS cc_start: 0.8739 (pptt) cc_final: 0.8369 (ptmt) REVERT: B 252 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8674 (pptt) REVERT: C 222 MET cc_start: 0.8580 (mtp) cc_final: 0.8279 (ptp) REVERT: C 292 GLN cc_start: 0.8198 (tt0) cc_final: 0.7952 (tt0) REVERT: C 322 ASP cc_start: 0.8361 (m-30) cc_final: 0.8077 (t70) REVERT: C 342 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8686 (ptm) REVERT: C 450 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: D 126 TYR cc_start: 0.8596 (m-80) cc_final: 0.8237 (m-80) REVERT: E 1 MET cc_start: 0.6334 (ptt) cc_final: 0.5986 (ptt) REVERT: E 152 ASP cc_start: 0.8037 (t0) cc_final: 0.7664 (t70) REVERT: E 202 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6854 (pp20) REVERT: E 209 LYS cc_start: 0.8947 (mmpt) cc_final: 0.8674 (mmmt) REVERT: E 248 LYS cc_start: 0.8769 (pptt) cc_final: 0.8359 (ptmt) REVERT: E 252 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8645 (pptt) REVERT: F 1 MET cc_start: 0.5880 (OUTLIER) cc_final: 0.5510 (ppp) REVERT: F 181 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: F 342 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.8614 (ptm) REVERT: F 369 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8711 (t0) REVERT: F 450 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8148 (tt0) outliers start: 28 outliers final: 9 residues processed: 153 average time/residue: 0.5860 time to fit residues: 98.6743 Evaluate side-chains 149 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 43 optimal weight: 4.9990 chunk 51 optimal weight: 0.0980 chunk 181 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 172 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN D 353 GLN E 66 GLN F 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.094647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.062258 restraints weight = 30312.170| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.51 r_work: 0.2664 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17114 Z= 0.148 Angle : 0.532 7.880 23216 Z= 0.273 Chirality : 0.046 0.166 2685 Planarity : 0.004 0.075 2921 Dihedral : 8.522 174.128 2304 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.49 % Favored : 97.37 % Rotamer: Outliers : 1.33 % Allowed : 11.97 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 2129 helix: 1.32 (0.20), residues: 724 sheet: -0.40 (0.24), residues: 448 loop : -0.35 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 108 TYR 0.019 0.001 TYR F 297 PHE 0.012 0.001 PHE C 272 TRP 0.009 0.001 TRP C 325 HIS 0.004 0.001 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (17114) covalent geometry : angle 0.53151 / 0.27 (23216) hydrogen bonds : bond 0.03473 / 2.30 ( 635) hydrogen bonds : angle 4.60874 / 3.14 ( 1782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8602 (m-80) cc_final: 0.8124 (m-80) REVERT: B 1 MET cc_start: 0.6583 (ttt) cc_final: 0.6369 (ttt) REVERT: B 26 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7413 (mt) REVERT: B 62 MET cc_start: 0.8253 (ttp) cc_final: 0.7981 (ttt) REVERT: B 108 ARG cc_start: 0.8673 (tpt90) cc_final: 0.8180 (tpp-160) REVERT: B 152 ASP cc_start: 0.8248 (t0) cc_final: 0.7975 (t70) REVERT: B 162 MET cc_start: 0.7794 (mpp) cc_final: 0.7553 (mmm) REVERT: B 248 LYS cc_start: 0.8762 (pptt) cc_final: 0.8400 (ptmt) REVERT: B 252 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8693 (pptt) REVERT: C 222 MET cc_start: 0.8527 (mtp) cc_final: 0.8249 (ptp) REVERT: C 292 GLN cc_start: 0.8232 (tt0) cc_final: 0.7984 (tt0) REVERT: C 342 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.8688 (ptm) REVERT: C 450 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: D 126 TYR cc_start: 0.8607 (m-80) cc_final: 0.8244 (m-80) REVERT: E 1 MET cc_start: 0.6172 (ptt) cc_final: 0.5833 (ptt) REVERT: E 62 MET cc_start: 0.8297 (ttp) cc_final: 0.8020 (ttt) REVERT: E 202 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6878 (pp20) REVERT: E 209 LYS cc_start: 0.8957 (mmpt) cc_final: 0.8689 (mmmt) REVERT: E 248 LYS cc_start: 0.8771 (pptt) cc_final: 0.8371 (ptmt) REVERT: E 252 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8665 (pptt) REVERT: F 1 MET cc_start: 0.5906 (OUTLIER) cc_final: 0.5535 (ppp) REVERT: F 181 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: F 222 MET cc_start: 0.8617 (mtp) cc_final: 0.8323 (ptp) REVERT: F 342 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8635 (ptm) REVERT: F 369 ASP cc_start: 0.9027 (m-30) cc_final: 0.8718 (t0) REVERT: F 450 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8203 (tt0) outliers start: 24 outliers final: 10 residues processed: 151 average time/residue: 0.6566 time to fit residues: 109.0017 Evaluate side-chains 146 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 0.0370 chunk 71 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN D 353 GLN E 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.095929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.062862 restraints weight = 38695.097| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.85 r_work: 0.2672 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17114 Z= 0.109 Angle : 0.509 8.496 23216 Z= 0.261 Chirality : 0.045 0.169 2685 Planarity : 0.004 0.073 2921 Dihedral : 8.412 173.705 2304 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.63 % Favored : 97.22 % Rotamer: Outliers : 1.05 % Allowed : 12.19 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 2129 helix: 1.43 (0.20), residues: 724 sheet: -0.36 (0.24), residues: 448 loop : -0.31 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 108 TYR 0.015 0.001 TYR C 297 PHE 0.012 0.001 PHE F 255 TRP 0.009 0.001 TRP C 325 HIS 0.004 0.001 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (17114) covalent geometry : angle 0.50916 / 0.26 (23216) hydrogen bonds : bond 0.03115 / 2.06 ( 635) hydrogen bonds : angle 4.51640 / 3.07 ( 1782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.539 Fit side-chains REVERT: A 126 TYR cc_start: 0.8564 (m-80) cc_final: 0.8081 (m-80) REVERT: B 26 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7453 (mt) REVERT: B 108 ARG cc_start: 0.8672 (tpt90) cc_final: 0.8180 (tpp-160) REVERT: B 152 ASP cc_start: 0.8122 (t0) cc_final: 0.7762 (t70) REVERT: B 162 MET cc_start: 0.7711 (mpp) cc_final: 0.7485 (mmm) REVERT: B 248 LYS cc_start: 0.8753 (pptt) cc_final: 0.8397 (ptmt) REVERT: B 252 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8690 (pptt) REVERT: C 222 MET cc_start: 0.8601 (mtp) cc_final: 0.8338 (ptp) REVERT: C 292 GLN cc_start: 0.8215 (tt0) cc_final: 0.7977 (tt0) REVERT: C 322 ASP cc_start: 0.8307 (m-30) cc_final: 0.8071 (t70) REVERT: C 450 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: D 126 TYR cc_start: 0.8563 (m-80) cc_final: 0.8191 (m-80) REVERT: E 1 MET cc_start: 0.6082 (ptt) cc_final: 0.5760 (ptt) REVERT: E 108 ARG cc_start: 0.8690 (tpt90) cc_final: 0.8210 (tpp-160) REVERT: E 152 ASP cc_start: 0.8074 (t0) cc_final: 0.7699 (t70) REVERT: E 162 MET cc_start: 0.7685 (mpp) cc_final: 0.7459 (mmm) REVERT: E 202 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6870 (pp20) REVERT: E 209 LYS cc_start: 0.8972 (mmpt) cc_final: 0.8720 (mmmt) REVERT: E 248 LYS cc_start: 0.8764 (pptt) cc_final: 0.8365 (ptmt) REVERT: E 252 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8658 (pptt) REVERT: F 1 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5488 (ppp) REVERT: F 342 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.8655 (ptm) REVERT: F 369 ASP cc_start: 0.8998 (m-30) cc_final: 0.8677 (t0) REVERT: F 450 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8180 (tt0) outliers start: 19 outliers final: 9 residues processed: 148 average time/residue: 0.6025 time to fit residues: 98.5461 Evaluate side-chains 145 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 129 optimal weight: 4.9990 chunk 101 optimal weight: 0.2980 chunk 174 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 chunk 159 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN D 353 GLN F 292 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.094464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.061810 restraints weight = 32817.554| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.60 r_work: 0.2653 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17114 Z= 0.163 Angle : 0.544 8.857 23216 Z= 0.278 Chirality : 0.046 0.164 2685 Planarity : 0.004 0.073 2921 Dihedral : 8.523 173.984 2304 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.49 % Favored : 97.37 % Rotamer: Outliers : 1.00 % Allowed : 12.58 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 2129 helix: 1.39 (0.20), residues: 724 sheet: -0.28 (0.24), residues: 444 loop : -0.31 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 108 TYR 0.019 0.001 TYR F 297 PHE 0.013 0.001 PHE C 272 TRP 0.008 0.001 TRP C 325 HIS 0.005 0.001 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (17114) covalent geometry : angle 0.54435 / 0.28 (23216) hydrogen bonds : bond 0.03528 / 2.33 ( 635) hydrogen bonds : angle 4.60127 / 3.13 ( 1782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.408 Fit side-chains REVERT: A 126 TYR cc_start: 0.8577 (m-80) cc_final: 0.8042 (m-80) REVERT: B 26 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7453 (mt) REVERT: B 108 ARG cc_start: 0.8666 (tpt90) cc_final: 0.8175 (tpp-160) REVERT: B 152 ASP cc_start: 0.8132 (t0) cc_final: 0.7824 (t70) REVERT: B 209 LYS cc_start: 0.8918 (mmpt) cc_final: 0.8675 (mmmt) REVERT: B 248 LYS cc_start: 0.8765 (pptt) cc_final: 0.8412 (ptmt) REVERT: B 252 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8695 (pptt) REVERT: C 181 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: C 222 MET cc_start: 0.8535 (mtp) cc_final: 0.8259 (ptp) REVERT: C 292 GLN cc_start: 0.8226 (tt0) cc_final: 0.7981 (tt0) REVERT: C 450 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: D 126 TYR cc_start: 0.8606 (m-80) cc_final: 0.8235 (m-80) REVERT: E 1 MET cc_start: 0.6237 (ptt) cc_final: 0.5893 (ptt) REVERT: E 108 ARG cc_start: 0.8682 (tpt90) cc_final: 0.8217 (tpp-160) REVERT: E 152 ASP cc_start: 0.8155 (t0) cc_final: 0.7780 (t70) REVERT: E 162 MET cc_start: 0.7656 (mpp) cc_final: 0.7434 (mmm) REVERT: E 202 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6993 (pp20) REVERT: E 209 LYS cc_start: 0.8964 (mmpt) cc_final: 0.8720 (mmmt) REVERT: E 248 LYS cc_start: 0.8772 (pptt) cc_final: 0.8392 (ptmt) REVERT: E 252 LYS cc_start: 0.8904 (ttmm) cc_final: 0.8666 (pptt) REVERT: F 1 MET cc_start: 0.5974 (OUTLIER) cc_final: 0.5612 (ppp) REVERT: F 342 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.8637 (ptm) REVERT: F 369 ASP cc_start: 0.9030 (m-30) cc_final: 0.8720 (t0) REVERT: F 450 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8208 (tt0) outliers start: 18 outliers final: 10 residues processed: 144 average time/residue: 0.6062 time to fit residues: 95.8713 Evaluate side-chains 147 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 19 optimal weight: 0.0770 chunk 49 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.094653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.062098 restraints weight = 32394.594| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.55 r_work: 0.2662 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 17114 Z= 0.162 Angle : 0.735 59.194 23216 Z= 0.422 Chirality : 0.046 0.375 2685 Planarity : 0.004 0.073 2921 Dihedral : 8.535 174.061 2304 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.54 % Favored : 97.32 % Rotamer: Outliers : 0.94 % Allowed : 12.85 % Favored : 86.20 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 2129 helix: 1.42 (0.20), residues: 724 sheet: -0.34 (0.24), residues: 448 loop : -0.28 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 108 TYR 0.019 0.001 TYR F 297 PHE 0.013 0.001 PHE C 437 TRP 0.008 0.001 TRP C 325 HIS 0.004 0.001 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (17114) covalent geometry : angle 0.73450 / 0.42 (23216) hydrogen bonds : bond 0.03507 / 2.31 ( 635) hydrogen bonds : angle 4.60440 / 3.14 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6988.87 seconds wall clock time: 119 minutes 22.92 seconds (7162.92 seconds total)