Starting phenix.real_space_refine on Wed Mar 4 22:43:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qh2_13960/03_2026/7qh2_13960.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qh2_13960/03_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_13960/03_2026/7qh2_13960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qh2_13960/03_2026/7qh2_13960.map" model { file = "/net/cci-nas-00/data/ceres_data/7qh2_13960/03_2026/7qh2_13960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qh2_13960/03_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-5986/lib/python3.9/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: 3.86, 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: 1.24 Conformation dependent library (CDL) restraints added in 882.4 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: 0.61 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: 2.33 Time building geometry restraints manager: 1.56 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: 10107 31.70 - 63.40: 367 63.40 - 95.10: 42 95.10 - 126.80: 0 126.80 - 158.50: 4 Dihedral angle restraints: 10520 sinusoidal: 4384 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 10517 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: 1.780 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:8.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 16.285 158.496 6586 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 covalent geometry : bond 0.00750 (17114) covalent geometry : angle 1.00837 (23216) hydrogen bonds : bond 0.28337 ( 635) hydrogen bonds : angle 9.94344 ( 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 : 0.451 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: 0.6908 time to fit residues: 174.3620 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 : 0.616 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3433 r_free = 0.3433 target = 0.096471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.063845 restraints weight = 36787.459| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.76 r_work: 0.2694 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 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 = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17114 Z= 0.127 Angle : 0.583 8.678 23216 Z= 0.307 Chirality : 0.046 0.257 2685 Planarity : 0.006 0.073 2921 Dihedral : 14.015 179.224 2616 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.07 % Favored : 97.70 % Rotamer: Outliers : 1.88 % Allowed : 8.59 % Favored : 89.53 % 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: -2.14 (0.16), residues: 2129 helix: -1.61 (0.16), residues: 720 sheet: -1.17 (0.22), residues: 436 loop : -1.22 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 238 TYR 0.022 0.001 TYR C 297 PHE 0.011 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 covalent geometry : bond 0.00280 (17114) covalent geometry : angle 0.58313 (23216) hydrogen bonds : bond 0.04209 ( 635) hydrogen bonds : angle 5.48187 ( 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 178 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.583 Fit side-chains REVERT: B 108 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8487 (tpt90) REVERT: B 227 GLN cc_start: 0.8787 (pm20) cc_final: 0.8508 (pm20) REVERT: B 248 LYS cc_start: 0.8704 (pptt) cc_final: 0.8210 (ptpt) REVERT: C 1 MET cc_start: 0.6302 (ptp) cc_final: 0.6064 (ptp) REVERT: C 292 GLN cc_start: 0.8318 (tt0) cc_final: 0.8054 (tt0) REVERT: C 322 ASP cc_start: 0.8371 (m-30) cc_final: 0.8074 (m-30) REVERT: C 342 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8989 (ptm) REVERT: D 126 TYR cc_start: 0.8739 (m-80) cc_final: 0.8263 (m-80) REVERT: D 242 PRO cc_start: 0.8943 (Cg_endo) cc_final: 0.8724 (Cg_exo) REVERT: E 1 MET cc_start: 0.6682 (ttp) cc_final: 0.6293 (ttm) REVERT: E 108 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8405 (tpt90) REVERT: E 202 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6813 (tm-30) REVERT: E 248 LYS cc_start: 0.8638 (pptt) cc_final: 0.8225 (ptpt) REVERT: F 181 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8536 (mp0) REVERT: F 256 MET cc_start: 0.9390 (ptm) cc_final: 0.9100 (ptp) REVERT: F 322 ASP cc_start: 0.8420 (m-30) cc_final: 0.8210 (t70) REVERT: F 342 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.8915 (ptm) REVERT: F 369 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8640 (t0) REVERT: F 450 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8334 (tt0) outliers start: 34 outliers final: 14 residues processed: 165 average time/residue: 0.6797 time to fit residues: 123.7032 Evaluate side-chains 152 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 108 ARG 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: 0.9980 chunk 118 optimal weight: 5.9990 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: 2.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 397 ASN B 141 HIS D 115 ASN D 353 GLN F 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.060511 restraints weight = 40680.116| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.73 r_work: 0.2614 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17114 Z= 0.222 Angle : 0.606 8.379 23216 Z= 0.313 Chirality : 0.048 0.192 2685 Planarity : 0.005 0.075 2921 Dihedral : 12.553 179.554 2572 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.35 % Favored : 97.51 % Rotamer: Outliers : 1.66 % Allowed : 9.92 % Favored : 88.42 % 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: -1.12 (0.17), residues: 2129 helix: -0.24 (0.18), residues: 722 sheet: -0.92 (0.22), residues: 442 loop : -0.90 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 238 TYR 0.024 0.002 TYR F 297 PHE 0.023 0.002 PHE C 272 TRP 0.011 0.002 TRP C 325 HIS 0.007 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00532 (17114) covalent geometry : angle 0.60558 (23216) hydrogen bonds : bond 0.04533 ( 635) hydrogen bonds : angle 5.10058 ( 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 157 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.673 Fit side-chains REVERT: A 126 TYR cc_start: 0.8714 (m-80) cc_final: 0.8259 (m-80) REVERT: B 1 MET cc_start: 0.7208 (ttt) cc_final: 0.6889 (ttm) REVERT: B 108 ARG cc_start: 0.8769 (mmm160) cc_final: 0.8566 (tpt90) REVERT: B 248 LYS cc_start: 0.8766 (pptt) cc_final: 0.8297 (ptpt) REVERT: C 222 MET cc_start: 0.8672 (mtp) cc_final: 0.8364 (ptp) REVERT: C 292 GLN cc_start: 0.8309 (tt0) cc_final: 0.8019 (tt0) REVERT: C 322 ASP cc_start: 0.8521 (m-30) cc_final: 0.8281 (m-30) REVERT: D 84 GLN cc_start: 0.8338 (tp40) cc_final: 0.8109 (mm-40) REVERT: D 126 TYR cc_start: 0.8787 (m-80) cc_final: 0.8298 (m-80) REVERT: E 108 ARG cc_start: 0.8709 (mmm160) cc_final: 0.8508 (tpt90) REVERT: E 202 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6780 (tm-30) REVERT: E 248 LYS cc_start: 0.8746 (pptt) cc_final: 0.8288 (ptpt) REVERT: F 1 MET cc_start: 0.6036 (ppp) cc_final: 0.5747 (ppp) REVERT: F 181 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8583 (mp0) REVERT: F 256 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9213 (ptp) REVERT: F 322 ASP cc_start: 0.8368 (m-30) cc_final: 0.8162 (t70) REVERT: F 369 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8759 (t0) REVERT: F 450 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8327 (tt0) outliers start: 30 outliers final: 12 residues processed: 143 average time/residue: 0.7043 time to fit residues: 110.6747 Evaluate side-chains 139 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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: 0.4980 chunk 135 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 353 GLN E 16 ASN ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.063035 restraints weight = 36148.597| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.61 r_work: 0.2677 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2110 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= 0.126 Angle : 0.533 8.328 23216 Z= 0.274 Chirality : 0.045 0.176 2685 Planarity : 0.004 0.074 2921 Dihedral : 11.766 176.278 2568 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.16 % Favored : 97.70 % Rotamer: Outliers : 2.11 % Allowed : 10.25 % Favored : 87.65 % 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: -0.50 (0.18), residues: 2129 helix: 0.55 (0.19), residues: 722 sheet: -0.74 (0.23), residues: 442 loop : -0.71 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 238 TYR 0.017 0.001 TYR C 297 PHE 0.010 0.001 PHE F 255 TRP 0.009 0.001 TRP C 325 HIS 0.005 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00294 (17114) covalent geometry : angle 0.53277 (23216) hydrogen bonds : bond 0.03436 ( 635) hydrogen bonds : angle 4.78525 ( 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 171 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.638 Fit side-chains REVERT: A 126 TYR cc_start: 0.8689 (m-80) cc_final: 0.8204 (m-80) REVERT: B 1 MET cc_start: 0.7074 (ttt) cc_final: 0.6757 (ttm) REVERT: B 26 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7413 (mt) REVERT: B 62 MET cc_start: 0.8811 (ttp) cc_final: 0.8581 (ttp) REVERT: B 81 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: B 199 LYS cc_start: 0.5920 (OUTLIER) cc_final: 0.5589 (mmmt) REVERT: B 248 LYS cc_start: 0.8777 (pptt) cc_final: 0.8380 (ptmt) REVERT: C 222 MET cc_start: 0.8700 (mtp) cc_final: 0.8442 (ptp) REVERT: C 292 GLN cc_start: 0.8301 (tt0) cc_final: 0.8039 (tt0) REVERT: C 322 ASP cc_start: 0.8518 (m-30) cc_final: 0.8288 (m-30) REVERT: D 126 TYR cc_start: 0.8740 (m-80) cc_final: 0.8266 (m-80) REVERT: E 81 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: E 202 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6744 (pp20) REVERT: E 227 GLN cc_start: 0.8783 (pm20) cc_final: 0.8201 (pm20) REVERT: E 248 LYS cc_start: 0.8768 (pptt) cc_final: 0.8328 (ptpt) REVERT: F 1 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5607 (ppp) REVERT: F 181 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: F 256 MET cc_start: 0.9388 (ptm) cc_final: 0.9156 (ptp) REVERT: F 292 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7945 (pt0) REVERT: F 342 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.8820 (ptm) REVERT: F 369 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8741 (t0) REVERT: F 450 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8244 (tt0) outliers start: 38 outliers final: 12 residues processed: 156 average time/residue: 0.6922 time to fit residues: 118.7003 Evaluate side-chains 149 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 16 ASN 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 199 LYS 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 81 GLU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 222 SER 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 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: 10.0000 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3375 r_free = 0.3375 target = 0.093172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.060591 restraints weight = 33208.429| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.61 r_work: 0.2628 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2211 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= 0.216 Angle : 0.582 9.246 23216 Z= 0.298 Chirality : 0.048 0.171 2685 Planarity : 0.005 0.075 2921 Dihedral : 11.905 175.318 2567 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.35 % Favored : 97.51 % Rotamer: Outliers : 1.72 % Allowed : 10.97 % Favored : 87.31 % 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: -0.28 (0.18), residues: 2129 helix: 0.80 (0.19), residues: 722 sheet: -0.66 (0.23), residues: 442 loop : -0.61 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 108 TYR 0.022 0.002 TYR F 297 PHE 0.016 0.001 PHE C 272 TRP 0.010 0.001 TRP F 325 HIS 0.007 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00522 (17114) covalent geometry : angle 0.58188 (23216) hydrogen bonds : bond 0.04069 ( 635) hydrogen bonds : angle 4.85751 ( 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 158 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.662 Fit side-chains REVERT: A 126 TYR cc_start: 0.8689 (m-80) cc_final: 0.8219 (m-80) REVERT: B 1 MET cc_start: 0.6994 (ttt) cc_final: 0.6639 (ttm) REVERT: B 26 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7367 (mt) REVERT: B 199 LYS cc_start: 0.5845 (OUTLIER) cc_final: 0.5418 (mmmt) REVERT: B 227 GLN cc_start: 0.8753 (pm20) cc_final: 0.8435 (pm20) REVERT: B 248 LYS cc_start: 0.8793 (pptt) cc_final: 0.8400 (ptmt) REVERT: B 252 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8722 (pptt) REVERT: C 222 MET cc_start: 0.8581 (mtp) cc_final: 0.8278 (ptp) REVERT: C 292 GLN cc_start: 0.8275 (tt0) cc_final: 0.8010 (tt0) REVERT: C 322 ASP cc_start: 0.8467 (m-30) cc_final: 0.8259 (m-30) REVERT: C 450 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: D 126 TYR cc_start: 0.8748 (m-80) cc_final: 0.8230 (m-80) REVERT: E 202 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6788 (tm-30) REVERT: E 209 LYS cc_start: 0.8952 (mmpt) cc_final: 0.8657 (mmmt) REVERT: E 248 LYS cc_start: 0.8767 (pptt) cc_final: 0.8334 (ptpt) REVERT: F 1 MET cc_start: 0.5979 (OUTLIER) cc_final: 0.5691 (ppp) REVERT: F 94 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8649 (tm-30) REVERT: F 181 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8553 (mp0) REVERT: F 369 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8728 (t0) REVERT: F 394 GLN cc_start: 0.8656 (tp40) cc_final: 0.8363 (tp-100) REVERT: F 450 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8304 (tt0) outliers start: 31 outliers final: 12 residues processed: 147 average time/residue: 0.7234 time to fit residues: 116.6173 Evaluate side-chains 142 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 B residue 199 LYS 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 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 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: 0.8980 chunk 102 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 353 GLN D 353 GLN E 66 GLN 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 = 0.3404 r_free = 0.3404 target = 0.095036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.062148 restraints weight = 37378.877| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.77 r_work: 0.2654 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17114 Z= 0.124 Angle : 0.526 9.877 23216 Z= 0.269 Chirality : 0.045 0.172 2685 Planarity : 0.004 0.075 2921 Dihedral : 11.424 174.674 2566 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.40 % Favored : 97.46 % Rotamer: Outliers : 1.83 % Allowed : 11.02 % Favored : 87.15 % 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: -0.03 (0.18), residues: 2129 helix: 1.08 (0.20), residues: 724 sheet: -0.55 (0.23), residues: 452 loop : -0.50 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 108 TYR 0.017 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 covalent geometry : bond 0.00291 (17114) covalent geometry : angle 0.52611 (23216) hydrogen bonds : bond 0.03319 ( 635) hydrogen bonds : angle 4.67278 ( 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 166 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.676 Fit side-chains REVERT: A 126 TYR cc_start: 0.8614 (m-80) cc_final: 0.8103 (m-80) REVERT: B 1 MET cc_start: 0.6795 (ttt) cc_final: 0.6552 (ttm) REVERT: B 26 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7363 (mt) REVERT: B 81 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: B 227 GLN cc_start: 0.8704 (pm20) cc_final: 0.8200 (pm20) REVERT: B 248 LYS cc_start: 0.8764 (pptt) cc_final: 0.8379 (ptmt) REVERT: B 252 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8672 (pptt) REVERT: C 222 MET cc_start: 0.8561 (mtp) cc_final: 0.8241 (ptp) REVERT: C 292 GLN cc_start: 0.8195 (tt0) cc_final: 0.7946 (tt0) REVERT: C 322 ASP cc_start: 0.8397 (m-30) cc_final: 0.8098 (t70) REVERT: C 342 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8675 (ptm) REVERT: C 450 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: D 126 TYR cc_start: 0.8671 (m-80) cc_final: 0.8157 (m-80) REVERT: E 202 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6776 (pp20) REVERT: E 209 LYS cc_start: 0.8929 (mmpt) cc_final: 0.8639 (mmmt) REVERT: E 227 GLN cc_start: 0.8737 (pm20) cc_final: 0.8161 (pm20) REVERT: E 248 LYS cc_start: 0.8742 (pptt) cc_final: 0.8316 (ptmt) REVERT: F 1 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5637 (ppp) REVERT: F 155 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8619 (mtt) REVERT: F 181 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8473 (mp0) REVERT: F 342 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.8649 (ptm) REVERT: F 369 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8748 (t0) REVERT: F 450 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8171 (tt0) outliers start: 33 outliers final: 11 residues processed: 155 average time/residue: 0.7276 time to fit residues: 123.3905 Evaluate side-chains 149 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 155 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: 5.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 194 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 52 optimal weight: 0.0020 overall best weight: 1.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 211 ASN D 353 GLN D 371 ASN E 66 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 = 0.3383 r_free = 0.3383 target = 0.093721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.061209 restraints weight = 30163.999| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.51 r_work: 0.2642 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- 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 = 0.41 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17114 Z= 0.177 Angle : 0.560 9.404 23216 Z= 0.286 Chirality : 0.047 0.170 2685 Planarity : 0.004 0.076 2921 Dihedral : 11.429 174.067 2562 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.45 % Favored : 97.41 % Rotamer: Outliers : 1.66 % Allowed : 11.19 % Favored : 87.15 % 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: 0.09 (0.18), residues: 2129 helix: 1.16 (0.20), residues: 722 sheet: -0.46 (0.24), residues: 438 loop : -0.44 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 108 TYR 0.021 0.001 TYR F 297 PHE 0.013 0.001 PHE C 272 TRP 0.010 0.001 TRP F 325 HIS 0.006 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00427 (17114) covalent geometry : angle 0.55982 (23216) hydrogen bonds : bond 0.03763 ( 635) hydrogen bonds : angle 4.72580 ( 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 159 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.507 Fit side-chains REVERT: A 126 TYR cc_start: 0.8636 (m-80) cc_final: 0.8145 (m-80) REVERT: B 1 MET cc_start: 0.6639 (ttt) cc_final: 0.6424 (ttm) REVERT: B 26 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7394 (mt) REVERT: B 81 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: B 162 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7536 (mmm) REVERT: B 248 LYS cc_start: 0.8785 (pptt) cc_final: 0.8405 (ptmt) REVERT: B 252 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8701 (pptt) REVERT: C 222 MET cc_start: 0.8535 (mtp) cc_final: 0.8180 (ptp) REVERT: C 292 GLN cc_start: 0.8228 (tt0) cc_final: 0.7976 (tt0) REVERT: C 342 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.8676 (ptm) REVERT: C 450 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: E 1 MET cc_start: 0.6268 (ptt) cc_final: 0.5921 (ptt) REVERT: E 202 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6847 (pp20) REVERT: E 209 LYS cc_start: 0.8965 (mmpt) cc_final: 0.8697 (mmmt) REVERT: E 248 LYS cc_start: 0.8794 (pptt) cc_final: 0.8353 (ptmt) REVERT: E 252 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8686 (pptt) REVERT: F 1 MET cc_start: 0.5945 (OUTLIER) cc_final: 0.5673 (ppp) REVERT: F 181 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: F 222 MET cc_start: 0.8626 (mmm) cc_final: 0.8402 (mtp) REVERT: F 342 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8648 (ptm) REVERT: F 369 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8758 (t0) REVERT: F 450 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8266 (tt0) outliers start: 30 outliers final: 11 residues processed: 148 average time/residue: 0.7454 time to fit residues: 121.1358 Evaluate side-chains 145 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 172 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 371 ASN D 353 GLN E 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.060892 restraints weight = 29913.129| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.49 r_work: 0.2639 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2508 r_free = 0.2508 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 = 0.2508 r_free = 0.2508 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17114 Z= 0.194 Angle : 0.565 8.016 23216 Z= 0.290 Chirality : 0.047 0.166 2685 Planarity : 0.004 0.075 2921 Dihedral : 11.605 174.193 2562 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.40 % Favored : 97.46 % Rotamer: Outliers : 1.50 % Allowed : 11.47 % Favored : 87.04 % 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: 0.12 (0.18), residues: 2129 helix: 1.20 (0.20), residues: 722 sheet: -0.46 (0.24), residues: 438 loop : -0.43 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 108 TYR 0.022 0.002 TYR F 297 PHE 0.014 0.001 PHE C 272 TRP 0.009 0.001 TRP F 325 HIS 0.006 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00469 (17114) covalent geometry : angle 0.56528 (23216) hydrogen bonds : bond 0.03846 ( 635) hydrogen bonds : angle 4.75990 ( 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: 27 poor density : 131 time to evaluate : 0.648 Fit side-chains REVERT: A 126 TYR cc_start: 0.8653 (m-80) cc_final: 0.8145 (m-80) REVERT: B 1 MET cc_start: 0.6562 (ttt) cc_final: 0.6327 (ttt) REVERT: B 26 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7394 (mt) REVERT: B 81 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7681 (pm20) REVERT: B 152 ASP cc_start: 0.8338 (t0) cc_final: 0.8052 (t70) REVERT: B 162 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7606 (mmm) REVERT: B 215 ASN cc_start: 0.7745 (t0) cc_final: 0.7542 (t0) REVERT: B 248 LYS cc_start: 0.8807 (pptt) cc_final: 0.8446 (ptmt) REVERT: B 252 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8704 (pptt) REVERT: C 222 MET cc_start: 0.8556 (mtp) cc_final: 0.8189 (ptp) REVERT: C 292 GLN cc_start: 0.8261 (tt0) cc_final: 0.8007 (tt0) REVERT: C 342 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8677 (ptm) REVERT: C 450 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: D 126 TYR cc_start: 0.8633 (m-80) cc_final: 0.8232 (m-80) REVERT: E 1 MET cc_start: 0.6333 (ptt) cc_final: 0.5916 (ptt) REVERT: E 162 MET cc_start: 0.7812 (mpp) cc_final: 0.7558 (mmm) REVERT: E 202 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7005 (pp20) REVERT: E 209 LYS cc_start: 0.8963 (mmpt) cc_final: 0.8715 (mmmt) REVERT: E 248 LYS cc_start: 0.8791 (pptt) cc_final: 0.8386 (ptmt) REVERT: E 252 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8704 (pptt) REVERT: F 1 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5561 (ppp) REVERT: F 94 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8676 (tm-30) REVERT: F 181 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: F 222 MET cc_start: 0.8686 (mmm) cc_final: 0.8204 (mtm) REVERT: F 342 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.8639 (ptm) REVERT: F 366 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8182 (ttmt) REVERT: F 369 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8749 (t0) REVERT: F 450 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8276 (tt0) outliers start: 27 outliers final: 9 residues processed: 147 average time/residue: 0.7253 time to fit residues: 116.9124 Evaluate side-chains 148 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 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 94 GLU 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 366 LYS Chi-restraints excluded: chain F residue 369 ASP 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: 0.9980 chunk 74 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3403 r_free = 0.3403 target = 0.094963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.061977 restraints weight = 38688.982| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.81 r_work: 0.2652 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 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 = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17114 Z= 0.128 Angle : 0.529 8.075 23216 Z= 0.270 Chirality : 0.045 0.169 2685 Planarity : 0.004 0.073 2921 Dihedral : 11.289 174.688 2562 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.68 % Favored : 97.18 % Rotamer: Outliers : 1.22 % Allowed : 11.80 % Favored : 86.98 % 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: 0.23 (0.19), residues: 2129 helix: 1.33 (0.20), residues: 724 sheet: -0.43 (0.24), residues: 448 loop : -0.36 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 108 TYR 0.017 0.001 TYR C 297 PHE 0.012 0.001 PHE F 255 TRP 0.010 0.001 TRP F 325 HIS 0.004 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00306 (17114) covalent geometry : angle 0.52856 (23216) hydrogen bonds : bond 0.03316 ( 635) hydrogen bonds : angle 4.61567 ( 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 160 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.697 Fit side-chains REVERT: A 126 TYR cc_start: 0.8613 (m-80) cc_final: 0.8090 (m-80) REVERT: B 18 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: B 26 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7362 (mt) REVERT: B 62 MET cc_start: 0.8239 (ttp) cc_final: 0.7988 (ttt) REVERT: B 152 ASP cc_start: 0.8275 (t0) cc_final: 0.8005 (t70) REVERT: B 209 LYS cc_start: 0.8924 (mmpt) cc_final: 0.8653 (mmmt) REVERT: B 215 ASN cc_start: 0.7697 (t0) cc_final: 0.7488 (t0) REVERT: B 248 LYS cc_start: 0.8791 (pptt) cc_final: 0.8435 (ptmt) REVERT: B 252 LYS cc_start: 0.8916 (ttmm) cc_final: 0.8696 (pptt) REVERT: C 222 MET cc_start: 0.8565 (mtp) cc_final: 0.8231 (ptp) REVERT: C 292 GLN cc_start: 0.8194 (tt0) cc_final: 0.7956 (tt0) REVERT: C 342 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.8712 (ptm) REVERT: C 450 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: D 126 TYR cc_start: 0.8575 (m-80) cc_final: 0.8159 (m-80) REVERT: E 1 MET cc_start: 0.6246 (ptt) cc_final: 0.5855 (ptt) REVERT: E 108 ARG cc_start: 0.8692 (tpt90) cc_final: 0.8241 (tpp-160) REVERT: E 162 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7452 (mmm) REVERT: E 202 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7082 (pp20) REVERT: E 209 LYS cc_start: 0.8958 (mmpt) cc_final: 0.8699 (mmmt) REVERT: E 248 LYS cc_start: 0.8771 (pptt) cc_final: 0.8371 (ptmt) REVERT: E 252 LYS cc_start: 0.8901 (ttmm) cc_final: 0.8686 (pptt) REVERT: F 1 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.5450 (ppp) REVERT: F 181 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8495 (mp0) REVERT: F 342 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.8642 (ptm) REVERT: F 369 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8730 (t0) REVERT: F 450 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8199 (tt0) outliers start: 22 outliers final: 9 residues processed: 150 average time/residue: 0.6951 time to fit residues: 114.5197 Evaluate side-chains 151 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 18 GLU 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 162 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 129 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 157 optimal weight: 0.2980 chunk 159 optimal weight: 0.4980 chunk 173 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3399 r_free = 0.3399 target = 0.094754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.062192 restraints weight = 32695.952| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.59 r_work: 0.2662 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 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 = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17114 Z= 0.139 Angle : 0.547 12.917 23216 Z= 0.277 Chirality : 0.046 0.166 2685 Planarity : 0.004 0.073 2921 Dihedral : 11.098 174.618 2562 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.68 % Favored : 97.18 % Rotamer: Outliers : 1.27 % Allowed : 12.13 % Favored : 86.59 % 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: 0.30 (0.19), residues: 2129 helix: 1.38 (0.20), residues: 724 sheet: -0.36 (0.24), residues: 444 loop : -0.34 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 108 TYR 0.018 0.001 TYR F 297 PHE 0.011 0.001 PHE F 255 TRP 0.010 0.001 TRP F 325 HIS 0.003 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00333 (17114) covalent geometry : angle 0.54673 (23216) hydrogen bonds : bond 0.03383 ( 635) hydrogen bonds : angle 4.59605 ( 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 156 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.658 Fit side-chains REVERT: A 126 TYR cc_start: 0.8630 (m-80) cc_final: 0.8115 (m-80) REVERT: B 18 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: B 26 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7442 (mt) REVERT: B 152 ASP cc_start: 0.8122 (t0) cc_final: 0.7824 (t70) REVERT: B 209 LYS cc_start: 0.8918 (mmpt) cc_final: 0.8655 (mmmt) REVERT: B 215 ASN cc_start: 0.7682 (t0) cc_final: 0.7471 (t0) REVERT: B 248 LYS cc_start: 0.8792 (pptt) cc_final: 0.8415 (ptmt) REVERT: B 252 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8701 (pptt) REVERT: C 222 MET cc_start: 0.8515 (mtp) cc_final: 0.8209 (ptp) REVERT: C 292 GLN cc_start: 0.8197 (tt0) cc_final: 0.7962 (tt0) REVERT: C 450 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: C 466 MET cc_start: 0.7241 (ttt) cc_final: 0.7019 (tmm) REVERT: D 126 TYR cc_start: 0.8575 (m-80) cc_final: 0.8161 (m-80) REVERT: E 1 MET cc_start: 0.6259 (ptt) cc_final: 0.5877 (ptt) REVERT: E 108 ARG cc_start: 0.8669 (tpt90) cc_final: 0.8205 (tpp80) REVERT: E 152 ASP cc_start: 0.8214 (t0) cc_final: 0.7918 (t70) REVERT: E 202 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7098 (pp20) REVERT: E 209 LYS cc_start: 0.8970 (mmpt) cc_final: 0.8724 (mmmt) REVERT: E 248 LYS cc_start: 0.8771 (pptt) cc_final: 0.8386 (ptmt) REVERT: E 252 LYS cc_start: 0.8904 (ttmm) cc_final: 0.8690 (pptt) REVERT: F 1 MET cc_start: 0.5934 (OUTLIER) cc_final: 0.5541 (ppp) REVERT: F 181 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: F 342 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8638 (ptm) REVERT: F 369 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8702 (t0) REVERT: F 450 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8209 (tt0) outliers start: 23 outliers final: 10 residues processed: 147 average time/residue: 0.7333 time to fit residues: 118.0906 Evaluate side-chains 148 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 18 GLU 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 81 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 19 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 116 optimal weight: 0.1980 chunk 69 optimal weight: 0.0570 chunk 60 optimal weight: 0.2980 overall best weight: 0.4700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3441 r_free = 0.3441 target = 0.097265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.065162 restraints weight = 33138.362| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.62 r_work: 0.2727 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17114 Z= 0.097 Angle : 0.506 11.754 23216 Z= 0.257 Chirality : 0.044 0.169 2685 Planarity : 0.004 0.073 2921 Dihedral : 10.499 172.730 2562 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.92 % Favored : 96.94 % Rotamer: Outliers : 1.00 % Allowed : 12.35 % Favored : 86.65 % 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: 0.46 (0.19), residues: 2129 helix: 1.55 (0.20), residues: 724 sheet: -0.30 (0.24), residues: 444 loop : -0.27 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 108 TYR 0.014 0.001 TYR C 297 PHE 0.012 0.001 PHE F 255 TRP 0.012 0.001 TRP F 325 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00221 (17114) covalent geometry : angle 0.50591 (23216) hydrogen bonds : bond 0.02807 ( 635) hydrogen bonds : angle 4.40897 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7986.92 seconds wall clock time: 136 minutes 13.08 seconds (8173.08 seconds total)