Starting phenix.real_space_refine on Sun Jun 15 05:33:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qh2_13960/06_2025/7qh2_13960.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qh2_13960/06_2025/7qh2_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_13960/06_2025/7qh2_13960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qh2_13960/06_2025/7qh2_13960.map" model { file = "/net/cci-nas-00/data/ceres_data/7qh2_13960/06_2025/7qh2_13960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qh2_13960/06_2025/7qh2_13960.cif" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.13, per 1000 atoms: 0.72 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: 4.87 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 2.44 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: 6.04 Time building geometry restraints manager: 5.33 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 467 or resid 501 through \ 502)) selection = (chain 'F' and (resid 1 through 41 or resid 43 through 467 or resid 501 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 44.000 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.860 ------------------------------------------------------------------------------- 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 : 6.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.002 TRP F 397 HIS 0.007 0.001 HIS C 441 PHE 0.016 0.002 PHE C 272 TYR 0.029 0.001 TYR C 297 ARG 0.009 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.28337 ( 635) hydrogen bonds : angle 9.94344 ( 1782) covalent geometry : bond 0.00750 (17114) covalent geometry : angle 1.00837 (23216) *********************** 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 : 1.982 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: 1.5366 time to fit residues: 389.1302 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 : 1.786 ------------------------------------------------------------------------------- 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 177 optimal weight: 0.9980 chunk 159 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 107 optimal weight: 0.0470 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.096792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.064850 restraints weight = 30745.542| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.51 r_work: 0.2727 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1641 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= 0.124 Angle : 0.577 8.461 23216 Z= 0.303 Chirality : 0.046 0.291 2685 Planarity : 0.006 0.073 2921 Dihedral : 13.953 179.492 2616 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.12 % Favored : 97.65 % Rotamer: Outliers : 1.94 % Allowed : 8.64 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.16), residues: 2129 helix: -1.74 (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 TRP 0.009 0.001 TRP C 325 HIS 0.007 0.001 HIS C 441 PHE 0.010 0.001 PHE F 272 TYR 0.022 0.001 TYR C 297 ARG 0.012 0.000 ARG D 238 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 635) hydrogen bonds : angle 5.48434 ( 1782) covalent geometry : bond 0.00268 (17114) covalent geometry : angle 0.57676 (23216) *********************** 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: 35 poor density : 143 time to evaluate : 1.959 Fit side-chains REVERT: B 227 GLN cc_start: 0.8795 (pm20) cc_final: 0.8528 (pm20) REVERT: B 248 LYS cc_start: 0.8721 (pptt) cc_final: 0.8235 (ptpt) REVERT: C 1 MET cc_start: 0.6351 (ptp) cc_final: 0.6120 (ptp) REVERT: C 222 MET cc_start: 0.8520 (mtp) cc_final: 0.8092 (ptp) REVERT: C 258 ARG cc_start: 0.8690 (ttt-90) cc_final: 0.8259 (tpp80) REVERT: C 292 GLN cc_start: 0.8368 (tt0) cc_final: 0.8111 (tt0) REVERT: C 322 ASP cc_start: 0.8367 (m-30) cc_final: 0.8091 (m-30) REVERT: C 342 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8982 (ptm) REVERT: D 126 TYR cc_start: 0.8743 (m-80) cc_final: 0.8253 (m-80) REVERT: D 242 PRO cc_start: 0.8943 (Cg_endo) cc_final: 0.8729 (Cg_exo) REVERT: E 1 MET cc_start: 0.6728 (ttp) cc_final: 0.6344 (ttm) REVERT: E 202 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6779 (tm-30) REVERT: E 248 LYS cc_start: 0.8650 (pptt) cc_final: 0.8246 (ptpt) REVERT: F 94 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8586 (tm-30) REVERT: F 181 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8484 (mp0) REVERT: F 222 MET cc_start: 0.8643 (mmm) cc_final: 0.7701 (mpp) REVERT: F 256 MET cc_start: 0.9381 (ptm) cc_final: 0.9115 (ptp) REVERT: F 342 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8920 (ptm) REVERT: F 369 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8666 (t0) REVERT: F 450 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8350 (tt0) outliers start: 35 outliers final: 14 residues processed: 165 average time/residue: 1.5479 time to fit residues: 282.3712 Evaluate side-chains 149 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 146 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 94 GLU 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 105 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 111 optimal weight: 0.0020 chunk 30 optimal weight: 0.0970 chunk 162 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 0.0570 chunk 184 optimal weight: 5.9990 overall best weight: 1.8308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 115 ASN D 353 GLN F 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.061746 restraints weight = 29840.618| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.47 r_work: 0.2656 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17114 Z= 0.193 Angle : 0.586 8.108 23216 Z= 0.303 Chirality : 0.047 0.190 2685 Planarity : 0.005 0.074 2921 Dihedral : 12.383 179.704 2572 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.26 % Favored : 97.60 % Rotamer: Outliers : 1.39 % Allowed : 9.86 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2129 helix: -0.26 (0.18), residues: 722 sheet: -0.85 (0.23), residues: 436 loop : -0.90 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 325 HIS 0.007 0.001 HIS C 441 PHE 0.020 0.001 PHE C 272 TYR 0.023 0.002 TYR F 297 ARG 0.007 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 635) hydrogen bonds : angle 5.06118 ( 1782) covalent geometry : bond 0.00461 (17114) covalent geometry : angle 0.58559 (23216) *********************** 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 158 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.792 Fit side-chains REVERT: A 126 TYR cc_start: 0.8695 (m-80) cc_final: 0.8235 (m-80) REVERT: B 1 MET cc_start: 0.7203 (ttt) cc_final: 0.6897 (ttm) REVERT: B 248 LYS cc_start: 0.8764 (pptt) cc_final: 0.8317 (ptpt) REVERT: C 292 GLN cc_start: 0.8317 (tt0) cc_final: 0.8031 (tt0) REVERT: C 322 ASP cc_start: 0.8504 (m-30) cc_final: 0.8267 (m-30) REVERT: D 84 GLN cc_start: 0.8343 (tp40) cc_final: 0.8094 (mm-40) REVERT: D 126 TYR cc_start: 0.8755 (m-80) cc_final: 0.8249 (m-80) REVERT: E 202 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6690 (pp20) REVERT: E 248 LYS cc_start: 0.8737 (pptt) cc_final: 0.8280 (ptpt) REVERT: F 1 MET cc_start: 0.5910 (ppp) cc_final: 0.5705 (ppp) REVERT: F 181 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8540 (mp0) REVERT: F 256 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.9177 (ptp) REVERT: F 369 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8736 (t0) REVERT: F 450 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8266 (tt0) outliers start: 25 outliers final: 12 residues processed: 147 average time/residue: 1.5196 time to fit residues: 246.4858 Evaluate side-chains 140 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 182 optimal weight: 3.9990 chunk 161 optimal weight: 0.0870 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 86 optimal weight: 0.2980 chunk 193 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 B 141 HIS D 353 GLN E 16 ASN E 141 HIS F 292 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.095653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.065139 restraints weight = 28831.471| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.33 r_work: 0.2724 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17114 Z= 0.110 Angle : 0.521 8.326 23216 Z= 0.267 Chirality : 0.045 0.178 2685 Planarity : 0.004 0.074 2921 Dihedral : 11.395 176.190 2568 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.12 % Favored : 97.74 % Rotamer: Outliers : 1.72 % Allowed : 10.58 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2129 helix: 0.61 (0.19), residues: 720 sheet: -0.68 (0.23), residues: 446 loop : -0.66 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 325 HIS 0.004 0.001 HIS C 441 PHE 0.011 0.001 PHE F 255 TYR 0.015 0.001 TYR C 297 ARG 0.007 0.000 ARG C 258 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 635) hydrogen bonds : angle 4.72109 ( 1782) covalent geometry : bond 0.00250 (17114) covalent geometry : angle 0.52132 (23216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.721 Fit side-chains REVERT: A 126 TYR cc_start: 0.8657 (m-80) cc_final: 0.8191 (m-80) REVERT: B 1 MET cc_start: 0.7210 (ttt) cc_final: 0.6842 (ttm) REVERT: B 26 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7443 (mt) REVERT: B 81 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: B 227 GLN cc_start: 0.8757 (pm20) cc_final: 0.8222 (pm20) REVERT: B 248 LYS cc_start: 0.8787 (pptt) cc_final: 0.8405 (ptmt) REVERT: C 292 GLN cc_start: 0.8335 (tt0) cc_final: 0.8080 (tt0) REVERT: C 322 ASP cc_start: 0.8465 (m-30) cc_final: 0.8237 (m-30) REVERT: D 84 GLN cc_start: 0.8380 (tp40) cc_final: 0.8158 (mm-40) REVERT: D 126 TYR cc_start: 0.8724 (m-80) cc_final: 0.8230 (m-80) REVERT: E 108 ARG cc_start: 0.8699 (tpt90) cc_final: 0.8227 (tpp-160) REVERT: E 202 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6741 (pp20) REVERT: E 248 LYS cc_start: 0.8780 (pptt) cc_final: 0.8368 (ptpt) REVERT: F 1 MET cc_start: 0.5947 (OUTLIER) cc_final: 0.5561 (ppp) REVERT: F 155 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8581 (mtt) REVERT: F 181 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8483 (mp0) REVERT: F 256 MET cc_start: 0.9386 (ptm) cc_final: 0.9159 (ptp) REVERT: F 292 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.8013 (pt0) REVERT: F 342 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.8817 (ptm) REVERT: F 369 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8650 (t0) REVERT: F 450 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8182 (tt0) outliers start: 31 outliers final: 9 residues processed: 158 average time/residue: 1.8810 time to fit residues: 326.3304 Evaluate side-chains 146 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 81 GLU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 126 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.092661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.060542 restraints weight = 45232.918| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.89 r_work: 0.2612 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 0.075 17114 Z= 0.211 Angle : 0.578 8.612 23216 Z= 0.295 Chirality : 0.048 0.174 2685 Planarity : 0.005 0.075 2921 Dihedral : 11.534 176.079 2562 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.35 % Favored : 97.51 % Rotamer: Outliers : 1.88 % Allowed : 10.91 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2129 helix: 0.86 (0.19), residues: 722 sheet: -0.63 (0.23), residues: 442 loop : -0.59 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 325 HIS 0.007 0.001 HIS C 441 PHE 0.018 0.001 PHE C 272 TYR 0.023 0.002 TYR F 297 ARG 0.004 0.000 ARG C 258 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 635) hydrogen bonds : angle 4.82609 ( 1782) covalent geometry : bond 0.00509 (17114) covalent geometry : angle 0.57782 (23216) *********************** 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 163 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.929 Fit side-chains revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8690 (m-80) cc_final: 0.8238 (m-80) REVERT: B 1 MET cc_start: 0.7019 (ttt) cc_final: 0.6654 (ttm) REVERT: B 26 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7373 (mt) REVERT: B 248 LYS cc_start: 0.8776 (pptt) cc_final: 0.8381 (ptmt) REVERT: B 252 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8721 (pptt) REVERT: C 181 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8597 (mp0) REVERT: C 292 GLN cc_start: 0.8352 (tt0) cc_final: 0.8102 (tt0) REVERT: C 322 ASP cc_start: 0.8513 (m-30) cc_final: 0.8189 (t70) REVERT: C 450 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: D 126 TYR cc_start: 0.8742 (m-80) cc_final: 0.8211 (m-80) REVERT: E 202 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6825 (pp20) REVERT: E 248 LYS cc_start: 0.8796 (pptt) cc_final: 0.8344 (ptpt) REVERT: E 252 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8638 (pptt) REVERT: F 1 MET cc_start: 0.5920 (OUTLIER) cc_final: 0.5567 (ppp) REVERT: F 181 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8576 (mp0) REVERT: F 369 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8796 (t0) REVERT: F 450 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8393 (tt0) outliers start: 34 outliers final: 14 residues processed: 150 average time/residue: 1.5400 time to fit residues: 254.0868 Evaluate side-chains 142 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 264 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 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 190 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 111 optimal weight: 0.0980 chunk 195 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 F 292 GLN F 394 GLN F 456 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.062959 restraints weight = 39868.727| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.85 r_work: 0.2672 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 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 = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17114 Z= 0.110 Angle : 0.513 9.913 23216 Z= 0.262 Chirality : 0.045 0.174 2685 Planarity : 0.004 0.074 2921 Dihedral : 11.024 174.945 2562 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.16 % Favored : 97.70 % Rotamer: Outliers : 2.11 % Allowed : 10.80 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2129 helix: 1.15 (0.20), residues: 724 sheet: -0.53 (0.23), residues: 452 loop : -0.47 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 325 HIS 0.004 0.001 HIS C 441 PHE 0.011 0.001 PHE F 255 TYR 0.016 0.001 TYR C 297 ARG 0.004 0.000 ARG C 258 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 635) hydrogen bonds : angle 4.60692 ( 1782) covalent geometry : bond 0.00253 (17114) covalent geometry : angle 0.51324 (23216) *********************** 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 173 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 1.892 Fit side-chains REVERT: A 126 TYR cc_start: 0.8605 (m-80) cc_final: 0.8105 (m-80) REVERT: B 1 MET cc_start: 0.6796 (ttt) cc_final: 0.6509 (ttm) REVERT: B 26 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7384 (mt) REVERT: B 152 ASP cc_start: 0.8159 (t0) cc_final: 0.7797 (t70) REVERT: B 227 GLN cc_start: 0.8663 (pm20) cc_final: 0.8146 (pm20) REVERT: B 248 LYS cc_start: 0.8743 (pptt) cc_final: 0.8367 (ptmt) REVERT: B 252 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8673 (pptt) REVERT: C 292 GLN cc_start: 0.8227 (tt0) cc_final: 0.7998 (tt0) REVERT: C 322 ASP cc_start: 0.8397 (m-30) cc_final: 0.8056 (t70) REVERT: C 342 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8703 (ptm) REVERT: C 450 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: E 202 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6815 (pp20) REVERT: E 209 LYS cc_start: 0.8916 (mmpt) cc_final: 0.8621 (mmmt) REVERT: E 248 LYS cc_start: 0.8777 (pptt) cc_final: 0.8339 (ptmt) REVERT: E 252 LYS cc_start: 0.8870 (ttmm) cc_final: 0.8643 (pptt) REVERT: F 1 MET cc_start: 0.5844 (OUTLIER) cc_final: 0.5420 (ppp) REVERT: F 120 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8534 (ptm) REVERT: F 181 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8471 (mp0) REVERT: F 222 MET cc_start: 0.8647 (mmm) cc_final: 0.8134 (mtm) REVERT: F 342 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.8660 (ptm) REVERT: F 369 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8689 (t0) REVERT: F 450 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8156 (tt0) outliers start: 38 outliers final: 13 residues processed: 158 average time/residue: 1.5347 time to fit residues: 267.0976 Evaluate side-chains 150 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.974 ------------------------------------------------------------------------------- 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 146 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 155 MET 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 222 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 120 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 93 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 74 optimal weight: 0.1980 chunk 193 optimal weight: 4.9990 chunk 192 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 211 ASN D 353 GLN E 66 GLN F 292 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.094325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.062130 restraints weight = 27226.892| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.38 r_work: 0.2666 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17114 Z= 0.167 Angle : 0.553 10.511 23216 Z= 0.281 Chirality : 0.046 0.170 2685 Planarity : 0.004 0.076 2921 Dihedral : 11.092 175.052 2562 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.54 % Favored : 97.32 % Rotamer: Outliers : 1.66 % Allowed : 11.47 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.19), residues: 2129 helix: 1.21 (0.20), residues: 724 sheet: -0.51 (0.24), residues: 452 loop : -0.43 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 325 HIS 0.005 0.001 HIS C 441 PHE 0.013 0.001 PHE C 272 TYR 0.020 0.001 TYR F 297 ARG 0.004 0.000 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 635) hydrogen bonds : angle 4.67583 ( 1782) covalent geometry : bond 0.00403 (17114) covalent geometry : angle 0.55320 (23216) *********************** 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 161 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 2.048 Fit side-chains revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8635 (m-80) cc_final: 0.8154 (m-80) REVERT: B 1 MET cc_start: 0.6693 (ttt) cc_final: 0.6429 (ttm) REVERT: B 26 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7412 (mt) REVERT: B 152 ASP cc_start: 0.8356 (t0) cc_final: 0.8052 (t70) REVERT: B 227 GLN cc_start: 0.8721 (pm20) cc_final: 0.8163 (pm20) REVERT: B 248 LYS cc_start: 0.8767 (pptt) cc_final: 0.8385 (ptmt) REVERT: B 252 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8702 (pptt) REVERT: C 322 ASP cc_start: 0.8391 (m-30) cc_final: 0.8143 (t70) REVERT: C 342 MET cc_start: 0.9398 (OUTLIER) cc_final: 0.8664 (ptm) REVERT: C 450 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: D 126 TYR cc_start: 0.8639 (m-80) cc_final: 0.8281 (m-80) REVERT: E 1 MET cc_start: 0.6238 (ptt) cc_final: 0.5970 (ptt) REVERT: E 202 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6813 (pp20) REVERT: E 209 LYS cc_start: 0.8977 (mmpt) cc_final: 0.8721 (mmmt) REVERT: E 248 LYS cc_start: 0.8781 (pptt) cc_final: 0.8362 (ptmt) REVERT: E 252 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8675 (pptt) REVERT: F 1 MET cc_start: 0.5933 (OUTLIER) cc_final: 0.5600 (ppp) REVERT: F 181 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: F 342 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8633 (ptm) REVERT: F 369 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8723 (t0) REVERT: F 450 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8250 (tt0) outliers start: 30 outliers final: 12 residues processed: 152 average time/residue: 1.5227 time to fit residues: 255.0919 Evaluate side-chains 147 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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 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 222 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 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 30 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 142 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN C 292 GLN 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 = 0.3408 r_free = 0.3408 target = 0.095212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.062296 restraints weight = 40938.546| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.85 r_work: 0.2658 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17114 Z= 0.123 Angle : 0.525 7.842 23216 Z= 0.268 Chirality : 0.045 0.261 2685 Planarity : 0.004 0.075 2921 Dihedral : 10.883 174.887 2562 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.49 % Favored : 97.37 % Rotamer: Outliers : 1.66 % Allowed : 11.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 2129 helix: 1.35 (0.20), residues: 724 sheet: -0.44 (0.24), residues: 448 loop : -0.37 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 325 HIS 0.004 0.001 HIS C 441 PHE 0.010 0.001 PHE F 255 TYR 0.016 0.001 TYR F 297 ARG 0.003 0.000 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 635) hydrogen bonds : angle 4.58586 ( 1782) covalent geometry : bond 0.00290 (17114) covalent geometry : angle 0.52494 (23216) *********************** 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 165 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8601 (m-80) cc_final: 0.8103 (m-80) REVERT: B 1 MET cc_start: 0.6650 (ttt) cc_final: 0.6376 (ttm) REVERT: B 26 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7364 (mt) REVERT: B 62 MET cc_start: 0.8269 (ttp) cc_final: 0.8050 (ttt) REVERT: B 152 ASP cc_start: 0.8234 (t0) cc_final: 0.7928 (t70) REVERT: B 162 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7526 (mmm) REVERT: B 227 GLN cc_start: 0.8679 (pm20) cc_final: 0.8131 (pm20) REVERT: B 248 LYS cc_start: 0.8746 (pptt) cc_final: 0.8380 (ptmt) REVERT: B 252 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8684 (pptt) REVERT: C 322 ASP cc_start: 0.8367 (m-30) cc_final: 0.8112 (t70) REVERT: C 342 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.8697 (ptm) REVERT: C 450 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: D 126 TYR cc_start: 0.8605 (m-80) cc_final: 0.8239 (m-80) REVERT: E 1 MET cc_start: 0.6183 (ptt) cc_final: 0.5828 (ptt) REVERT: E 62 MET cc_start: 0.8262 (ttp) cc_final: 0.8035 (ttt) REVERT: E 152 ASP cc_start: 0.8067 (t0) cc_final: 0.7681 (t70) REVERT: E 202 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6838 (pp20) REVERT: E 209 LYS cc_start: 0.8957 (mmpt) cc_final: 0.8702 (mmmt) REVERT: E 248 LYS cc_start: 0.8780 (pptt) cc_final: 0.8378 (ptmt) REVERT: E 252 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8649 (pptt) REVERT: F 1 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.5488 (ppp) REVERT: F 181 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: F 342 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.8642 (ptm) REVERT: F 369 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8725 (t0) REVERT: F 450 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8198 (tt0) outliers start: 30 outliers final: 10 residues processed: 152 average time/residue: 1.4442 time to fit residues: 242.5434 Evaluate side-chains 148 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 146 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 D 371 ASN E 66 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 = 0.3349 r_free = 0.3349 target = 0.091562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.058292 restraints weight = 41235.744| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.86 r_work: 0.2572 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.118 17114 Z= 0.341 Angle : 0.671 8.991 23216 Z= 0.340 Chirality : 0.052 0.173 2685 Planarity : 0.005 0.075 2921 Dihedral : 11.770 176.639 2562 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.87 % Favored : 96.99 % Rotamer: Outliers : 1.50 % Allowed : 11.80 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2129 helix: 0.99 (0.19), residues: 728 sheet: -0.44 (0.24), residues: 438 loop : -0.46 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 397 HIS 0.009 0.002 HIS C 441 PHE 0.023 0.002 PHE C 272 TYR 0.028 0.002 TYR F 297 ARG 0.005 0.001 ARG E 230 Details of bonding type rmsd hydrogen bonds : bond 0.04679 ( 635) hydrogen bonds : angle 4.97042 ( 1782) covalent geometry : bond 0.00833 (17114) covalent geometry : angle 0.67102 (23216) *********************** 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 152 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 2.031 Fit side-chains REVERT: A 126 TYR cc_start: 0.8706 (m-80) cc_final: 0.8245 (m-80) REVERT: B 1 MET cc_start: 0.6665 (ttt) cc_final: 0.6331 (ttm) REVERT: B 162 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7535 (mmm) REVERT: B 215 ASN cc_start: 0.7758 (t0) cc_final: 0.7511 (t0) REVERT: B 248 LYS cc_start: 0.8817 (pptt) cc_final: 0.8457 (ptmt) REVERT: B 252 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8709 (pptt) REVERT: C 342 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.8677 (ptm) REVERT: C 450 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: D 126 TYR cc_start: 0.8677 (m-80) cc_final: 0.8235 (m-80) REVERT: E 1 MET cc_start: 0.6267 (ptt) cc_final: 0.5923 (ptt) REVERT: E 162 MET cc_start: 0.7765 (mpp) cc_final: 0.7535 (mmm) REVERT: E 202 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6949 (pp20) REVERT: E 209 LYS cc_start: 0.8969 (mmpt) cc_final: 0.8719 (mmmt) REVERT: E 248 LYS cc_start: 0.8803 (pptt) cc_final: 0.8409 (ptmt) REVERT: E 252 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8690 (pptt) REVERT: F 1 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5716 (ppp) REVERT: F 94 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8702 (tm-30) REVERT: F 181 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8613 (mp0) REVERT: F 342 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.8616 (ptm) REVERT: F 366 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8228 (ttmt) REVERT: F 369 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8820 (t0) REVERT: F 450 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8346 (tt0) outliers start: 27 outliers final: 12 residues processed: 141 average time/residue: 1.6484 time to fit residues: 255.5631 Evaluate side-chains 146 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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 28 ARG Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 223 THR 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 222 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 292 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 108 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 161 optimal weight: 0.0060 chunk 131 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 292 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 = 0.3406 r_free = 0.3406 target = 0.095117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.062920 restraints weight = 34939.962| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.65 r_work: 0.2675 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 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 = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17114 Z= 0.113 Angle : 0.539 13.123 23216 Z= 0.275 Chirality : 0.045 0.170 2685 Planarity : 0.004 0.073 2921 Dihedral : 11.363 174.719 2562 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.65 % Rotamer: Outliers : 1.05 % Allowed : 12.24 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 2129 helix: 1.29 (0.20), residues: 724 sheet: -0.51 (0.24), residues: 442 loop : -0.36 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 325 HIS 0.003 0.001 HIS C 441 PHE 0.012 0.001 PHE F 255 TYR 0.016 0.001 TYR C 297 ARG 0.004 0.000 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 635) hydrogen bonds : angle 4.65401 ( 1782) covalent geometry : bond 0.00260 (17114) covalent geometry : angle 0.53923 (23216) ********************** 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 158 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.867 Fit side-chains REVERT: A 126 TYR cc_start: 0.8665 (m-80) cc_final: 0.8161 (m-80) REVERT: B 1 MET cc_start: 0.6594 (ttt) cc_final: 0.6341 (ttt) REVERT: B 108 ARG cc_start: 0.8606 (tpt90) cc_final: 0.8219 (tpp-160) REVERT: B 152 ASP cc_start: 0.8229 (t0) cc_final: 0.7934 (t70) REVERT: B 209 LYS cc_start: 0.8931 (mmpt) cc_final: 0.8690 (mmmt) REVERT: B 215 ASN cc_start: 0.7734 (t0) cc_final: 0.7515 (t0) REVERT: B 227 GLN cc_start: 0.8637 (pm20) cc_final: 0.8138 (pm20) REVERT: B 248 LYS cc_start: 0.8791 (pptt) cc_final: 0.8435 (ptmt) REVERT: B 252 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8711 (pptt) REVERT: C 342 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.8703 (ptm) REVERT: C 450 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: D 126 TYR cc_start: 0.8649 (m-80) cc_final: 0.8191 (m-80) REVERT: E 1 MET cc_start: 0.6270 (ptt) cc_final: 0.5859 (ptt) REVERT: E 108 ARG cc_start: 0.8671 (tpt90) cc_final: 0.8237 (tpp-160) REVERT: E 162 MET cc_start: 0.7795 (mpp) cc_final: 0.7571 (mmm) REVERT: E 202 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7039 (pp20) REVERT: E 209 LYS cc_start: 0.8976 (mmpt) cc_final: 0.8734 (mmmt) REVERT: E 248 LYS cc_start: 0.8802 (pptt) cc_final: 0.8375 (ptmt) REVERT: E 252 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8686 (pptt) REVERT: F 1 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5565 (ppp) REVERT: F 181 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: F 342 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.8633 (ptm) REVERT: F 369 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8740 (t0) REVERT: F 450 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8211 (tt0) outliers start: 19 outliers final: 9 residues processed: 149 average time/residue: 1.4316 time to fit residues: 236.2362 Evaluate side-chains 148 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 2.005 ------------------------------------------------------------------------------- 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 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 222 SER 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 9 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 185 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 34 optimal weight: 0.0270 chunk 3 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 F 292 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.097032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.065030 restraints weight = 32631.697| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.59 r_work: 0.2721 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17114 Z= 0.098 Angle : 0.508 8.725 23216 Z= 0.258 Chirality : 0.044 0.169 2685 Planarity : 0.004 0.073 2921 Dihedral : 10.595 171.474 2562 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.92 % Favored : 96.94 % Rotamer: Outliers : 1.00 % Allowed : 12.58 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 2129 helix: 1.53 (0.20), residues: 724 sheet: -0.41 (0.24), residues: 448 loop : -0.28 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 325 HIS 0.002 0.001 HIS F 441 PHE 0.012 0.001 PHE F 255 TYR 0.015 0.001 TYR C 297 ARG 0.005 0.000 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.02898 ( 635) hydrogen bonds : angle 4.44309 ( 1782) covalent geometry : bond 0.00225 (17114) covalent geometry : angle 0.50750 (23216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17808.56 seconds wall clock time: 308 minutes 40.58 seconds (18520.58 seconds total)