Starting phenix.real_space_refine on Sat Aug 8 01:54:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lq7_63295/08_2026/9lq7_63295.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lq7_63295/08_2026/9lq7_63295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lq7_63295/08_2026/9lq7_63295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lq7_63295/08_2026/9lq7_63295.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lq7_63295/08_2026/9lq7_63295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lq7_63295/08_2026/9lq7_63295.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.597 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 Mn 1 7.51 5 P 81 5.49 5 S 107 5.16 5 C 15529 2.51 5 N 4136 2.21 5 O 4911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24765 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3904 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 17, 'TRANS': 451} Chain: "B" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4788 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 20, 'TRANS': 569} Chain breaks: 2 Chain: "C" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3044 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 1 Chain: "D" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2214 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "E" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2214 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "F" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2214 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "G" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1071 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "H" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1071 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "I" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2534 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 16, 'TRANS': 297} Chain: "K" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 779 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 18} Link IDs: {'rna2p': 6, 'rna3p': 30} Chain: "J" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 873 Classifications: {'RNA': 41} Modifications used: {'p5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna2p': 17, 'rna3p': 23} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MN': 1, 'ATP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 5.18, per 1000 atoms: 0.21 Number of scatterers: 24765 At special positions: 0 Unit cell: (102.52, 113.704, 200.38, 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) Mn 1 24.99 S 107 16.00 P 81 15.00 O 4911 8.00 N 4136 7.00 C 15529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5434 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 35 sheets defined 41.8% alpha, 16.2% beta 28 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 143 through 149 Processing helix chain 'A' and resid 168 through 186 Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.612A pdb=" N ASN A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.588A pdb=" N TYR A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.543A pdb=" N LYS A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 297 Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.586A pdb=" N ALA A 333 " --> pdb=" O TYR A 330 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 334 " --> pdb=" O ILE A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 334' Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 20 through 45 removed outlier: 3.802A pdb=" N PHE B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.879A pdb=" N GLN B 59 " --> pdb=" O ASN B 55 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 60' Processing helix chain 'B' and resid 79 through 97 removed outlier: 3.915A pdb=" N LEU B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 135 through 151 Proline residue: B 141 - end of helix removed outlier: 3.740A pdb=" N TYR B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 197 through 204 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 267 through 270 Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 296 through 319 removed outlier: 4.150A pdb=" N LEU B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 362 Processing helix chain 'B' and resid 362 through 372 removed outlier: 3.670A pdb=" N GLU B 371 " --> pdb=" O ASN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 409 through 419 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 455 through 469 removed outlier: 4.213A pdb=" N VAL B 459 " --> pdb=" O GLY B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 4.152A pdb=" N GLN B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 505 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 529 through 561 removed outlier: 5.807A pdb=" N ASN B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 573 Processing helix chain 'B' and resid 575 through 596 Processing helix chain 'C' and resid 84 through 100 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 239 through 242 No H-bonds generated for 'chain 'C' and resid 239 through 242' Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 328 through 330 No H-bonds generated for 'chain 'C' and resid 328 through 330' Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.994A pdb=" N LEU C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 410 Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'D' and resid 42 through 55 Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 104 through 118 Processing helix chain 'D' and resid 121 through 141 removed outlier: 3.823A pdb=" N TYR D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 189 through 197 Processing helix chain 'D' and resid 240 through 253 Processing helix chain 'E' and resid 42 through 55 Processing helix chain 'E' and resid 57 through 65 Processing helix chain 'E' and resid 104 through 118 Processing helix chain 'E' and resid 121 through 141 removed outlier: 3.973A pdb=" N TYR E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 154 removed outlier: 3.647A pdb=" N GLN E 154 " --> pdb=" O PRO E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 Processing helix chain 'E' and resid 189 through 198 Processing helix chain 'E' and resid 240 through 252 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'F' and resid 42 through 54 Processing helix chain 'F' and resid 57 through 65 Processing helix chain 'F' and resid 104 through 118 Processing helix chain 'F' and resid 121 through 141 removed outlier: 4.073A pdb=" N TYR F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 154 removed outlier: 3.622A pdb=" N GLN F 154 " --> pdb=" O PRO F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 Processing helix chain 'F' and resid 189 through 198 Processing helix chain 'F' and resid 240 through 253 Processing helix chain 'G' and resid 4 through 18 Processing helix chain 'G' and resid 29 through 45 removed outlier: 4.321A pdb=" N GLY G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY G 39 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA G 40 " --> pdb=" O SER G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 65 through 83 removed outlier: 4.106A pdb=" N ILE G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 112 through 130 Processing helix chain 'G' and resid 131 through 133 No H-bonds generated for 'chain 'G' and resid 131 through 133' Processing helix chain 'H' and resid 4 through 18 Processing helix chain 'H' and resid 29 through 45 removed outlier: 4.431A pdb=" N GLY H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 65 through 82 removed outlier: 3.965A pdb=" N ILE H 69 " --> pdb=" O ARG H 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 91 removed outlier: 3.879A pdb=" N ILE H 90 " --> pdb=" O THR H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 109 Processing helix chain 'H' and resid 112 through 131 Processing helix chain 'I' and resid 12 through 19 Processing helix chain 'I' and resid 32 through 38 Processing helix chain 'I' and resid 38 through 53 Processing helix chain 'I' and resid 61 through 72 Processing helix chain 'I' and resid 116 through 126 Processing helix chain 'I' and resid 127 through 132 removed outlier: 6.987A pdb=" N PHE I 130 " --> pdb=" O MET I 127 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU I 132 " --> pdb=" O PRO I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 161 removed outlier: 3.677A pdb=" N GLU I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR I 152 " --> pdb=" O GLU I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 Processing helix chain 'I' and resid 261 through 271 Processing helix chain 'I' and resid 275 through 277 No H-bonds generated for 'chain 'I' and resid 275 through 277' Processing helix chain 'I' and resid 283 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 78 removed outlier: 6.632A pdb=" N THR A 5 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 204 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 7 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 removed outlier: 6.316A pdb=" N GLY A 119 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 129 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 139 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 375 removed outlier: 3.802A pdb=" N ILE A 379 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 223 " --> pdb=" O GLY A 383 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 224 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 262 removed outlier: 3.534A pdb=" N ILE A 268 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 342 removed outlier: 3.775A pdb=" N THR A 403 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR A 416 " --> pdb=" O THR A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 75 removed outlier: 3.776A pdb=" N PHE B 126 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU B 128 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS C 185 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB1, first strand: chain 'B' and resid 183 through 184 removed outlier: 4.009A pdb=" N ARG B 193 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 321 through 326 removed outlier: 6.677A pdb=" N LEU B 331 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 325 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS B 434 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 337 through 338 Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 146 removed outlier: 6.553A pdb=" N THR C 284 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE C 146 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR C 282 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU C 151 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 163 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN C 229 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 143 through 146 removed outlier: 6.553A pdb=" N THR C 284 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE C 146 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR C 282 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N PHE C 277 " --> pdb=" O PRO C 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 76 through 77 Processing sheet with id=AB7, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AB8, first strand: chain 'C' and resid 335 through 336 Processing sheet with id=AB9, first strand: chain 'C' and resid 366 through 367 removed outlier: 4.023A pdb=" N ILE C 379 " --> pdb=" O GLN C 367 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.505A pdb=" N ARG D 229 " --> pdb=" O LEU D 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 229 through 235 current: chain 'D' and resid 185 through 188 Processing sheet with id=AC2, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.505A pdb=" N ARG D 229 " --> pdb=" O LEU D 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 84 through 92 current: chain 'D' and resid 274 through 275 Processing sheet with id=AC3, first strand: chain 'D' and resid 26 through 28 removed outlier: 5.244A pdb=" N ILE D 26 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLN D 222 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN D 28 " --> pdb=" O GLN D 222 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN D 209 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU D 218 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG D 207 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR D 220 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU D 205 " --> pdb=" O TYR D 220 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 157 through 158 removed outlier: 3.732A pdb=" N ILE D 163 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AC6, first strand: chain 'E' and resid 40 through 41 removed outlier: 6.530A pdb=" N ARG E 229 " --> pdb=" O LEU E 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 229 through 236 current: chain 'E' and resid 185 through 188 Processing sheet with id=AC7, first strand: chain 'E' and resid 79 through 81 removed outlier: 6.530A pdb=" N ARG E 229 " --> pdb=" O LEU E 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 92 current: chain 'E' and resid 270 through 275 Processing sheet with id=AC8, first strand: chain 'E' and resid 26 through 28 removed outlier: 4.939A pdb=" N ILE E 26 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLN E 222 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN E 28 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N SER E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU E 211 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 157 through 158 removed outlier: 3.684A pdb=" N ILE E 163 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 40 through 41 removed outlier: 6.530A pdb=" N ARG F 229 " --> pdb=" O LEU F 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 229 through 235 current: chain 'F' and resid 185 through 188 Processing sheet with id=AD2, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.530A pdb=" N ARG F 229 " --> pdb=" O LEU F 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 84 through 92 current: chain 'F' and resid 270 through 275 Processing sheet with id=AD3, first strand: chain 'F' and resid 26 through 28 removed outlier: 5.182A pdb=" N ILE F 26 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLN F 222 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN F 28 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN F 209 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU F 218 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG F 207 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR F 220 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU F 205 " --> pdb=" O TYR F 220 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 26 through 27 Processing sheet with id=AD5, first strand: chain 'I' and resid 114 through 115 removed outlier: 6.551A pdb=" N THR I 242 " --> pdb=" O ALA I 205 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL I 241 " --> pdb=" O THR I 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 198 through 199 Processing sheet with id=AD7, first strand: chain 'I' and resid 213 through 218 Processing sheet with id=AD8, first strand: chain 'I' and resid 258 through 260 removed outlier: 4.194A pdb=" N HIS I 253 " --> pdb=" O CYS I 260 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2844 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7590 1.34 - 1.46: 4935 1.46 - 1.58: 12574 1.58 - 1.70: 159 1.70 - 1.82: 181 Bond restraints: 25439 Sorted by residual: bond pdb=" CA ASP C 157 " pdb=" CB ASP C 157 " ideal model delta sigma weight residual 1.524 1.557 -0.032 1.53e-02 4.27e+03 4.47e+00 bond pdb=" C TYR A 280 " pdb=" N PRO A 281 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.19e-02 7.06e+03 3.07e+00 bond pdb=" CB GLU B 161 " pdb=" CG GLU B 161 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.42e+00 bond pdb=" N9 A J 20 " pdb=" C4 A J 20 " ideal model delta sigma weight residual 1.374 1.365 0.009 6.00e-03 2.78e+04 2.11e+00 bond pdb=" CB PRO B 52 " pdb=" CG PRO B 52 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.99e+00 ... (remaining 25434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.73: 34697 5.73 - 11.47: 34 11.47 - 17.20: 0 17.20 - 22.94: 1 22.94 - 28.67: 1 Bond angle restraints: 34733 Sorted by residual: angle pdb=" O3' G J 38 " pdb=" P C J 39 " pdb=" OP1 C J 39 " ideal model delta sigma weight residual 108.00 79.33 28.67 3.00e+00 1.11e-01 9.13e+01 angle pdb=" O3' G J 38 " pdb=" P C J 39 " pdb=" OP2 C J 39 " ideal model delta sigma weight residual 108.00 85.16 22.84 3.00e+00 1.11e-01 5.80e+01 angle pdb=" O4' A J 9 " pdb=" C1' A J 9 " pdb=" N9 A J 9 " ideal model delta sigma weight residual 108.20 112.94 -4.74 8.00e-01 1.56e+00 3.52e+01 angle pdb=" N VAL B 179 " pdb=" CA VAL B 179 " pdb=" C VAL B 179 " ideal model delta sigma weight residual 113.53 107.89 5.64 9.80e-01 1.04e+00 3.31e+01 angle pdb=" C ARG A 264 " pdb=" CA ARG A 264 " pdb=" CB ARG A 264 " ideal model delta sigma weight residual 115.79 109.73 6.06 1.19e+00 7.06e-01 2.59e+01 ... (remaining 34728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 14775 35.72 - 71.45: 737 71.45 - 107.17: 46 107.17 - 142.89: 0 142.89 - 178.61: 4 Dihedral angle restraints: 15562 sinusoidal: 7139 harmonic: 8423 Sorted by residual: dihedral pdb=" CA TYR I 81 " pdb=" C TYR I 81 " pdb=" N PRO I 82 " pdb=" CA PRO I 82 " ideal model delta harmonic sigma weight residual 180.00 119.63 60.37 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" O4' C J 12 " pdb=" C1' C J 12 " pdb=" N1 C J 12 " pdb=" C2 C J 12 " ideal model delta sinusoidal sigma weight residual 200.00 43.30 156.70 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" O4' U J 41 " pdb=" C1' U J 41 " pdb=" N1 U J 41 " pdb=" C2 U J 41 " ideal model delta sinusoidal sigma weight residual 232.00 53.39 178.61 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.387: 3907 0.387 - 0.775: 0 0.775 - 1.162: 0 1.162 - 1.550: 0 1.550 - 1.937: 1 Chirality restraints: 3908 Sorted by residual: chirality pdb=" P C J 39 " pdb=" OP1 C J 39 " pdb=" OP2 C J 39 " pdb=" O5' C J 39 " both_signs ideal model delta sigma weight residual True 2.41 0.47 1.94 2.00e-01 2.50e+01 9.38e+01 chirality pdb=" CA ASP C 157 " pdb=" N ASP C 157 " pdb=" C ASP C 157 " pdb=" CB ASP C 157 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA PRO B 52 " pdb=" N PRO B 52 " pdb=" C PRO B 52 " pdb=" CB PRO B 52 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 3905 not shown) Planarity restraints: 4154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 51 " -0.093 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO B 52 " 0.242 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR I 81 " 0.087 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO I 82 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO I 82 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO I 82 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 106 " -0.077 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO C 107 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO C 107 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 107 " -0.063 5.00e-02 4.00e+02 ... (remaining 4151 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 885 2.70 - 3.25: 23922 3.25 - 3.80: 41367 3.80 - 4.35: 54321 4.35 - 4.90: 89900 Nonbonded interactions: 210395 Sorted by model distance: nonbonded pdb=" O PRO I 229 " pdb=" O2' U K 17 " model vdw 2.156 3.040 nonbonded pdb=" OD2 ASP B 279 " pdb="MN MN B 703 " model vdw 2.189 2.320 nonbonded pdb=" OD2 ASP B 328 " pdb="MN MN B 703 " model vdw 2.190 2.320 nonbonded pdb=" O SER E 67 " pdb=" O2' C J 12 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG G 131 " pdb=" OP1 C K 31 " model vdw 2.206 3.120 ... (remaining 210390 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 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.880 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 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 : 0.003 0.070 25439 Z= 0.142 Angle : 0.660 28.671 34733 Z= 0.390 Chirality : 0.054 1.937 3908 Planarity : 0.006 0.140 4154 Dihedral : 19.216 178.615 10128 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.49 % Favored : 95.08 % Rotamer: Outliers : 3.15 % Allowed : 30.74 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.16), residues: 2828 helix: 1.34 (0.16), residues: 1091 sheet: 0.54 (0.24), residues: 449 loop : -0.81 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 264 TYR 0.013 0.001 TYR I 145 PHE 0.018 0.001 PHE B 461 TRP 0.009 0.001 TRP A 147 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (25439) covalent geometry : angle 0.66025 / 0.39 (34733) hydrogen bonds : bond 0.15538 / 10.36 ( 1054) hydrogen bonds : angle 5.92011 / 4.17 ( 2980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 295 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 TYR cc_start: 0.8091 (t80) cc_final: 0.7841 (t80) REVERT: A 344 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7956 (tm-30) REVERT: A 361 ASN cc_start: 0.8093 (m-40) cc_final: 0.7793 (m110) REVERT: A 406 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6826 (ptpp) REVERT: A 417 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7892 (mm-30) REVERT: B 1 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.7838 (mtm) REVERT: B 98 HIS cc_start: 0.9246 (OUTLIER) cc_final: 0.8714 (m170) REVERT: B 128 GLU cc_start: 0.7784 (pp20) cc_final: 0.7233 (pp20) REVERT: B 224 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6068 (mp) REVERT: B 233 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7995 (mt) REVERT: B 370 SER cc_start: 0.8647 (m) cc_final: 0.8271 (p) REVERT: B 392 MET cc_start: 0.8806 (tmm) cc_final: 0.8541 (tmt) REVERT: C 112 LYS cc_start: 0.8970 (mppt) cc_final: 0.8749 (mppt) REVERT: C 233 GLN cc_start: 0.8316 (mp10) cc_final: 0.8088 (pm20) REVERT: C 255 VAL cc_start: 0.8701 (t) cc_final: 0.8471 (m) REVERT: C 313 GLU cc_start: 0.8026 (pm20) cc_final: 0.7613 (pp20) REVERT: C 314 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7854 (tp30) REVERT: C 409 MET cc_start: 0.9193 (mtm) cc_final: 0.8913 (mtt) REVERT: F 207 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.7338 (mtm-85) outliers start: 81 outliers final: 59 residues processed: 352 average time/residue: 0.6498 time to fit residues: 260.1690 Evaluate side-chains 345 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 279 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN A 463 ASN B 342 ASN C 105 GLN C 178 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN H 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.051276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.041885 restraints weight = 61196.262| |-----------------------------------------------------------------------------| r_work (start): 0.2394 rms_B_bonded: 1.85 r_work: 0.2306 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2208 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25439 Z= 0.156 Angle : 0.628 28.074 34733 Z= 0.330 Chirality : 0.052 1.856 3908 Planarity : 0.006 0.141 4154 Dihedral : 14.682 179.503 4474 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.49 % Favored : 95.05 % Rotamer: Outliers : 4.55 % Allowed : 27.36 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.16), residues: 2828 helix: 1.47 (0.16), residues: 1097 sheet: 0.80 (0.25), residues: 417 loop : -0.73 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 312 TYR 0.016 0.001 TYR B 125 PHE 0.019 0.002 PHE B 126 TRP 0.009 0.001 TRP B 25 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (25439) covalent geometry : angle 0.62848 / 0.33 (34733) hydrogen bonds : bond 0.04762 / 3.18 ( 1054) hydrogen bonds : angle 4.84797 / 3.40 ( 2980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 302 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 361 ASN cc_start: 0.8084 (m-40) cc_final: 0.7782 (m110) REVERT: A 406 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6844 (ptpp) REVERT: A 417 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7867 (mm-30) REVERT: B 94 GLU cc_start: 0.6903 (tp30) cc_final: 0.6518 (tp30) REVERT: B 98 HIS cc_start: 0.9316 (OUTLIER) cc_final: 0.8689 (m170) REVERT: B 128 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7268 (pp20) REVERT: B 161 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7144 (tm-30) REVERT: B 224 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6073 (mp) REVERT: B 233 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8107 (mt) REVERT: B 370 SER cc_start: 0.8838 (m) cc_final: 0.8494 (p) REVERT: B 392 MET cc_start: 0.8804 (tmm) cc_final: 0.8535 (tmt) REVERT: C 112 LYS cc_start: 0.9042 (mppt) cc_final: 0.8674 (mmmm) REVERT: C 115 GLU cc_start: 0.8795 (mp0) cc_final: 0.8542 (mp0) REVERT: C 233 GLN cc_start: 0.8470 (mp10) cc_final: 0.8187 (pm20) REVERT: C 255 VAL cc_start: 0.8728 (t) cc_final: 0.8505 (m) REVERT: C 313 GLU cc_start: 0.8095 (pm20) cc_final: 0.7633 (pp20) REVERT: C 406 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8485 (tmmm) REVERT: C 409 MET cc_start: 0.9177 (mtm) cc_final: 0.8864 (mtt) REVERT: E 188 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9150 (mp) REVERT: G 13 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: G 20 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8788 (mt) REVERT: I 181 ASN cc_start: 0.9164 (OUTLIER) cc_final: 0.8715 (t0) REVERT: I 238 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8124 (mtp85) outliers start: 117 outliers final: 51 residues processed: 391 average time/residue: 0.6831 time to fit residues: 305.5110 Evaluate side-chains 341 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 279 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 183 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 171 optimal weight: 0.0970 chunk 45 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 248 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN A 463 ASN B 265 GLN C 105 GLN C 197 ASN E 31 GLN G 23 ASN G 111 ASN H 59 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.051384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.042109 restraints weight = 61414.686| |-----------------------------------------------------------------------------| r_work (start): 0.2402 rms_B_bonded: 1.86 r_work: 0.2315 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2217 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25439 Z= 0.141 Angle : 0.610 28.542 34733 Z= 0.320 Chirality : 0.051 1.854 3908 Planarity : 0.005 0.139 4154 Dihedral : 14.305 179.026 4387 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.35 % Favored : 95.16 % Rotamer: Outliers : 4.51 % Allowed : 27.75 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 2828 helix: 1.53 (0.16), residues: 1100 sheet: 0.91 (0.26), residues: 383 loop : -0.73 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 374 TYR 0.014 0.001 TYR F 270 PHE 0.021 0.001 PHE B 74 TRP 0.008 0.001 TRP B 25 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (25439) covalent geometry : angle 0.60997 / 0.32 (34733) hydrogen bonds : bond 0.04283 / 2.87 ( 1054) hydrogen bonds : angle 4.65853 / 3.27 ( 2980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 296 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.8948 (mm-30) REVERT: A 361 ASN cc_start: 0.8019 (m-40) cc_final: 0.7723 (m110) REVERT: A 406 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6819 (ptpp) REVERT: A 417 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7911 (mm-30) REVERT: B 1 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7605 (mtm) REVERT: B 98 HIS cc_start: 0.9312 (OUTLIER) cc_final: 0.8755 (m170) REVERT: B 128 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7196 (pp20) REVERT: B 193 ARG cc_start: 0.8722 (mtm-85) cc_final: 0.8506 (mtm-85) REVERT: B 224 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6077 (mp) REVERT: B 233 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8110 (mt) REVERT: B 370 SER cc_start: 0.8869 (m) cc_final: 0.8518 (p) REVERT: B 392 MET cc_start: 0.8815 (tmm) cc_final: 0.8536 (tmt) REVERT: B 409 ASP cc_start: 0.9203 (OUTLIER) cc_final: 0.8845 (m-30) REVERT: C 112 LYS cc_start: 0.9074 (mppt) cc_final: 0.8536 (mmmm) REVERT: C 115 GLU cc_start: 0.8802 (mp0) cc_final: 0.8581 (mp0) REVERT: C 233 GLN cc_start: 0.8457 (mp10) cc_final: 0.8176 (pm20) REVERT: C 255 VAL cc_start: 0.8733 (t) cc_final: 0.8513 (m) REVERT: C 313 GLU cc_start: 0.8079 (pm20) cc_final: 0.7616 (pp20) REVERT: C 406 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8529 (tmmm) REVERT: C 409 MET cc_start: 0.9151 (mtm) cc_final: 0.8782 (mtt) REVERT: C 415 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8507 (mtp180) REVERT: E 188 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9109 (mt) REVERT: G 13 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: G 20 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8778 (mt) REVERT: H 126 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8791 (mtm) REVERT: I 150 MET cc_start: 0.9157 (tpp) cc_final: 0.8925 (tpp) REVERT: I 181 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8706 (t0) REVERT: I 238 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8053 (mtp85) outliers start: 116 outliers final: 59 residues processed: 383 average time/residue: 0.6463 time to fit residues: 282.2022 Evaluate side-chains 352 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 277 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 213 LYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 126 MET Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 342 ASN B 345 ASN C 105 GLN E 31 GLN G 23 ASN G 111 ASN H 59 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.048272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.038987 restraints weight = 61384.897| |-----------------------------------------------------------------------------| r_work (start): 0.2310 rms_B_bonded: 1.85 r_work: 0.2219 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2119 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 25439 Z= 0.260 Angle : 0.709 29.430 34733 Z= 0.372 Chirality : 0.054 1.829 3908 Planarity : 0.006 0.141 4154 Dihedral : 14.334 179.325 4380 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.88 % Favored : 94.55 % Rotamer: Outliers : 6.06 % Allowed : 26.70 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.16), residues: 2828 helix: 1.28 (0.16), residues: 1109 sheet: 0.74 (0.25), residues: 417 loop : -0.83 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 374 TYR 0.018 0.002 TYR I 114 PHE 0.021 0.002 PHE C 281 TRP 0.012 0.002 TRP F 219 HIS 0.006 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.26 (25439) covalent geometry : angle 0.70893 / 0.37 (34733) hydrogen bonds : bond 0.05105 / 3.41 ( 1054) hydrogen bonds : angle 4.69511 / 3.30 ( 2980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 278 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8557 (tmtt) REVERT: A 417 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 1 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7684 (mtm) REVERT: B 94 GLU cc_start: 0.6999 (tp30) cc_final: 0.6609 (tp30) REVERT: B 98 HIS cc_start: 0.9339 (OUTLIER) cc_final: 0.8839 (m170) REVERT: B 128 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7172 (pp20) REVERT: B 193 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8485 (mtm-85) REVERT: B 224 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6399 (mp) REVERT: B 233 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8190 (mt) REVERT: B 370 SER cc_start: 0.8901 (m) cc_final: 0.8554 (p) REVERT: B 392 MET cc_start: 0.8813 (tmm) cc_final: 0.8411 (tmm) REVERT: B 409 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8786 (m-30) REVERT: C 112 LYS cc_start: 0.9118 (mppt) cc_final: 0.8544 (mmmm) REVERT: C 115 GLU cc_start: 0.8849 (mp0) cc_final: 0.8620 (mp0) REVERT: C 213 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8682 (mtmm) REVERT: C 233 GLN cc_start: 0.8605 (mp10) cc_final: 0.8358 (pm20) REVERT: C 255 VAL cc_start: 0.8822 (t) cc_final: 0.8603 (m) REVERT: C 313 GLU cc_start: 0.8071 (pm20) cc_final: 0.7617 (pp20) REVERT: C 320 GLU cc_start: 0.8696 (tp30) cc_final: 0.8396 (tp30) REVERT: C 406 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8534 (tmmm) REVERT: C 415 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8645 (mtp180) REVERT: E 4 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.7186 (ptp90) REVERT: E 188 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9205 (mp) REVERT: G 13 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: G 20 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9026 (mt) REVERT: G 117 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8614 (ttpp) REVERT: I 156 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8922 (mp) REVERT: I 181 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8723 (t0) outliers start: 156 outliers final: 87 residues processed: 393 average time/residue: 0.6312 time to fit residues: 283.2993 Evaluate side-chains 379 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 275 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 213 LYS Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 114 TYR Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 112 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 197 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 463 ASN C 105 GLN C 178 ASN E 31 GLN G 23 ASN G 111 ASN H 59 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.048966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2331 r_free = 0.2331 target = 0.039650 restraints weight = 61129.072| |-----------------------------------------------------------------------------| r_work (start): 0.2330 rms_B_bonded: 1.85 r_work: 0.2239 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2139 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25439 Z= 0.203 Angle : 0.659 29.227 34733 Z= 0.346 Chirality : 0.053 1.836 3908 Planarity : 0.006 0.139 4154 Dihedral : 14.312 178.917 4374 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.53 % Favored : 94.94 % Rotamer: Outliers : 5.60 % Allowed : 27.44 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.16), residues: 2828 helix: 1.33 (0.16), residues: 1103 sheet: 0.72 (0.25), residues: 417 loop : -0.82 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 418 TYR 0.017 0.002 TYR A 435 PHE 0.019 0.002 PHE B 74 TRP 0.011 0.001 TRP B 25 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (25439) covalent geometry : angle 0.65933 / 0.35 (34733) hydrogen bonds : bond 0.04658 / 3.13 ( 1054) hydrogen bonds : angle 4.63563 / 3.26 ( 2980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 282 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8551 (tmtt) REVERT: A 417 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7972 (mm-30) REVERT: B 1 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7648 (mtm) REVERT: B 74 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7774 (t80) REVERT: B 94 GLU cc_start: 0.6925 (tp30) cc_final: 0.6681 (tp30) REVERT: B 98 HIS cc_start: 0.9310 (OUTLIER) cc_final: 0.8752 (m170) REVERT: B 128 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7088 (pp20) REVERT: B 224 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6362 (mp) REVERT: B 233 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8185 (mt) REVERT: B 271 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8849 (mttp) REVERT: B 370 SER cc_start: 0.8913 (m) cc_final: 0.8642 (p) REVERT: B 392 MET cc_start: 0.8794 (tmm) cc_final: 0.8514 (tmt) REVERT: B 409 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8705 (m-30) REVERT: C 112 LYS cc_start: 0.9111 (mppt) cc_final: 0.8606 (mmmm) REVERT: C 115 GLU cc_start: 0.8867 (mp0) cc_final: 0.8623 (mp0) REVERT: C 178 ASN cc_start: 0.8721 (t0) cc_final: 0.8456 (t0) REVERT: C 233 GLN cc_start: 0.8606 (mp10) cc_final: 0.8336 (pm20) REVERT: C 255 VAL cc_start: 0.8831 (t) cc_final: 0.8602 (m) REVERT: C 313 GLU cc_start: 0.8080 (pm20) cc_final: 0.7616 (pp20) REVERT: C 320 GLU cc_start: 0.8699 (tp30) cc_final: 0.8379 (tp30) REVERT: C 406 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8529 (tmmm) REVERT: C 415 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8631 (mtp180) REVERT: E 4 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.6779 (ptp90) REVERT: E 188 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9172 (mp) REVERT: G 13 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: G 20 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9010 (mt) REVERT: G 68 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8927 (pt) REVERT: I 181 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8700 (t0) outliers start: 144 outliers final: 83 residues processed: 392 average time/residue: 0.6596 time to fit residues: 295.3951 Evaluate side-chains 380 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 280 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 213 LYS Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 114 TYR Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 130 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 258 optimal weight: 0.4980 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN C 178 ASN E 31 GLN G 23 ASN G 111 ASN H 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.049909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.040602 restraints weight = 60846.713| |-----------------------------------------------------------------------------| r_work (start): 0.2358 rms_B_bonded: 1.85 r_work: 0.2270 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2171 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25439 Z= 0.158 Angle : 0.631 28.876 34733 Z= 0.331 Chirality : 0.052 1.848 3908 Planarity : 0.006 0.137 4154 Dihedral : 14.271 178.617 4374 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.46 % Favored : 95.01 % Rotamer: Outliers : 5.17 % Allowed : 27.98 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 2828 helix: 1.42 (0.16), residues: 1105 sheet: 0.73 (0.25), residues: 415 loop : -0.78 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 264 TYR 0.017 0.001 TYR A 435 PHE 0.018 0.002 PHE B 461 TRP 0.010 0.001 TRP B 25 HIS 0.005 0.001 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (25439) covalent geometry : angle 0.63101 / 0.33 (34733) hydrogen bonds : bond 0.04242 / 2.85 ( 1054) hydrogen bonds : angle 4.54549 / 3.19 ( 2980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 293 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 TYR cc_start: 0.8527 (t80) cc_final: 0.8325 (t80) REVERT: A 406 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6913 (ptpp) REVERT: A 417 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7921 (mm-30) REVERT: B 74 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7791 (t80) REVERT: B 98 HIS cc_start: 0.9299 (OUTLIER) cc_final: 0.8779 (m170) REVERT: B 128 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7218 (pp20) REVERT: B 184 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7395 (p90) REVERT: B 193 ARG cc_start: 0.8801 (mtm-85) cc_final: 0.7957 (ptm-80) REVERT: B 224 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6352 (mp) REVERT: B 271 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8881 (mttp) REVERT: B 370 SER cc_start: 0.8924 (m) cc_final: 0.8653 (p) REVERT: B 392 MET cc_start: 0.8798 (tmm) cc_final: 0.8523 (tmt) REVERT: B 409 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8671 (m-30) REVERT: C 112 LYS cc_start: 0.9121 (mppt) cc_final: 0.8611 (mmmm) REVERT: C 115 GLU cc_start: 0.8837 (mp0) cc_final: 0.8602 (mp0) REVERT: C 178 ASN cc_start: 0.8650 (t0) cc_final: 0.8436 (t0) REVERT: C 233 GLN cc_start: 0.8538 (mp10) cc_final: 0.8266 (pm20) REVERT: C 255 VAL cc_start: 0.8832 (t) cc_final: 0.8612 (m) REVERT: C 313 GLU cc_start: 0.8065 (pm20) cc_final: 0.7601 (pp20) REVERT: C 320 GLU cc_start: 0.8685 (tp30) cc_final: 0.8351 (tp30) REVERT: C 406 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8527 (tmmm) REVERT: C 415 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8597 (mtp180) REVERT: E 4 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.6800 (ptp90) REVERT: E 124 GLN cc_start: 0.8488 (mt0) cc_final: 0.8246 (mp10) REVERT: E 188 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9143 (mp) REVERT: G 13 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: G 20 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8929 (mt) REVERT: G 68 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8886 (pt) REVERT: G 117 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8613 (ttpp) REVERT: I 181 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8711 (t0) outliers start: 133 outliers final: 77 residues processed: 389 average time/residue: 0.6641 time to fit residues: 294.9379 Evaluate side-chains 378 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 284 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 213 LYS Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 11 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 231 optimal weight: 0.5980 chunk 239 optimal weight: 0.5980 chunk 245 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 238 optimal weight: 0.3980 chunk 175 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 HIS A 149 GLN A 463 ASN B 166 HIS C 105 GLN C 315 ASN C 367 GLN E 31 GLN G 23 ASN G 111 ASN H 59 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.050910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.041671 restraints weight = 61089.083| |-----------------------------------------------------------------------------| r_work (start): 0.2389 rms_B_bonded: 1.85 r_work: 0.2302 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2203 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 25439 Z= 0.131 Angle : 0.616 28.453 34733 Z= 0.322 Chirality : 0.051 1.862 3908 Planarity : 0.005 0.136 4154 Dihedral : 14.228 178.363 4370 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.31 % Favored : 95.16 % Rotamer: Outliers : 4.66 % Allowed : 28.72 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2828 helix: 1.56 (0.16), residues: 1098 sheet: 0.69 (0.25), residues: 432 loop : -0.76 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 418 TYR 0.015 0.001 TYR A 435 PHE 0.025 0.001 PHE A 263 TRP 0.009 0.001 TRP B 25 HIS 0.005 0.001 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (25439) covalent geometry : angle 0.61642 / 0.32 (34733) hydrogen bonds : bond 0.03935 / 2.65 ( 1054) hydrogen bonds : angle 4.47138 / 3.14 ( 2980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 290 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6880 (ptpp) REVERT: A 417 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7896 (mm-30) REVERT: B 74 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7782 (t80) REVERT: B 94 GLU cc_start: 0.7003 (tp30) cc_final: 0.6501 (tp30) REVERT: B 98 HIS cc_start: 0.9294 (OUTLIER) cc_final: 0.8806 (m170) REVERT: B 128 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7320 (pp20) REVERT: B 184 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7660 (p90) REVERT: B 193 ARG cc_start: 0.8777 (mtm-85) cc_final: 0.8267 (mtm-85) REVERT: B 224 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6414 (mp) REVERT: B 233 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8219 (mt) REVERT: B 271 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8858 (mttp) REVERT: B 370 SER cc_start: 0.8945 (m) cc_final: 0.8672 (p) REVERT: B 374 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7715 (mtm110) REVERT: B 392 MET cc_start: 0.8794 (tmm) cc_final: 0.8525 (tmt) REVERT: B 409 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8660 (m-30) REVERT: C 112 LYS cc_start: 0.9105 (mppt) cc_final: 0.8601 (mmmm) REVERT: C 115 GLU cc_start: 0.8844 (mp0) cc_final: 0.8609 (mp0) REVERT: C 233 GLN cc_start: 0.8494 (mp10) cc_final: 0.8216 (pm20) REVERT: C 255 VAL cc_start: 0.8817 (t) cc_final: 0.8603 (m) REVERT: C 320 GLU cc_start: 0.8667 (tp30) cc_final: 0.8328 (tp30) REVERT: C 406 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8517 (tmmm) REVERT: E 124 GLN cc_start: 0.8474 (mt0) cc_final: 0.8203 (mp10) REVERT: E 188 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9062 (mt) REVERT: F 207 ARG cc_start: 0.9369 (OUTLIER) cc_final: 0.7309 (mtm-85) REVERT: G 13 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: G 20 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8863 (mt) REVERT: G 68 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8856 (pt) REVERT: G 117 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8608 (ttpp) REVERT: I 238 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.7725 (mtp85) outliers start: 120 outliers final: 70 residues processed: 381 average time/residue: 0.6533 time to fit residues: 284.3852 Evaluate side-chains 372 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 285 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 213 LYS Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 260 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 265 optimal weight: 0.3980 chunk 259 optimal weight: 0.7980 chunk 206 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 151 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 ASN C 105 GLN C 197 ASN C 261 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN H 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.051162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.041932 restraints weight = 60783.820| |-----------------------------------------------------------------------------| r_work (start): 0.2397 rms_B_bonded: 1.83 r_work: 0.2310 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2212 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 25439 Z= 0.134 Angle : 0.618 28.322 34733 Z= 0.322 Chirality : 0.051 1.867 3908 Planarity : 0.005 0.135 4154 Dihedral : 14.203 178.299 4370 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.53 % Favored : 94.94 % Rotamer: Outliers : 4.47 % Allowed : 28.92 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2828 helix: 1.59 (0.16), residues: 1101 sheet: 0.71 (0.25), residues: 429 loop : -0.74 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 418 TYR 0.015 0.001 TYR A 435 PHE 0.026 0.001 PHE A 263 TRP 0.009 0.001 TRP B 25 HIS 0.005 0.001 HIS G 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (25439) covalent geometry : angle 0.61838 / 0.32 (34733) hydrogen bonds : bond 0.03855 / 2.59 ( 1054) hydrogen bonds : angle 4.43574 / 3.12 ( 2980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 290 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6871 (ptpp) REVERT: A 417 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7894 (mm-30) REVERT: B 74 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7746 (t80) REVERT: B 94 GLU cc_start: 0.6989 (tp30) cc_final: 0.6571 (tp30) REVERT: B 98 HIS cc_start: 0.9288 (OUTLIER) cc_final: 0.8814 (m170) REVERT: B 128 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7276 (pp20) REVERT: B 184 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7746 (p90) REVERT: B 193 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8295 (mtm-85) REVERT: B 224 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6404 (mp) REVERT: B 233 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8238 (mt) REVERT: B 271 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8865 (mttp) REVERT: B 370 SER cc_start: 0.8948 (m) cc_final: 0.8671 (p) REVERT: B 392 MET cc_start: 0.8801 (tmm) cc_final: 0.8532 (tmt) REVERT: B 409 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8641 (m-30) REVERT: C 112 LYS cc_start: 0.9117 (mppt) cc_final: 0.8606 (mmmm) REVERT: C 115 GLU cc_start: 0.8838 (mp0) cc_final: 0.8605 (mp0) REVERT: C 233 GLN cc_start: 0.8483 (mp10) cc_final: 0.8179 (pm20) REVERT: C 255 VAL cc_start: 0.8812 (t) cc_final: 0.8602 (m) REVERT: C 320 GLU cc_start: 0.8656 (tp30) cc_final: 0.8317 (tp30) REVERT: C 406 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8521 (tmmm) REVERT: C 415 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8560 (mtp180) REVERT: E 188 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9070 (mt) REVERT: F 207 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.7317 (mtm-85) REVERT: G 13 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: G 20 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8813 (mt) REVERT: G 68 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8850 (pt) REVERT: G 117 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8606 (ttpp) REVERT: I 238 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8024 (mtp85) outliers start: 115 outliers final: 71 residues processed: 375 average time/residue: 0.7316 time to fit residues: 312.4877 Evaluate side-chains 372 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 283 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 213 LYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 103 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 235 optimal weight: 0.5980 chunk 284 optimal weight: 8.9990 chunk 199 optimal weight: 0.0670 chunk 187 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN A 463 ASN C 105 GLN E 31 GLN G 23 ASN G 111 ASN H 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.051235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.041957 restraints weight = 60840.264| |-----------------------------------------------------------------------------| r_work (start): 0.2398 rms_B_bonded: 1.85 r_work: 0.2312 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2214 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 25439 Z= 0.140 Angle : 0.628 28.260 34733 Z= 0.326 Chirality : 0.051 1.872 3908 Planarity : 0.006 0.135 4154 Dihedral : 14.182 178.311 4370 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.35 % Favored : 95.12 % Rotamer: Outliers : 4.20 % Allowed : 29.27 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.16), residues: 2828 helix: 1.62 (0.16), residues: 1101 sheet: 0.81 (0.25), residues: 419 loop : -0.75 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 70 TYR 0.015 0.001 TYR F 270 PHE 0.025 0.001 PHE A 263 TRP 0.009 0.001 TRP B 25 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (25439) covalent geometry : angle 0.62776 / 0.33 (34733) hydrogen bonds : bond 0.03856 / 2.60 ( 1054) hydrogen bonds : angle 4.40667 / 3.10 ( 2980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 288 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6912 (ptpp) REVERT: A 417 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7893 (mm-30) REVERT: B 94 GLU cc_start: 0.7009 (tp30) cc_final: 0.6630 (tp30) REVERT: B 98 HIS cc_start: 0.9281 (OUTLIER) cc_final: 0.8791 (m170) REVERT: B 128 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7296 (pp20) REVERT: B 184 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7838 (p90) REVERT: B 193 ARG cc_start: 0.8743 (mtm-85) cc_final: 0.8337 (mtm-85) REVERT: B 224 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6445 (mp) REVERT: B 233 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8258 (mt) REVERT: B 271 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8856 (mttp) REVERT: B 370 SER cc_start: 0.8964 (m) cc_final: 0.8676 (p) REVERT: B 392 MET cc_start: 0.8814 (tmm) cc_final: 0.8543 (tmt) REVERT: B 409 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8630 (m-30) REVERT: C 112 LYS cc_start: 0.9099 (mppt) cc_final: 0.8587 (mmmm) REVERT: C 115 GLU cc_start: 0.8844 (mp0) cc_final: 0.8607 (mp0) REVERT: C 233 GLN cc_start: 0.8465 (mp10) cc_final: 0.8187 (pm20) REVERT: C 255 VAL cc_start: 0.8788 (t) cc_final: 0.8585 (m) REVERT: C 320 GLU cc_start: 0.8680 (tp30) cc_final: 0.8346 (tp30) REVERT: C 406 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8526 (tmmm) REVERT: C 415 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8570 (mtp180) REVERT: D 55 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8786 (pttp) REVERT: E 124 GLN cc_start: 0.8464 (mt0) cc_final: 0.8183 (mp10) REVERT: E 188 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9065 (mt) REVERT: F 207 ARG cc_start: 0.9369 (OUTLIER) cc_final: 0.7321 (mtm-85) REVERT: G 13 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: G 20 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8774 (mt) REVERT: G 68 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8851 (pt) outliers start: 108 outliers final: 71 residues processed: 370 average time/residue: 0.7381 time to fit residues: 310.9861 Evaluate side-chains 368 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 281 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 213 LYS Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 258 optimal weight: 0.0870 chunk 194 optimal weight: 0.0570 chunk 251 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 121 optimal weight: 0.0000 chunk 234 optimal weight: 1.9990 overall best weight: 0.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN A 463 ASN C 105 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN G 111 ASN H 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.051975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.042728 restraints weight = 60931.896| |-----------------------------------------------------------------------------| r_work (start): 0.2420 rms_B_bonded: 1.83 r_work: 0.2334 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2236 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 25439 Z= 0.124 Angle : 0.626 28.023 34733 Z= 0.324 Chirality : 0.051 1.879 3908 Planarity : 0.006 0.135 4154 Dihedral : 14.175 178.138 4369 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.28 % Favored : 95.19 % Rotamer: Outliers : 3.58 % Allowed : 29.85 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2828 helix: 1.67 (0.16), residues: 1101 sheet: 0.74 (0.24), residues: 423 loop : -0.72 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 136 TYR 0.030 0.001 TYR I 81 PHE 0.023 0.001 PHE A 263 TRP 0.009 0.001 TRP B 25 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (25439) covalent geometry : angle 0.62560 / 0.32 (34733) hydrogen bonds : bond 0.03665 / 2.47 ( 1054) hydrogen bonds : angle 4.37495 / 3.08 ( 2980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 287 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6890 (ptpp) REVERT: A 417 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7871 (mm-30) REVERT: B 94 GLU cc_start: 0.7006 (tp30) cc_final: 0.6606 (tp30) REVERT: B 98 HIS cc_start: 0.9265 (OUTLIER) cc_final: 0.8746 (m170) REVERT: B 128 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7261 (pp20) REVERT: B 184 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.8031 (p90) REVERT: B 224 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6490 (mp) REVERT: B 233 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8251 (mt) REVERT: B 271 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8861 (mttp) REVERT: B 392 MET cc_start: 0.8812 (tmm) cc_final: 0.8549 (tmt) REVERT: B 409 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8597 (m-30) REVERT: C 112 LYS cc_start: 0.9094 (mppt) cc_final: 0.8582 (mmmm) REVERT: C 115 GLU cc_start: 0.8850 (mp0) cc_final: 0.8571 (mp0) REVERT: C 233 GLN cc_start: 0.8453 (mp10) cc_final: 0.8124 (pm20) REVERT: C 313 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7626 (pp20) REVERT: C 316 SER cc_start: 0.7727 (p) cc_final: 0.7344 (m) REVERT: C 320 GLU cc_start: 0.8666 (tp30) cc_final: 0.8328 (tp30) REVERT: C 406 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8523 (tmmm) REVERT: C 415 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8559 (mtp180) REVERT: D 55 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8787 (pttp) REVERT: F 207 ARG cc_start: 0.9355 (OUTLIER) cc_final: 0.7346 (mtm-85) REVERT: G 13 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: G 20 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8698 (mt) REVERT: G 68 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8832 (pt) outliers start: 92 outliers final: 59 residues processed: 354 average time/residue: 0.7571 time to fit residues: 304.7651 Evaluate side-chains 349 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 274 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 213 LYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 304 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 266 optimal weight: 3.9990 chunk 284 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 268 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 ASN C 105 GLN C 178 ASN C 217 HIS ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN I 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.051769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.042547 restraints weight = 61038.924| |-----------------------------------------------------------------------------| r_work (start): 0.2416 rms_B_bonded: 1.84 r_work: 0.2330 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2232 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 25439 Z= 0.179 Angle : 0.745 59.200 34733 Z= 0.414 Chirality : 0.054 1.881 3908 Planarity : 0.006 0.134 4154 Dihedral : 14.154 178.136 4365 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.28 % Favored : 95.19 % Rotamer: Outliers : 3.42 % Allowed : 30.00 % Favored : 66.58 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.16), residues: 2828 helix: 1.65 (0.16), residues: 1101 sheet: 0.74 (0.24), residues: 423 loop : -0.73 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 264 TYR 0.027 0.001 TYR I 81 PHE 0.048 0.002 PHE A 263 TRP 0.008 0.001 TRP B 25 HIS 0.006 0.001 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (25439) covalent geometry : angle 0.74452 / 0.41 (34733) hydrogen bonds : bond 0.03725 / 2.52 ( 1054) hydrogen bonds : angle 4.37159 / 3.08 ( 2980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7842.89 seconds wall clock time: 134 minutes 41.59 seconds (8081.59 seconds total)