Starting phenix.real_space_refine on Sun Jul 5 03:18:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lq7_63295/07_2026/9lq7_63295.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lq7_63295/07_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_63295/07_2026/9lq7_63295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lq7_63295/07_2026/9lq7_63295.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lq7_63295/07_2026/9lq7_63295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lq7_63295/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 58 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'ATP': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain breaks: 1 Time building chain proxies: 5.17, 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: 1.61 Conformation dependent library (CDL) restraints added in 1.1 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: 2.87 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: 5.20 Time building geometry restraints manager: 2.12 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=" 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 angle pdb=" C ALA A 359 " pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 121.54 130.86 -9.32 1.91e+00 2.74e-01 2.38e+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 3.060 nonbonded pdb=" OD2 ASP B 328 " pdb="MN MN B 703 " model vdw 2.190 3.060 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: 4.300 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.930 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.170 ------------------------------------------------------------------------------- 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= 0.137 Angle : 0.635 28.671 34733 Z= 0.356 Chirality : 0.051 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 0.00286 / 0.14 (25439) covalent geometry : angle 0.63506 / 0.36 (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 : 0.938 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: 0.7307 time to fit residues: 291.8102 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 : 0.869 ------------------------------------------------------------------------------- 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 = 0.051279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.041849 restraints weight = 61110.596| |-----------------------------------------------------------------------------| r_work (start): 0.2394 rms_B_bonded: 1.87 r_work: 0.2305 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2207 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.0677 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= 0.158 Angle : 0.631 28.804 34733 Z= 0.331 Chirality : 0.052 1.908 3908 Planarity : 0.006 0.141 4154 Dihedral : 14.705 179.984 4474 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.56 % Favored : 94.98 % Rotamer: Outliers : 4.59 % Allowed : 27.32 % 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: 1.48 (0.16), residues: 1097 sheet: 0.79 (0.25), residues: 417 loop : -0.74 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 312 TYR 0.016 0.001 TYR B 125 PHE 0.019 0.002 PHE B 126 TRP 0.008 0.001 TRP B 25 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (25439) covalent geometry : angle 0.63099 / 0.33 (34733) hydrogen bonds : bond 0.04630 / 3.08 ( 1054) hydrogen bonds : angle 4.84254 / 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: 118 poor density : 301 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7859 (tm-30) REVERT: A 361 ASN cc_start: 0.8098 (m-40) cc_final: 0.7786 (m110) REVERT: A 406 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6856 (ptpp) REVERT: A 417 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7860 (mm-30) REVERT: B 94 GLU cc_start: 0.6907 (tp30) cc_final: 0.6526 (tp30) REVERT: B 98 HIS cc_start: 0.9309 (OUTLIER) cc_final: 0.8676 (m170) REVERT: B 128 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7271 (pp20) REVERT: B 161 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7157 (tm-30) REVERT: B 224 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6075 (mp) REVERT: B 233 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8111 (mt) REVERT: B 370 SER cc_start: 0.8868 (m) cc_final: 0.8524 (p) REVERT: B 392 MET cc_start: 0.8804 (tmm) cc_final: 0.8532 (tmt) REVERT: C 112 LYS cc_start: 0.9037 (mppt) cc_final: 0.8533 (mppt) REVERT: C 115 GLU cc_start: 0.8799 (mp0) cc_final: 0.8553 (mp0) REVERT: C 233 GLN cc_start: 0.8467 (mp10) cc_final: 0.8185 (pm20) REVERT: C 255 VAL cc_start: 0.8728 (t) cc_final: 0.8506 (m) REVERT: C 313 GLU cc_start: 0.8094 (pm20) cc_final: 0.7634 (pp20) REVERT: C 406 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8489 (tmmm) REVERT: C 409 MET cc_start: 0.9184 (mtm) cc_final: 0.8871 (mtt) REVERT: E 188 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9149 (mp) REVERT: G 13 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8049 (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: 118 outliers final: 52 residues processed: 391 average time/residue: 0.6903 time to fit residues: 307.8355 Evaluate side-chains 342 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 279 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 335 LEU 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: 2.9990 chunk 159 optimal weight: 0.1980 chunk 131 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.050800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.041529 restraints weight = 61403.084| |-----------------------------------------------------------------------------| r_work (start): 0.2386 rms_B_bonded: 1.86 r_work: 0.2297 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2197 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.0879 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= 0.158 Angle : 0.619 29.271 34733 Z= 0.325 Chirality : 0.052 1.872 3908 Planarity : 0.005 0.140 4154 Dihedral : 14.344 178.717 4387 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.63 % Favored : 94.87 % Rotamer: Outliers : 4.59 % Allowed : 27.63 % Favored : 67.78 % 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: 1.50 (0.16), residues: 1100 sheet: 0.91 (0.26), residues: 383 loop : -0.75 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 418 TYR 0.014 0.001 TYR F 270 PHE 0.023 0.002 PHE B 74 TRP 0.009 0.001 TRP B 25 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (25439) covalent geometry : angle 0.61915 / 0.32 (34733) hydrogen bonds : bond 0.04394 / 2.93 ( 1054) hydrogen bonds : angle 4.66101 / 3.28 ( 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 409 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 291 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8439 (tmtt) REVERT: A 263 PHE cc_start: 0.7437 (t80) cc_final: 0.7143 (t80) REVERT: A 264 ARG cc_start: 0.8362 (tpp80) cc_final: 0.8158 (tpp80) REVERT: A 308 ILE cc_start: 0.9368 (mm) cc_final: 0.9135 (mp) REVERT: A 361 ASN cc_start: 0.8007 (m-40) cc_final: 0.7706 (m110) REVERT: A 406 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6857 (ptpp) REVERT: A 417 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7932 (mm-30) REVERT: B 1 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7606 (mtm) REVERT: B 98 HIS cc_start: 0.9306 (OUTLIER) cc_final: 0.8756 (m170) REVERT: B 128 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7172 (pp20) REVERT: B 224 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6174 (mp) REVERT: B 233 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8114 (mt) REVERT: B 370 SER cc_start: 0.8889 (m) cc_final: 0.8543 (p) REVERT: B 392 MET cc_start: 0.8808 (tmm) cc_final: 0.8527 (tmt) REVERT: B 409 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8812 (m-30) REVERT: C 112 LYS cc_start: 0.9089 (mppt) cc_final: 0.8539 (mmmm) REVERT: C 115 GLU cc_start: 0.8809 (mp0) cc_final: 0.8585 (mp0) REVERT: C 233 GLN cc_start: 0.8494 (mp10) cc_final: 0.8204 (pm20) REVERT: C 255 VAL cc_start: 0.8741 (t) cc_final: 0.8520 (m) REVERT: C 313 GLU cc_start: 0.8078 (pm20) cc_final: 0.7611 (pp20) REVERT: C 406 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8536 (tmmm) REVERT: C 409 MET cc_start: 0.9160 (mtm) cc_final: 0.8785 (mtt) REVERT: C 415 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8525 (mtp180) REVERT: E 188 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9125 (mt) REVERT: G 13 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: G 20 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8826 (mt) REVERT: H 126 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8897 (mtm) REVERT: I 181 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8718 (t0) REVERT: I 238 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8146 (mtp85) outliers start: 118 outliers final: 60 residues processed: 380 average time/residue: 0.6588 time to fit residues: 285.0315 Evaluate side-chains 352 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 276 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 170 ASP 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 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 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 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 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 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: 0.8980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 GLN A 463 ASN B 342 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 = 0.2627 r_free = 0.2627 target = 0.050137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.040794 restraints weight = 61032.335| |-----------------------------------------------------------------------------| r_work (start): 0.2365 rms_B_bonded: 1.86 r_work: 0.2276 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2176 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25439 Z= 0.177 Angle : 0.628 29.283 34733 Z= 0.330 Chirality : 0.052 1.879 3908 Planarity : 0.005 0.139 4154 Dihedral : 14.307 178.317 4380 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.42 % Favored : 95.08 % Rotamer: Outliers : 5.29 % Allowed : 27.21 % Favored : 67.51 % 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: 0.54 (0.16), residues: 2828 helix: 1.49 (0.16), residues: 1100 sheet: 0.75 (0.25), residues: 417 loop : -0.74 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 46 TYR 0.015 0.001 TYR A 435 PHE 0.016 0.002 PHE C 281 TRP 0.009 0.001 TRP F 219 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (25439) covalent geometry : angle 0.62796 / 0.33 (34733) hydrogen bonds : bond 0.04375 / 2.92 ( 1054) hydrogen bonds : angle 4.58071 / 3.22 ( 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 421 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 285 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8344 (pm20) cc_final: 0.7993 (pm20) REVERT: A 252 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8455 (tmtt) REVERT: A 263 PHE cc_start: 0.7613 (t80) cc_final: 0.7371 (t80) REVERT: A 361 ASN cc_start: 0.8027 (m-40) cc_final: 0.7729 (m110) REVERT: A 417 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 1 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7567 (mtm) REVERT: B 57 GLU cc_start: 0.8424 (tp30) cc_final: 0.8221 (mm-30) REVERT: B 94 GLU cc_start: 0.7013 (tp30) cc_final: 0.6636 (tp30) REVERT: B 98 HIS cc_start: 0.9328 (OUTLIER) cc_final: 0.8843 (m170) REVERT: B 128 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7159 (pp20) REVERT: B 184 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7661 (p90) REVERT: B 193 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8320 (mtm-85) REVERT: B 224 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6284 (mp) REVERT: B 233 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8178 (mt) REVERT: B 370 SER cc_start: 0.8867 (m) cc_final: 0.8523 (p) REVERT: B 392 MET cc_start: 0.8809 (tmm) cc_final: 0.8531 (tmt) REVERT: B 409 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8715 (m-30) REVERT: C 112 LYS cc_start: 0.9105 (mppt) cc_final: 0.8534 (mmmm) REVERT: C 115 GLU cc_start: 0.8841 (mp0) cc_final: 0.8612 (mp0) REVERT: C 233 GLN cc_start: 0.8531 (mp10) cc_final: 0.8252 (pm20) REVERT: C 255 VAL cc_start: 0.8779 (t) cc_final: 0.8554 (m) REVERT: C 313 GLU cc_start: 0.8081 (pm20) cc_final: 0.7618 (pp20) REVERT: C 406 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8528 (tmmm) REVERT: C 409 MET cc_start: 0.9184 (mtm) cc_final: 0.8879 (mtt) REVERT: C 415 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8537 (mtp180) REVERT: E 188 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9126 (mt) REVERT: G 13 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: G 20 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8903 (mt) REVERT: G 68 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8893 (pt) REVERT: H 126 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8905 (mtm) REVERT: I 181 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8703 (t0) REVERT: I 238 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.7894 (mtp85) outliers start: 136 outliers final: 78 residues processed: 386 average time/residue: 0.6550 time to fit residues: 288.7234 Evaluate side-chains 378 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 283 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 208 LYS Chi-restraints excluded: chain A residue 210 ILE 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 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 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 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 184 ASP 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 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 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 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 1 MET 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 126 MET 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 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: 0.9990 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 B 345 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.048029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2304 r_free = 0.2304 target = 0.038763 restraints weight = 61338.045| |-----------------------------------------------------------------------------| r_work (start): 0.2303 rms_B_bonded: 1.83 r_work: 0.2211 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2111 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 25439 Z= 0.281 Angle : 0.706 30.078 34733 Z= 0.372 Chirality : 0.055 1.858 3908 Planarity : 0.006 0.141 4154 Dihedral : 14.333 178.972 4374 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.70 % Favored : 94.77 % Rotamer: Outliers : 6.22 % Allowed : 26.47 % Favored : 67.31 % 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: 0.33 (0.16), residues: 2828 helix: 1.25 (0.16), residues: 1109 sheet: 0.69 (0.25), residues: 420 loop : -0.84 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 418 TYR 0.018 0.002 TYR A 435 PHE 0.022 0.002 PHE C 281 TRP 0.013 0.002 TRP F 219 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.28 (25439) covalent geometry : angle 0.70581 / 0.37 (34733) hydrogen bonds : bond 0.05073 / 3.39 ( 1054) hydrogen bonds : angle 4.66631 / 3.28 ( 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 441 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 281 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ARG cc_start: 0.8265 (tpp80) cc_final: 0.8044 (tpp80) REVERT: A 406 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6986 (ptpp) REVERT: A 417 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8002 (mm-30) REVERT: B 1 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7716 (mtm) REVERT: B 98 HIS cc_start: 0.9293 (OUTLIER) cc_final: 0.8779 (m170) REVERT: B 128 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7189 (pp20) REVERT: B 184 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7872 (p90) REVERT: B 224 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6506 (mp) REVERT: B 233 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8203 (mt) REVERT: B 271 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8802 (mttp) REVERT: B 370 SER cc_start: 0.8914 (m) cc_final: 0.8640 (p) REVERT: B 392 MET cc_start: 0.8803 (tmm) cc_final: 0.8399 (tmm) REVERT: B 409 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8788 (m-30) REVERT: B 540 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9072 (tp) REVERT: C 112 LYS cc_start: 0.9143 (mppt) cc_final: 0.8592 (mmmm) REVERT: C 115 GLU cc_start: 0.8861 (mp0) cc_final: 0.8624 (mp0) REVERT: C 213 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8667 (mtmm) REVERT: C 255 VAL cc_start: 0.8847 (t) cc_final: 0.8629 (m) REVERT: C 313 GLU cc_start: 0.8061 (pm20) cc_final: 0.7615 (pp20) REVERT: C 406 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8539 (tmmm) REVERT: C 415 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8652 (mtp180) REVERT: E 4 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.6792 (ptp90) REVERT: E 188 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9194 (mp) REVERT: G 13 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: G 20 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9068 (mt) REVERT: G 117 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8618 (ttpp) REVERT: H 126 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8913 (mtm) REVERT: I 156 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8934 (mp) REVERT: I 181 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8718 (t0) outliers start: 160 outliers final: 90 residues processed: 399 average time/residue: 0.6335 time to fit residues: 289.6248 Evaluate side-chains 391 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 280 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 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 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 A residue 440 THR Chi-restraints excluded: chain A residue 444 LEU 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 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 540 LEU 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 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 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 44 SER Chi-restraints excluded: chain E residue 123 THR 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 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 86 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 104 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 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 297 CYS 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: 0.9980 chunk 142 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 201 optimal weight: 0.0770 chunk 230 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 258 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 166 HIS B 356 GLN C 105 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.2631 r_free = 0.2631 target = 0.050270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2372 r_free = 0.2372 target = 0.041019 restraints weight = 60934.050| |-----------------------------------------------------------------------------| r_work (start): 0.2368 rms_B_bonded: 1.84 r_work: 0.2281 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2182 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.1187 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= 0.143 Angle : 0.621 29.332 34733 Z= 0.326 Chirality : 0.052 1.876 3908 Planarity : 0.006 0.137 4154 Dihedral : 14.320 178.547 4374 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.31 % Favored : 95.12 % Rotamer: Outliers : 5.09 % Allowed : 27.94 % 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: 0.50 (0.16), residues: 2828 helix: 1.47 (0.16), residues: 1100 sheet: 0.66 (0.25), residues: 417 loop : -0.75 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 418 TYR 0.017 0.001 TYR A 267 PHE 0.018 0.001 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 0.00326 / 0.14 (25439) covalent geometry : angle 0.62129 / 0.33 (34733) hydrogen bonds : bond 0.04112 / 2.77 ( 1054) hydrogen bonds : angle 4.52255 / 3.18 ( 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 423 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 292 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 PHE cc_start: 0.7519 (t80) cc_final: 0.7230 (t80) REVERT: A 406 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6893 (ptpp) REVERT: A 417 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7912 (mm-30) REVERT: B 74 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7798 (t80) REVERT: B 94 GLU cc_start: 0.6998 (tp30) cc_final: 0.6512 (tp30) REVERT: B 98 HIS cc_start: 0.9315 (OUTLIER) cc_final: 0.8783 (m170) REVERT: B 128 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7055 (pp20) REVERT: B 184 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7757 (p90) REVERT: B 193 ARG cc_start: 0.8760 (mtm-85) cc_final: 0.8024 (ptm-80) REVERT: B 224 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6478 (mp) REVERT: B 233 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8175 (mt) REVERT: B 370 SER cc_start: 0.8913 (m) cc_final: 0.8643 (p) REVERT: B 392 MET cc_start: 0.8797 (tmm) cc_final: 0.8523 (tmt) REVERT: B 409 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8680 (m-30) REVERT: C 112 LYS cc_start: 0.9123 (mppt) cc_final: 0.8612 (mmmm) REVERT: C 115 GLU cc_start: 0.8838 (mp0) cc_final: 0.8612 (mp0) REVERT: C 255 VAL cc_start: 0.8823 (t) cc_final: 0.8607 (m) REVERT: C 313 GLU cc_start: 0.8063 (pm20) cc_final: 0.7602 (pp20) REVERT: C 406 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8525 (tmmm) REVERT: C 415 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8587 (mtp180) REVERT: E 188 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9133 (mt) REVERT: G 13 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: G 20 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8925 (mt) REVERT: G 68 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8872 (pt) REVERT: G 117 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8613 (ttpp) REVERT: H 126 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8896 (mtm) REVERT: I 150 MET cc_start: 0.9171 (tpp) cc_final: 0.8928 (tpp) REVERT: I 181 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8712 (t0) REVERT: I 238 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.7620 (mtp85) outliers start: 131 outliers final: 70 residues processed: 388 average time/residue: 0.6860 time to fit residues: 303.1879 Evaluate side-chains 370 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 282 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 120 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 240 ILE 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 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 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 282 SER 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 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 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 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 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 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 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 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 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: 3.9990 chunk 231 optimal weight: 3.9990 chunk 239 optimal weight: 0.6980 chunk 245 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 HIS ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 356 GLN C 105 GLN C 315 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.048834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2328 r_free = 0.2328 target = 0.039545 restraints weight = 61357.422| |-----------------------------------------------------------------------------| r_work (start): 0.2325 rms_B_bonded: 1.86 r_work: 0.2236 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2137 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 25439 Z= 0.222 Angle : 0.675 29.697 34733 Z= 0.354 Chirality : 0.053 1.867 3908 Planarity : 0.006 0.138 4154 Dihedral : 14.305 178.912 4372 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.63 % Favored : 94.80 % Rotamer: Outliers : 5.13 % Allowed : 27.98 % Favored : 66.89 % 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: 0.42 (0.16), residues: 2828 helix: 1.40 (0.16), residues: 1098 sheet: 0.66 (0.25), residues: 418 loop : -0.81 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 418 TYR 0.020 0.002 TYR A 267 PHE 0.019 0.002 PHE C 281 TRP 0.010 0.002 TRP F 219 HIS 0.006 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (25439) covalent geometry : angle 0.67482 / 0.35 (34733) hydrogen bonds : bond 0.04618 / 3.09 ( 1054) hydrogen bonds : angle 4.56275 / 3.20 ( 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 418 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 286 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6925 (ptpp) REVERT: A 417 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8006 (mm-30) REVERT: B 94 GLU cc_start: 0.7042 (tp30) cc_final: 0.6620 (tp30) REVERT: B 98 HIS cc_start: 0.9306 (OUTLIER) cc_final: 0.8629 (m170) REVERT: B 128 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7268 (pp20) REVERT: B 184 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7979 (p90) REVERT: B 193 ARG cc_start: 0.8797 (mtm-85) cc_final: 0.8266 (ptm-80) REVERT: B 224 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6538 (mp) REVERT: B 233 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8236 (mt) REVERT: B 271 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8819 (mttp) REVERT: B 370 SER cc_start: 0.8953 (m) cc_final: 0.8677 (p) REVERT: B 392 MET cc_start: 0.8808 (tmm) cc_final: 0.8528 (tmt) REVERT: B 409 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8718 (m-30) REVERT: B 540 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9017 (tp) REVERT: C 112 LYS cc_start: 0.9133 (mppt) cc_final: 0.8612 (mmmm) REVERT: C 115 GLU cc_start: 0.8851 (mp0) cc_final: 0.8603 (mp0) REVERT: C 178 ASN cc_start: 0.8723 (t0) cc_final: 0.8426 (t0) REVERT: C 255 VAL cc_start: 0.8857 (t) cc_final: 0.8643 (m) REVERT: C 406 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8540 (tmmm) REVERT: C 415 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8644 (mtp180) REVERT: E 188 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9183 (mp) REVERT: F 207 ARG cc_start: 0.9394 (OUTLIER) cc_final: 0.7305 (mtm-85) REVERT: G 13 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: G 20 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8999 (mt) REVERT: G 68 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8904 (pt) REVERT: G 117 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8618 (ttpp) REVERT: H 126 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8918 (mtm) REVERT: I 150 MET cc_start: 0.9176 (tpp) cc_final: 0.8925 (tpp) REVERT: I 156 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8942 (mp) REVERT: I 181 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8716 (t0) outliers start: 132 outliers final: 83 residues processed: 383 average time/residue: 0.6824 time to fit residues: 297.9589 Evaluate side-chains 385 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 282 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 120 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 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 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 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 540 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 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 2 THR 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 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 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 G residue 117 LYS Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 104 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 260 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 265 optimal weight: 0.0010 chunk 259 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 GLN A 463 ASN B 356 GLN C 261 ASN C 370 ASN E 31 GLN G 23 ASN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.050138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.040879 restraints weight = 60845.988| |-----------------------------------------------------------------------------| r_work (start): 0.2365 rms_B_bonded: 1.84 r_work: 0.2277 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2179 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.1259 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= 0.149 Angle : 0.643 29.274 34733 Z= 0.336 Chirality : 0.052 1.880 3908 Planarity : 0.006 0.137 4154 Dihedral : 14.299 178.579 4372 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.56 % Favored : 94.91 % Rotamer: Outliers : 4.55 % Allowed : 28.64 % Favored : 66.81 % 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: 0.51 (0.16), residues: 2828 helix: 1.49 (0.16), residues: 1100 sheet: 0.65 (0.25), residues: 430 loop : -0.77 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 418 TYR 0.017 0.001 TYR A 435 PHE 0.018 0.001 PHE B 461 TRP 0.010 0.001 TRP B 25 HIS 0.006 0.001 HIS G 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (25439) covalent geometry : angle 0.64339 / 0.34 (34733) hydrogen bonds : bond 0.04113 / 2.76 ( 1054) hydrogen bonds : angle 4.50679 / 3.16 ( 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 410 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 293 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 PHE cc_start: 0.7504 (t80) cc_final: 0.7279 (t80) REVERT: A 406 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6885 (ptpp) REVERT: A 417 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7975 (mm-30) REVERT: B 98 HIS cc_start: 0.9279 (OUTLIER) cc_final: 0.8800 (m170) REVERT: B 128 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7272 (pp20) REVERT: B 184 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7736 (p90) REVERT: B 193 ARG cc_start: 0.8734 (mtm-85) cc_final: 0.8019 (ptm-80) REVERT: B 224 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6516 (mp) REVERT: B 233 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8250 (mt) REVERT: B 370 SER cc_start: 0.8959 (m) cc_final: 0.8685 (p) REVERT: B 392 MET cc_start: 0.8801 (tmm) cc_final: 0.8525 (tmt) REVERT: B 409 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8662 (m-30) REVERT: C 112 LYS cc_start: 0.9128 (mppt) cc_final: 0.8609 (mmmm) REVERT: C 115 GLU cc_start: 0.8836 (mp0) cc_final: 0.8606 (mp0) REVERT: C 178 ASN cc_start: 0.8682 (t0) cc_final: 0.8460 (t0) REVERT: C 255 VAL cc_start: 0.8836 (t) cc_final: 0.8622 (m) REVERT: C 406 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8527 (tmmm) REVERT: C 415 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8627 (mtp180) REVERT: D 73 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8497 (pptt) REVERT: E 188 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9119 (mp) REVERT: G 13 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: G 20 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8909 (mt) REVERT: G 68 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8870 (pt) REVERT: G 117 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8622 (ttpp) REVERT: H 126 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8900 (mtm) REVERT: I 181 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8691 (t0) REVERT: I 238 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7960 (mtp85) outliers start: 117 outliers final: 71 residues processed: 383 average time/residue: 0.6660 time to fit residues: 291.2605 Evaluate side-chains 377 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 288 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 240 ILE 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 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 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 298 THR 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 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 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 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 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 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 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 112 THR Chi-restraints excluded: chain G residue 117 LYS 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 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: 0.4980 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 125 optimal weight: 0.3980 chunk 132 optimal weight: 3.9990 chunk 235 optimal weight: 0.5980 chunk 284 optimal weight: 7.9990 chunk 199 optimal weight: 0.0270 chunk 187 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN A 463 ASN B 356 GLN C 197 ASN C 367 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.051104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.041861 restraints weight = 60762.811| |-----------------------------------------------------------------------------| r_work (start): 0.2395 rms_B_bonded: 1.84 r_work: 0.2308 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2210 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 25439 Z= 0.132 Angle : 0.639 28.967 34733 Z= 0.333 Chirality : 0.051 1.889 3908 Planarity : 0.006 0.135 4154 Dihedral : 14.258 178.198 4372 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.49 % Favored : 94.98 % Rotamer: Outliers : 3.77 % Allowed : 29.38 % 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: 0.57 (0.16), residues: 2828 helix: 1.55 (0.16), residues: 1102 sheet: 0.65 (0.25), residues: 429 loop : -0.73 (0.18), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 136 TYR 0.020 0.001 TYR A 267 PHE 0.018 0.001 PHE B 461 TRP 0.010 0.001 TRP B 25 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (25439) covalent geometry : angle 0.63931 / 0.33 (34733) hydrogen bonds : bond 0.03833 / 2.58 ( 1054) hydrogen bonds : angle 4.43233 / 3.11 ( 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 388 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 291 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6887 (ptpp) REVERT: A 417 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7930 (mm-30) REVERT: B 94 GLU cc_start: 0.7016 (tp30) cc_final: 0.6530 (tp30) REVERT: B 98 HIS cc_start: 0.9280 (OUTLIER) cc_final: 0.8817 (m170) REVERT: B 128 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7260 (pp20) REVERT: B 184 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7692 (p90) REVERT: B 193 ARG cc_start: 0.8723 (mtm-85) cc_final: 0.8020 (ptm-80) REVERT: B 224 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6535 (mp) REVERT: B 233 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8248 (mt) REVERT: B 370 SER cc_start: 0.8966 (m) cc_final: 0.8672 (p) REVERT: B 392 MET cc_start: 0.8803 (tmm) cc_final: 0.8530 (tmt) REVERT: B 409 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8636 (m-30) REVERT: C 91 MET cc_start: 0.9189 (ttp) cc_final: 0.8966 (tmm) REVERT: C 112 LYS cc_start: 0.9110 (mppt) cc_final: 0.8681 (mmmm) REVERT: C 115 GLU cc_start: 0.8842 (mp0) cc_final: 0.8539 (mp0) REVERT: C 178 ASN cc_start: 0.8717 (t0) cc_final: 0.8464 (t0) REVERT: C 406 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8513 (tmmm) REVERT: D 73 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8460 (pptt) REVERT: E 188 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9101 (mp) REVERT: F 207 ARG cc_start: 0.9360 (OUTLIER) cc_final: 0.7305 (mtm-85) REVERT: G 13 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: G 20 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8841 (mt) REVERT: G 68 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8820 (pt) REVERT: H 126 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8880 (mtm) outliers start: 97 outliers final: 66 residues processed: 363 average time/residue: 0.6840 time to fit residues: 282.0943 Evaluate side-chains 364 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 283 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 120 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 240 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 311 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 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 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 508 LYS 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 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 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 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 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 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 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 223 GLU Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 275 SER 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 258 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 356 GLN C 217 HIS ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN H 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.051008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.041787 restraints weight = 61036.744| |-----------------------------------------------------------------------------| r_work (start): 0.2392 rms_B_bonded: 1.83 r_work: 0.2306 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2208 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 25439 Z= 0.185 Angle : 0.847 59.052 34733 Z= 0.451 Chirality : 0.052 1.891 3908 Planarity : 0.006 0.135 4154 Dihedral : 14.255 178.193 4370 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.53 % Favored : 94.94 % Rotamer: Outliers : 3.34 % Allowed : 29.85 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.04 % 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: 0.56 (0.16), residues: 2828 helix: 1.54 (0.16), residues: 1102 sheet: 0.66 (0.25), residues: 429 loop : -0.75 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 136 TYR 0.017 0.001 TYR A 267 PHE 0.018 0.001 PHE B 461 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 0.00404 / 0.18 (25439) covalent geometry : angle 0.84657 / 0.45 (34733) hydrogen bonds : bond 0.03862 / 2.60 ( 1054) hydrogen bonds : angle 4.43143 / 3.11 ( 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 370 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 284 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6893 (ptpp) REVERT: A 417 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 94 GLU cc_start: 0.7016 (tp30) cc_final: 0.6532 (tp30) REVERT: B 98 HIS cc_start: 0.9283 (OUTLIER) cc_final: 0.8813 (m170) REVERT: B 128 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7256 (pp20) REVERT: B 184 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7875 (p90) REVERT: B 193 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8177 (ptm-80) REVERT: B 224 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6545 (mp) REVERT: B 233 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8242 (mt) REVERT: B 370 SER cc_start: 0.8954 (m) cc_final: 0.8654 (p) REVERT: B 392 MET cc_start: 0.8804 (tmm) cc_final: 0.8533 (tmt) REVERT: B 409 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8648 (m-30) REVERT: C 91 MET cc_start: 0.9195 (ttp) cc_final: 0.8975 (tmm) REVERT: C 112 LYS cc_start: 0.9108 (mppt) cc_final: 0.8680 (mmmm) REVERT: C 115 GLU cc_start: 0.8840 (mp0) cc_final: 0.8537 (mp0) REVERT: C 178 ASN cc_start: 0.8723 (t0) cc_final: 0.8476 (t0) REVERT: C 406 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8515 (tmmm) REVERT: D 73 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8472 (pptt) REVERT: E 188 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9105 (mp) REVERT: F 207 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.7311 (mtm-85) REVERT: G 13 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: G 20 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8845 (mt) REVERT: G 68 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8823 (pt) REVERT: H 126 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8886 (mtm) outliers start: 86 outliers final: 66 residues processed: 348 average time/residue: 0.7193 time to fit residues: 284.5761 Evaluate side-chains 363 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 282 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 208 LYS 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 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 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 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 508 LYS 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 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 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 235 MET 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 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 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 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 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 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 266 optimal weight: 2.9990 chunk 284 optimal weight: 7.9990 chunk 114 optimal weight: 0.3980 chunk 223 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 268 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 356 GLN 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.051001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.041759 restraints weight = 60907.252| |-----------------------------------------------------------------------------| r_work (start): 0.2393 rms_B_bonded: 1.84 r_work: 0.2306 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2207 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 25439 Z= 0.182 Angle : 0.845 59.196 34733 Z= 0.450 Chirality : 0.052 1.891 3908 Planarity : 0.006 0.137 4154 Dihedral : 14.255 178.193 4370 Min Nonbonded Distance : 0.936 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.53 % Favored : 94.94 % Rotamer: Outliers : 3.26 % Allowed : 29.97 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.04 % 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: 0.56 (0.16), residues: 2828 helix: 1.54 (0.16), residues: 1102 sheet: 0.66 (0.25), residues: 429 loop : -0.75 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 136 TYR 0.016 0.001 TYR A 267 PHE 0.018 0.001 PHE B 461 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 0.00400 / 0.18 (25439) covalent geometry : angle 0.84507 / 0.45 (34733) hydrogen bonds : bond 0.03862 / 2.60 ( 1054) hydrogen bonds : angle 4.43142 / 3.11 ( 2980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7712.51 seconds wall clock time: 132 minutes 44.82 seconds (7964.82 seconds total)