Starting phenix.real_space_refine on Fri Feb 6 11:44:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lq7_63295/02_2026/9lq7_63295.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lq7_63295/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9lq7_63295/02_2026/9lq7_63295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lq7_63295/02_2026/9lq7_63295.map" model { file = "/net/cci-nas-00/data/ceres_data/9lq7_63295/02_2026/9lq7_63295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lq7_63295/02_2026/9lq7_63295.cif" } 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24765 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3904 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 17, 'TRANS': 451} Chain: "B" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4788 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 20, 'TRANS': 569} Chain breaks: 2 Chain: "C" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3044 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 1 Chain: "D" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2214 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "E" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2214 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "F" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2214 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "G" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1071 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "H" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1071 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "I" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2534 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 16, 'TRANS': 297} Chain: "K" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 779 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 18} Link IDs: {'rna2p': 6, 'rna3p': 30} Chain: "J" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 873 Classifications: {'RNA': 41} Modifications used: {'p5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna2p': 17, 'rna3p': 23} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MN': 1, 'ATP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 4.99, per 1000 atoms: 0.20 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: 2.06 Conformation dependent library (CDL) restraints added in 950.3 milliseconds 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: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 143 through 149 Processing helix chain 'A' and resid 168 through 186 Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.612A pdb=" N ASN A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.588A pdb=" N TYR A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.543A pdb=" N LYS A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 297 Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.586A pdb=" N ALA A 333 " --> pdb=" O TYR A 330 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 334 " --> pdb=" O ILE A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 334' Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 20 through 45 removed outlier: 3.802A pdb=" N PHE B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.879A pdb=" N GLN B 59 " --> pdb=" O ASN B 55 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 60' Processing helix chain 'B' and resid 79 through 97 removed outlier: 3.915A pdb=" N LEU B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 135 through 151 Proline residue: B 141 - end of helix removed outlier: 3.740A pdb=" N TYR B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 197 through 204 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 267 through 270 Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 296 through 319 removed outlier: 4.150A pdb=" N LEU B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 362 Processing helix chain 'B' and resid 362 through 372 removed outlier: 3.670A pdb=" N GLU B 371 " --> pdb=" O ASN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 409 through 419 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 455 through 469 removed outlier: 4.213A pdb=" N VAL B 459 " --> pdb=" O GLY B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 4.152A pdb=" N GLN B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 505 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 529 through 561 removed outlier: 5.807A pdb=" N ASN B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 573 Processing helix chain 'B' and resid 575 through 596 Processing helix chain 'C' and resid 84 through 100 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 239 through 242 No H-bonds generated for 'chain 'C' and resid 239 through 242' Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 328 through 330 No H-bonds generated for 'chain 'C' and resid 328 through 330' Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.994A pdb=" N LEU C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 410 Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'D' and resid 42 through 55 Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 104 through 118 Processing helix chain 'D' and resid 121 through 141 removed outlier: 3.823A pdb=" N TYR D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 189 through 197 Processing helix chain 'D' and resid 240 through 253 Processing helix chain 'E' and resid 42 through 55 Processing helix chain 'E' and resid 57 through 65 Processing helix chain 'E' and resid 104 through 118 Processing helix chain 'E' and resid 121 through 141 removed outlier: 3.973A pdb=" N TYR E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 154 removed outlier: 3.647A pdb=" N GLN E 154 " --> pdb=" O PRO E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 Processing helix chain 'E' and resid 189 through 198 Processing helix chain 'E' and resid 240 through 252 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'F' and resid 42 through 54 Processing helix chain 'F' and resid 57 through 65 Processing helix chain 'F' and resid 104 through 118 Processing helix chain 'F' and resid 121 through 141 removed outlier: 4.073A pdb=" N TYR F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 154 removed outlier: 3.622A pdb=" N GLN F 154 " --> pdb=" O PRO F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 Processing helix chain 'F' and resid 189 through 198 Processing helix chain 'F' and resid 240 through 253 Processing helix chain 'G' and resid 4 through 18 Processing helix chain 'G' and resid 29 through 45 removed outlier: 4.321A pdb=" N GLY G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY G 39 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA G 40 " --> pdb=" O SER G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 65 through 83 removed outlier: 4.106A pdb=" N ILE G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 112 through 130 Processing helix chain 'G' and resid 131 through 133 No H-bonds generated for 'chain 'G' and resid 131 through 133' Processing helix chain 'H' and resid 4 through 18 Processing helix chain 'H' and resid 29 through 45 removed outlier: 4.431A pdb=" N GLY H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 65 through 82 removed outlier: 3.965A pdb=" N ILE H 69 " --> pdb=" O ARG H 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 91 removed outlier: 3.879A pdb=" N ILE H 90 " --> pdb=" O THR H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 109 Processing helix chain 'H' and resid 112 through 131 Processing helix chain 'I' and resid 12 through 19 Processing helix chain 'I' and resid 32 through 38 Processing helix chain 'I' and resid 38 through 53 Processing helix chain 'I' and resid 61 through 72 Processing helix chain 'I' and resid 116 through 126 Processing helix chain 'I' and resid 127 through 132 removed outlier: 6.987A pdb=" N PHE I 130 " --> pdb=" O MET I 127 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU I 132 " --> pdb=" O PRO I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 161 removed outlier: 3.677A pdb=" N GLU I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR I 152 " --> pdb=" O GLU I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 Processing helix chain 'I' and resid 261 through 271 Processing helix chain 'I' and resid 275 through 277 No H-bonds generated for 'chain 'I' and resid 275 through 277' Processing helix chain 'I' and resid 283 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 78 removed outlier: 6.632A pdb=" N THR A 5 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 204 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 7 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 removed outlier: 6.316A pdb=" N GLY A 119 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 129 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 139 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 375 removed outlier: 3.802A pdb=" N ILE A 379 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 223 " --> pdb=" O GLY A 383 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 224 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 262 removed outlier: 3.534A pdb=" N ILE A 268 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 342 removed outlier: 3.775A pdb=" N THR A 403 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR A 416 " --> pdb=" O THR A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 75 removed outlier: 3.776A pdb=" N PHE B 126 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU B 128 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS C 185 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB1, first strand: chain 'B' and resid 183 through 184 removed outlier: 4.009A pdb=" N ARG B 193 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 321 through 326 removed outlier: 6.677A pdb=" N LEU B 331 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 325 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS B 434 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 337 through 338 Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 146 removed outlier: 6.553A pdb=" N THR C 284 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE C 146 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR C 282 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU C 151 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 163 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN C 229 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 143 through 146 removed outlier: 6.553A pdb=" N THR C 284 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE C 146 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR C 282 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N PHE C 277 " --> pdb=" O PRO C 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 76 through 77 Processing sheet with id=AB7, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AB8, first strand: chain 'C' and resid 335 through 336 Processing sheet with id=AB9, first strand: chain 'C' and resid 366 through 367 removed outlier: 4.023A pdb=" N ILE C 379 " --> pdb=" O GLN C 367 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.505A pdb=" N ARG D 229 " --> pdb=" O LEU D 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 229 through 235 current: chain 'D' and resid 185 through 188 Processing sheet with id=AC2, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.505A pdb=" N ARG D 229 " --> pdb=" O LEU D 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 84 through 92 current: chain 'D' and resid 274 through 275 Processing sheet with id=AC3, first strand: chain 'D' and resid 26 through 28 removed outlier: 5.244A pdb=" N ILE D 26 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLN D 222 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN D 28 " --> pdb=" O GLN D 222 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN D 209 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU D 218 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG D 207 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR D 220 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU D 205 " --> pdb=" O TYR D 220 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 157 through 158 removed outlier: 3.732A pdb=" N ILE D 163 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AC6, first strand: chain 'E' and resid 40 through 41 removed outlier: 6.530A pdb=" N ARG E 229 " --> pdb=" O LEU E 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 229 through 236 current: chain 'E' and resid 185 through 188 Processing sheet with id=AC7, first strand: chain 'E' and resid 79 through 81 removed outlier: 6.530A pdb=" N ARG E 229 " --> pdb=" O LEU E 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 92 current: chain 'E' and resid 270 through 275 Processing sheet with id=AC8, first strand: chain 'E' and resid 26 through 28 removed outlier: 4.939A pdb=" N ILE E 26 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLN E 222 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN E 28 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N SER E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU E 211 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 157 through 158 removed outlier: 3.684A pdb=" N ILE E 163 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 40 through 41 removed outlier: 6.530A pdb=" N ARG F 229 " --> pdb=" O LEU F 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 229 through 235 current: chain 'F' and resid 185 through 188 Processing sheet with id=AD2, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.530A pdb=" N ARG F 229 " --> pdb=" O LEU F 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 84 through 92 current: chain 'F' and resid 270 through 275 Processing sheet with id=AD3, first strand: chain 'F' and resid 26 through 28 removed outlier: 5.182A pdb=" N ILE F 26 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLN F 222 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN F 28 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN F 209 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU F 218 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG F 207 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR F 220 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU F 205 " --> pdb=" O TYR F 220 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 26 through 27 Processing sheet with id=AD5, first strand: chain 'I' and resid 114 through 115 removed outlier: 6.551A pdb=" N THR I 242 " --> pdb=" O ALA I 205 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL I 241 " --> pdb=" O THR I 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 198 through 199 Processing sheet with id=AD7, first strand: chain 'I' and resid 213 through 218 Processing sheet with id=AD8, first strand: chain 'I' and resid 258 through 260 removed outlier: 4.194A pdb=" N HIS I 253 " --> pdb=" O CYS I 260 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2844 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 4.17 Time building geometry restraints manager: 2.65 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=" 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 bond pdb=" CB LYS C 144 " pdb=" CG LYS C 144 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.87e+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 2.320 nonbonded pdb=" OD2 ASP B 328 " pdb="MN MN B 703 " model vdw 2.190 2.320 nonbonded pdb=" O SER E 67 " pdb=" O2' C J 12 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG G 131 " pdb=" OP1 C K 31 " model vdw 2.206 3.120 ... (remaining 210390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.770 Find NCS groups from input model: 0.140 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:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 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= 0.129 Angle : 0.635 28.671 34733 Z= 0.331 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 covalent geometry : bond 0.00286 (25439) covalent geometry : angle 0.63504 (34733) hydrogen bonds : bond 0.15538 ( 1054) hydrogen bonds : angle 5.92011 ( 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 : 0.704 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: 0.7229 time to fit residues: 288.0029 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 : 1.071 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2647 r_free = 0.2647 target = 0.050900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.041604 restraints weight = 61482.342| |-----------------------------------------------------------------------------| r_work (start): 0.2387 rms_B_bonded: 1.87 r_work: 0.2298 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2199 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25439 Z= 0.157 Angle : 0.623 29.403 34733 Z= 0.323 Chirality : 0.052 1.898 3908 Planarity : 0.005 0.140 4154 Dihedral : 14.645 179.534 4474 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.63 % Favored : 94.91 % Rotamer: Outliers : 4.51 % Allowed : 27.32 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.16), residues: 2828 helix: 1.47 (0.16), residues: 1099 sheet: 0.85 (0.25), residues: 413 loop : -0.74 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 312 TYR 0.014 0.001 TYR F 270 PHE 0.015 0.001 PHE B 461 TRP 0.008 0.001 TRP A 147 HIS 0.005 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00356 (25439) covalent geometry : angle 0.62313 (34733) hydrogen bonds : bond 0.04315 ( 1054) hydrogen bonds : angle 4.72435 ( 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 417 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 301 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8892 (mm-30) REVERT: A 130 LYS cc_start: 0.9396 (mmmm) cc_final: 0.9044 (mmmm) REVERT: A 344 GLN cc_start: 0.8236 (tm-30) cc_final: 0.8011 (tm-30) REVERT: A 361 ASN cc_start: 0.8023 (m-40) cc_final: 0.7723 (m110) REVERT: A 406 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6904 (ptpp) REVERT: A 417 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8003 (mm-30) REVERT: B 98 HIS cc_start: 0.9309 (OUTLIER) cc_final: 0.8778 (m170) REVERT: B 128 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7023 (pp20) REVERT: B 161 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7224 (tm-30) REVERT: B 224 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6178 (mp) REVERT: B 233 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8120 (mt) REVERT: B 370 SER cc_start: 0.8863 (m) cc_final: 0.8499 (p) REVERT: B 392 MET cc_start: 0.8823 (tmm) cc_final: 0.8544 (tmt) REVERT: C 112 LYS cc_start: 0.9056 (mppt) cc_final: 0.8542 (mmmm) REVERT: C 115 GLU cc_start: 0.8802 (mp0) cc_final: 0.8576 (mp0) REVERT: C 155 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8997 (mtmm) REVERT: C 233 GLN cc_start: 0.8469 (mp10) cc_final: 0.8180 (pm20) REVERT: C 255 VAL cc_start: 0.8732 (t) cc_final: 0.8505 (m) REVERT: C 313 GLU cc_start: 0.8078 (pm20) cc_final: 0.7605 (pp20) REVERT: C 406 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8546 (tmmm) REVERT: C 409 MET cc_start: 0.9157 (mtm) cc_final: 0.8833 (mtt) REVERT: E 188 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9128 (mt) REVERT: G 13 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: G 20 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8818 (mt) REVERT: I 156 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8902 (mp) REVERT: I 181 ASN cc_start: 0.9159 (OUTLIER) cc_final: 0.8746 (t0) REVERT: I 238 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7929 (mtp85) outliers start: 116 outliers final: 51 residues processed: 392 average time/residue: 0.6593 time to fit residues: 294.2574 Evaluate side-chains 343 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 279 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 213 VAL 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 435 TYR 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 164 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 331 LEU 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 118 ILE 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 343 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain D residue 127 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 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 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 95 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 86 THR 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 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: 0.7980 chunk 197 optimal weight: 2.9990 chunk 159 optimal weight: 0.4980 chunk 131 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN A 463 ASN B 265 GLN C 105 GLN C 197 ASN E 31 GLN G 23 ASN G 111 ASN H 59 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.051027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.041751 restraints weight = 61469.531| |-----------------------------------------------------------------------------| r_work (start): 0.2391 rms_B_bonded: 1.86 r_work: 0.2304 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2206 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25439 Z= 0.147 Angle : 0.611 28.939 34733 Z= 0.315 Chirality : 0.051 1.895 3908 Planarity : 0.005 0.138 4154 Dihedral : 14.250 178.756 4380 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.38 % Favored : 95.16 % Rotamer: Outliers : 4.86 % Allowed : 26.93 % Favored : 68.21 % 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: 0.60 (0.16), residues: 2828 helix: 1.54 (0.16), residues: 1100 sheet: 0.92 (0.26), residues: 397 loop : -0.74 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 288 TYR 0.015 0.001 TYR F 270 PHE 0.022 0.001 PHE B 74 TRP 0.008 0.001 TRP B 25 HIS 0.005 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00334 (25439) covalent geometry : angle 0.61068 (34733) hydrogen bonds : bond 0.04058 ( 1054) hydrogen bonds : angle 4.53815 ( 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 419 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 294 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8495 (tmtt) REVERT: A 308 ILE cc_start: 0.9359 (mm) cc_final: 0.9122 (mp) REVERT: A 417 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7977 (mm-30) REVERT: B 98 HIS cc_start: 0.9305 (OUTLIER) cc_final: 0.8769 (m170) REVERT: B 128 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7048 (pp20) REVERT: B 184 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.8080 (p90) REVERT: B 224 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6349 (mp) REVERT: B 233 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8149 (mt) REVERT: B 370 SER cc_start: 0.8859 (m) cc_final: 0.8510 (p) REVERT: B 392 MET cc_start: 0.8809 (tmm) cc_final: 0.8517 (tmt) REVERT: C 112 LYS cc_start: 0.9087 (mppt) cc_final: 0.8675 (mmmm) REVERT: C 115 GLU cc_start: 0.8832 (mp0) cc_final: 0.8570 (mp0) REVERT: C 233 GLN cc_start: 0.8472 (mp10) cc_final: 0.8218 (pm20) REVERT: C 255 VAL cc_start: 0.8769 (t) cc_final: 0.8557 (m) REVERT: C 313 GLU cc_start: 0.8088 (pm20) cc_final: 0.7618 (pp20) REVERT: C 406 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8529 (tmmm) REVERT: C 415 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8562 (mtp180) REVERT: D 191 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8737 (ptpp) REVERT: E 188 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9085 (mt) REVERT: G 13 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: G 20 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8805 (mt) REVERT: G 68 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8864 (pt) REVERT: G 117 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8613 (ttpp) REVERT: I 156 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8899 (mp) REVERT: I 181 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8682 (t0) REVERT: I 238 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.7822 (mtp85) outliers start: 125 outliers final: 62 residues processed: 389 average time/residue: 0.7523 time to fit residues: 330.7283 Evaluate side-chains 362 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 283 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 229 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 252 LYS 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 B residue 8 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 248 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 439 LEU Chi-restraints excluded: chain B residue 570 GLU 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 160 SER 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 383 SER Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 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 191 LYS 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 14 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain 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 104 GLN Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 123 THR 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 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: 2.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 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 = 0.2599 r_free = 0.2599 target = 0.049110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.039807 restraints weight = 61299.824| |-----------------------------------------------------------------------------| r_work (start): 0.2334 rms_B_bonded: 1.86 r_work: 0.2244 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2145 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25439 Z= 0.206 Angle : 0.657 29.736 34733 Z= 0.340 Chirality : 0.053 1.869 3908 Planarity : 0.006 0.139 4154 Dihedral : 14.264 178.880 4372 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.70 % Favored : 94.73 % Rotamer: Outliers : 5.87 % Allowed : 26.27 % Favored : 67.86 % 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: 0.48 (0.16), residues: 2828 helix: 1.41 (0.16), residues: 1103 sheet: 0.78 (0.24), residues: 431 loop : -0.79 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 46 TYR 0.016 0.002 TYR A 435 PHE 0.018 0.002 PHE C 281 TRP 0.011 0.001 TRP F 219 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00480 (25439) covalent geometry : angle 0.65657 (34733) hydrogen bonds : bond 0.04474 ( 1054) hydrogen bonds : angle 4.57140 ( 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 444 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 293 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6986 (ptpp) REVERT: A 417 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8016 (mm-30) REVERT: B 98 HIS cc_start: 0.9298 (OUTLIER) cc_final: 0.8822 (m170) REVERT: B 128 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7268 (pp20) REVERT: B 184 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7417 (p90) REVERT: B 193 ARG cc_start: 0.8768 (mtm-85) cc_final: 0.8142 (mtm-85) REVERT: B 224 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6420 (mp) REVERT: B 233 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8216 (mt) REVERT: B 370 SER cc_start: 0.8913 (m) cc_final: 0.8636 (p) REVERT: B 392 MET cc_start: 0.8800 (tmm) cc_final: 0.8511 (tmt) REVERT: C 233 GLN cc_start: 0.8595 (mp10) cc_final: 0.8328 (pm20) REVERT: C 255 VAL cc_start: 0.8836 (t) cc_final: 0.8626 (m) REVERT: C 313 GLU cc_start: 0.8088 (pm20) cc_final: 0.7626 (pp20) REVERT: C 406 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8531 (tmmm) REVERT: C 415 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.8629 (mtp180) REVERT: D 191 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8780 (ptpp) REVERT: E 188 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9166 (mp) REVERT: G 13 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: G 20 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8972 (mt) REVERT: G 68 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8924 (pt) REVERT: G 117 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8610 (ttpp) REVERT: I 156 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8905 (mp) REVERT: I 181 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8723 (t0) outliers start: 151 outliers final: 80 residues processed: 402 average time/residue: 0.7390 time to fit residues: 337.6643 Evaluate side-chains 376 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 280 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 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 434 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 248 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 CYS Chi-restraints excluded: chain B residue 338 CYS 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 456 LYS Chi-restraints excluded: chain B residue 570 GLU 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 160 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 213 LYS Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 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 127 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 191 LYS 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 14 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 117 LYS 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 I residue 1 MET Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 114 TYR Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 112 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 463 ASN B 166 HIS B 356 GLN C 105 GLN E 31 GLN G 23 ASN G 111 ASN H 59 ASN I 50 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.049438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.040223 restraints weight = 61319.246| |-----------------------------------------------------------------------------| r_work (start): 0.2345 rms_B_bonded: 1.83 r_work: 0.2257 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2159 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 25439 Z= 0.186 Angle : 0.650 29.536 34733 Z= 0.336 Chirality : 0.052 1.876 3908 Planarity : 0.006 0.138 4154 Dihedral : 14.261 178.826 4370 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.38 % Favored : 95.12 % Rotamer: Outliers : 5.44 % Allowed : 26.82 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 2828 helix: 1.46 (0.16), residues: 1095 sheet: 0.74 (0.24), residues: 431 loop : -0.82 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 264 TYR 0.017 0.001 TYR A 435 PHE 0.017 0.002 PHE B 74 TRP 0.010 0.001 TRP B 25 HIS 0.005 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00433 (25439) covalent geometry : angle 0.64971 (34733) hydrogen bonds : bond 0.04271 ( 1054) hydrogen bonds : angle 4.52133 ( 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 434 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 294 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6897 (ptpp) REVERT: A 417 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 94 GLU cc_start: 0.6995 (tp30) cc_final: 0.6633 (tp30) REVERT: B 98 HIS cc_start: 0.9284 (OUTLIER) cc_final: 0.8716 (m170) REVERT: B 128 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7146 (pp20) REVERT: B 184 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7859 (p90) REVERT: B 193 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8420 (mtm-85) REVERT: B 224 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6448 (mp) REVERT: B 233 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8248 (mt) REVERT: B 271 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8852 (mttp) REVERT: B 370 SER cc_start: 0.8946 (m) cc_final: 0.8663 (p) REVERT: B 392 MET cc_start: 0.8794 (tmm) cc_final: 0.8509 (tmt) REVERT: C 112 LYS cc_start: 0.9248 (mmmm) cc_final: 0.8800 (mmmm) REVERT: C 115 GLU cc_start: 0.8840 (mp0) cc_final: 0.8623 (mp0) REVERT: C 233 GLN cc_start: 0.8577 (mp10) cc_final: 0.8302 (pm20) REVERT: C 255 VAL cc_start: 0.8848 (t) cc_final: 0.8637 (m) REVERT: C 406 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8519 (tmmm) REVERT: C 409 MET cc_start: 0.9095 (mtm) cc_final: 0.8875 (mtt) REVERT: C 415 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8630 (mtp180) REVERT: D 191 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8775 (ptpp) REVERT: E 188 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9168 (mp) REVERT: G 13 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: G 20 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8949 (mt) REVERT: G 68 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8894 (pt) REVERT: G 117 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8619 (ttpp) REVERT: I 156 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8906 (mp) REVERT: I 181 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8713 (t0) REVERT: I 238 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7652 (mtp85) outliers start: 140 outliers final: 79 residues processed: 399 average time/residue: 0.6935 time to fit residues: 315.4615 Evaluate side-chains 383 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 286 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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 317 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 434 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 342 ASN Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 213 LYS Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 252 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 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 24 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 314 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 130 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 264 optimal weight: 2.9990 chunk 258 optimal weight: 0.2980 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 463 ASN B 342 ASN C 105 GLN 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 = 0.051176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.041934 restraints weight = 60996.705| |-----------------------------------------------------------------------------| r_work (start): 0.2395 rms_B_bonded: 1.85 r_work: 0.2308 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2211 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25439 Z= 0.135 Angle : 0.610 29.016 34733 Z= 0.314 Chirality : 0.051 1.890 3908 Planarity : 0.005 0.135 4154 Dihedral : 14.183 177.981 4370 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.38 % Favored : 95.12 % Rotamer: Outliers : 4.97 % Allowed : 27.79 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 2828 helix: 1.58 (0.16), residues: 1100 sheet: 0.80 (0.26), residues: 399 loop : -0.75 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 418 TYR 0.015 0.001 TYR F 270 PHE 0.018 0.001 PHE B 461 TRP 0.009 0.001 TRP B 25 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00309 (25439) covalent geometry : angle 0.61020 (34733) hydrogen bonds : bond 0.03729 ( 1054) hydrogen bonds : angle 4.39018 ( 2980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 298 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6946 (ptpp) REVERT: A 417 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7965 (mm-30) REVERT: B 128 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7230 (pp20) REVERT: B 193 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8422 (mtm-85) REVERT: B 224 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6504 (mp) REVERT: B 233 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8249 (mt) REVERT: B 370 SER cc_start: 0.8972 (m) cc_final: 0.8676 (p) REVERT: B 392 MET cc_start: 0.8805 (tmm) cc_final: 0.8522 (tmt) REVERT: C 233 GLN cc_start: 0.8504 (mp10) cc_final: 0.8257 (pm20) REVERT: C 406 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8520 (tmmm) REVERT: C 409 MET cc_start: 0.9116 (mtm) cc_final: 0.8835 (mtt) REVERT: C 415 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8567 (mtp180) REVERT: D 191 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8740 (ptpp) REVERT: E 188 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9111 (mp) REVERT: G 13 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: G 20 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8790 (mt) REVERT: G 68 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8847 (pt) REVERT: G 117 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8609 (ttpp) REVERT: I 181 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8714 (t0) outliers start: 128 outliers final: 68 residues processed: 395 average time/residue: 0.6987 time to fit residues: 314.6796 Evaluate side-chains 366 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 285 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 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 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 248 SER Chi-restraints excluded: chain B residue 331 LEU 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 B residue 570 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 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 160 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 213 LYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 252 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 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 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 150 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 11 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 239 optimal weight: 0.5980 chunk 245 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 36 optimal weight: 0.0370 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 342 ASN C 217 HIS E 31 GLN G 23 ASN G 111 ASN H 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.050529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.041183 restraints weight = 61102.542| |-----------------------------------------------------------------------------| r_work (start): 0.2373 rms_B_bonded: 1.88 r_work: 0.2286 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2188 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25439 Z= 0.161 Angle : 0.642 29.182 34733 Z= 0.330 Chirality : 0.052 1.888 3908 Planarity : 0.005 0.136 4154 Dihedral : 14.166 178.297 4366 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.28 % Favored : 95.16 % Rotamer: Outliers : 4.78 % Allowed : 27.91 % Favored : 67.31 % 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: 0.58 (0.16), residues: 2828 helix: 1.57 (0.16), residues: 1100 sheet: 0.80 (0.26), residues: 399 loop : -0.76 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 312 TYR 0.025 0.001 TYR I 81 PHE 0.017 0.002 PHE B 461 TRP 0.009 0.001 TRP F 219 HIS 0.008 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00376 (25439) covalent geometry : angle 0.64169 (34733) hydrogen bonds : bond 0.03932 ( 1054) hydrogen bonds : angle 4.41470 ( 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 415 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 292 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6986 (ptpp) REVERT: A 417 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 74 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7747 (t80) REVERT: B 94 GLU cc_start: 0.6961 (tp30) cc_final: 0.6577 (tp30) REVERT: B 98 HIS cc_start: 0.9242 (OUTLIER) cc_final: 0.8687 (m170) REVERT: B 128 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7253 (pp20) REVERT: B 224 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6572 (mp) REVERT: B 233 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8259 (mt) REVERT: B 370 SER cc_start: 0.8985 (m) cc_final: 0.8677 (p) REVERT: B 392 MET cc_start: 0.8798 (tmm) cc_final: 0.8507 (tmt) REVERT: C 112 LYS cc_start: 0.9262 (mmmm) cc_final: 0.8790 (mmmm) REVERT: C 115 GLU cc_start: 0.8857 (mp0) cc_final: 0.8477 (mp0) REVERT: C 233 GLN cc_start: 0.8531 (mp10) cc_final: 0.8238 (pm20) REVERT: C 406 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8523 (tmmm) REVERT: C 409 MET cc_start: 0.9174 (mtm) cc_final: 0.8943 (mtt) REVERT: C 415 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8590 (mtp180) REVERT: D 55 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8774 (pttp) REVERT: D 191 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8757 (ptpp) REVERT: E 124 GLN cc_start: 0.8435 (mt0) cc_final: 0.8159 (mp10) REVERT: E 188 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9080 (mt) REVERT: G 13 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: G 20 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8852 (mt) REVERT: G 68 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8861 (pt) REVERT: G 117 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8603 (ttpp) REVERT: I 181 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8688 (t0) REVERT: I 238 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8157 (mtp85) outliers start: 123 outliers final: 77 residues processed: 383 average time/residue: 0.7222 time to fit residues: 313.5277 Evaluate side-chains 378 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 284 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 170 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 317 SER 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 434 ASN Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 248 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 439 LEU 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 65 ARG 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 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 160 SER 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 312 ILE 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 55 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 191 LYS Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 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 111 ASN Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 4 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 260 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 265 optimal weight: 0.5980 chunk 259 optimal weight: 0.4980 chunk 206 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 151 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN A 463 ASN C 217 HIS C 261 ASN C 315 ASN E 31 GLN G 23 ASN G 111 ASN H 59 ASN I 50 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.051572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.042306 restraints weight = 60866.445| |-----------------------------------------------------------------------------| r_work (start): 0.2405 rms_B_bonded: 1.86 r_work: 0.2319 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2222 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25439 Z= 0.134 Angle : 0.624 28.882 34733 Z= 0.319 Chirality : 0.051 1.897 3908 Planarity : 0.005 0.135 4154 Dihedral : 14.135 177.724 4366 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.03 % Favored : 95.44 % Rotamer: Outliers : 4.16 % Allowed : 28.53 % 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: 0.65 (0.16), residues: 2828 helix: 1.63 (0.16), residues: 1104 sheet: 0.79 (0.26), residues: 399 loop : -0.72 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 418 TYR 0.025 0.001 TYR I 81 PHE 0.018 0.001 PHE B 461 TRP 0.008 0.001 TRP B 25 HIS 0.008 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00312 (25439) covalent geometry : angle 0.62365 (34733) hydrogen bonds : bond 0.03664 ( 1054) hydrogen bonds : angle 4.34749 ( 2980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 298 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8396 (tp30) cc_final: 0.7862 (tp30) REVERT: A 406 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6945 (ptpp) REVERT: A 417 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7937 (mm-30) REVERT: B 74 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7711 (t80) REVERT: B 128 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7202 (pp20) REVERT: B 184 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7725 (p90) REVERT: B 193 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8033 (ptm-80) REVERT: B 224 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6647 (mp) REVERT: B 233 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8247 (mt) REVERT: B 370 SER cc_start: 0.8973 (m) cc_final: 0.8672 (p) REVERT: B 392 MET cc_start: 0.8794 (tmm) cc_final: 0.8472 (tmm) REVERT: C 112 LYS cc_start: 0.9248 (mmmm) cc_final: 0.8723 (mmmm) REVERT: C 115 GLU cc_start: 0.8863 (mp0) cc_final: 0.8464 (mp0) REVERT: C 233 GLN cc_start: 0.8495 (mp10) cc_final: 0.8205 (pm20) REVERT: C 406 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8521 (tmmm) REVERT: C 409 MET cc_start: 0.9173 (mtm) cc_final: 0.8915 (mtt) REVERT: C 415 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8557 (mtp180) REVERT: D 55 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8768 (pttp) REVERT: D 73 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8431 (pptt) REVERT: D 75 LEU cc_start: 0.9226 (mp) cc_final: 0.8986 (mm) REVERT: D 191 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8737 (ptpp) REVERT: E 124 GLN cc_start: 0.8424 (mt0) cc_final: 0.8152 (mp10) REVERT: E 188 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9046 (mt) REVERT: G 13 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: G 20 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8732 (mt) REVERT: G 68 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8840 (pt) REVERT: I 181 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8688 (t0) outliers start: 107 outliers final: 66 residues processed: 381 average time/residue: 0.7056 time to fit residues: 304.6631 Evaluate side-chains 366 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 284 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 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 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 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 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 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 160 SER 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 3 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 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 191 LYS Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain G residue 112 THR 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 113 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 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: 0.9990 chunk 120 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 235 optimal weight: 0.5980 chunk 284 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 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 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 = 0.2668 r_free = 0.2668 target = 0.051750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.042457 restraints weight = 60827.538| |-----------------------------------------------------------------------------| r_work (start): 0.2411 rms_B_bonded: 1.87 r_work: 0.2325 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2228 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25439 Z= 0.136 Angle : 0.637 28.834 34733 Z= 0.325 Chirality : 0.051 1.899 3908 Planarity : 0.005 0.135 4154 Dihedral : 14.103 177.708 4366 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.21 % Favored : 95.30 % Rotamer: Outliers : 4.00 % Allowed : 29.03 % 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: 0.66 (0.16), residues: 2828 helix: 1.64 (0.16), residues: 1105 sheet: 0.77 (0.26), residues: 399 loop : -0.70 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 312 TYR 0.023 0.001 TYR I 81 PHE 0.017 0.001 PHE B 461 TRP 0.008 0.001 TRP B 25 HIS 0.008 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00320 (25439) covalent geometry : angle 0.63666 (34733) hydrogen bonds : bond 0.03631 ( 1054) hydrogen bonds : angle 4.31783 ( 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 398 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 295 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6984 (ptpp) REVERT: A 417 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7907 (mm-30) REVERT: B 74 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7697 (t80) REVERT: B 94 GLU cc_start: 0.7022 (tp30) cc_final: 0.6466 (tp30) REVERT: B 98 HIS cc_start: 0.9254 (OUTLIER) cc_final: 0.8694 (m170) REVERT: B 128 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7188 (pp20) REVERT: B 168 LYS cc_start: 0.8905 (mtmm) cc_final: 0.8591 (ptpp) REVERT: B 184 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7838 (p90) REVERT: B 193 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8113 (ptm-80) REVERT: B 224 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6643 (mp) REVERT: B 233 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8264 (mt) REVERT: B 392 MET cc_start: 0.8796 (tmm) cc_final: 0.8461 (tmm) REVERT: C 112 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8610 (mmmm) REVERT: C 115 GLU cc_start: 0.8854 (mp0) cc_final: 0.8415 (mp0) REVERT: C 233 GLN cc_start: 0.8493 (mp10) cc_final: 0.8193 (pm20) REVERT: C 406 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8516 (tmmm) REVERT: C 409 MET cc_start: 0.9157 (mtm) cc_final: 0.8882 (mtt) REVERT: C 415 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8557 (mtp180) REVERT: D 55 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8767 (pttp) REVERT: D 73 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8425 (pptt) REVERT: D 75 LEU cc_start: 0.9214 (mp) cc_final: 0.8949 (mm) REVERT: D 191 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8740 (ptpp) REVERT: E 124 GLN cc_start: 0.8412 (mt0) cc_final: 0.8137 (mp10) REVERT: E 188 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9078 (mp) REVERT: G 13 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: G 20 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8687 (mt) REVERT: G 68 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8841 (pt) REVERT: I 181 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8712 (t0) REVERT: I 238 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7643 (mtp85) outliers start: 103 outliers final: 62 residues processed: 373 average time/residue: 0.7682 time to fit residues: 323.7820 Evaluate side-chains 367 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 287 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 CYS 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 570 GLU 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 114 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 160 SER 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 3 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 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 191 LYS Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain 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 112 THR 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 113 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 258 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 chunk 251 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 28 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 234 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 342 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN G 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.051826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.042515 restraints weight = 61194.001| |-----------------------------------------------------------------------------| r_work (start): 0.2411 rms_B_bonded: 1.88 r_work: 0.2326 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2229 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25439 Z= 0.139 Angle : 0.640 28.793 34733 Z= 0.327 Chirality : 0.051 1.900 3908 Planarity : 0.005 0.136 4154 Dihedral : 14.076 177.756 4364 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.31 % Favored : 95.19 % Rotamer: Outliers : 3.19 % Allowed : 29.97 % 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: 0.65 (0.16), residues: 2828 helix: 1.64 (0.16), residues: 1106 sheet: 0.76 (0.26), residues: 399 loop : -0.71 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 374 TYR 0.023 0.001 TYR I 81 PHE 0.018 0.001 PHE A 263 TRP 0.008 0.001 TRP B 25 HIS 0.008 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00324 (25439) covalent geometry : angle 0.64039 (34733) hydrogen bonds : bond 0.03627 ( 1054) hydrogen bonds : angle 4.32318 ( 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 373 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 291 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6997 (ptpp) REVERT: A 417 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7894 (mm-30) REVERT: B 74 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7681 (t80) REVERT: B 94 GLU cc_start: 0.7019 (tp30) cc_final: 0.6557 (tp30) REVERT: B 98 HIS cc_start: 0.9233 (OUTLIER) cc_final: 0.8775 (m170) REVERT: B 128 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7176 (pp20) REVERT: B 161 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7313 (tm-30) REVERT: B 168 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8553 (ptpp) REVERT: B 184 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7832 (p90) REVERT: B 193 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8101 (ptm-80) REVERT: B 233 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8269 (mt) REVERT: B 370 SER cc_start: 0.8994 (m) cc_final: 0.8685 (p) REVERT: B 392 MET cc_start: 0.8803 (tmm) cc_final: 0.8465 (tmm) REVERT: C 112 LYS cc_start: 0.9248 (mmmm) cc_final: 0.8691 (mmmm) REVERT: C 115 GLU cc_start: 0.8856 (mp0) cc_final: 0.8414 (mp0) REVERT: C 233 GLN cc_start: 0.8490 (mp10) cc_final: 0.8169 (pm20) REVERT: C 406 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8510 (tmmm) REVERT: C 409 MET cc_start: 0.9154 (mtm) cc_final: 0.8880 (mtt) REVERT: C 415 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8553 (mtp180) REVERT: D 55 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8781 (pttp) REVERT: D 73 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8437 (pptt) REVERT: D 75 LEU cc_start: 0.9205 (mp) cc_final: 0.8946 (mm) REVERT: D 191 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8733 (ptpp) REVERT: E 124 GLN cc_start: 0.8416 (mt0) cc_final: 0.8135 (mp10) REVERT: G 13 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: G 20 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8678 (mt) REVERT: G 68 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8839 (pt) REVERT: I 181 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8713 (t0) REVERT: I 238 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.7948 (mtp85) outliers start: 82 outliers final: 58 residues processed: 353 average time/residue: 0.7872 time to fit residues: 314.2527 Evaluate side-chains 359 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 285 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 440 THR 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 233 LEU 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 570 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 LYS 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 344 ASP Chi-restraints excluded: chain C residue 406 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 LYS 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 191 LYS Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain 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 112 THR 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 113 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 266 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 223 optimal weight: 0.0010 chunk 138 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 342 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN G 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.050644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.041356 restraints weight = 61136.805| |-----------------------------------------------------------------------------| r_work (start): 0.2379 rms_B_bonded: 1.87 r_work: 0.2293 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2195 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25439 Z= 0.168 Angle : 0.687 30.409 34733 Z= 0.344 Chirality : 0.052 1.888 3908 Planarity : 0.006 0.211 4154 Dihedral : 14.092 178.312 4362 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.49 % Favored : 95.01 % Rotamer: Outliers : 3.54 % Allowed : 29.65 % 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: 0.60 (0.16), residues: 2828 helix: 1.59 (0.16), residues: 1100 sheet: 0.75 (0.26), residues: 401 loop : -0.73 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 136 TYR 0.019 0.001 TYR I 81 PHE 0.020 0.002 PHE A 263 TRP 0.010 0.001 TRP F 219 HIS 0.006 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00396 (25439) covalent geometry : angle 0.68711 (34733) hydrogen bonds : bond 0.03936 ( 1054) hydrogen bonds : angle 4.38085 ( 2980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8013.00 seconds wall clock time: 137 minutes 39.76 seconds (8259.76 seconds total)