Starting phenix.real_space_refine on Thu Aug 6 12:54:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l6o_62860/08_2026/9l6o_62860.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l6o_62860/08_2026/9l6o_62860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l6o_62860/08_2026/9l6o_62860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l6o_62860/08_2026/9l6o_62860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l6o_62860/08_2026/9l6o_62860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l6o_62860/08_2026/9l6o_62860.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 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: 5 Type Number sf(0) Gaussians Mn 4 7.51 5 S 47 5.16 5 C 9469 2.51 5 N 2484 2.21 5 O 2844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14848 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2566 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 305} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4518 Classifications: {'peptide': 566} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 543} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2358 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 278} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 5402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5402 Classifications: {'peptide': 667} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 642} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.48, per 1000 atoms: 0.23 Number of scatterers: 14848 At special positions: 0 Unit cell: (93.72, 134.19, 149.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 4 24.99 S 47 16.00 O 2844 8.00 N 2484 7.00 C 9469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 394 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 691.7 milliseconds 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3486 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 8 sheets defined 48.5% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 17 through 20 Processing helix chain 'A' and resid 21 through 27 removed outlier: 3.529A pdb=" N HIS A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.767A pdb=" N TRP A 46 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN A 47 " --> pdb=" O PRO A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 47' Processing helix chain 'A' and resid 53 through 76 removed outlier: 4.091A pdb=" N THR A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLY A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 80 Processing helix chain 'A' and resid 88 through 107 removed outlier: 3.656A pdb=" N LEU A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS A 102 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ALA A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 106 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.745A pdb=" N TYR A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 157 removed outlier: 4.694A pdb=" N ARG A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 173 removed outlier: 3.692A pdb=" N SER A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 168 " --> pdb=" O TYR A 164 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 183 through 188 removed outlier: 4.241A pdb=" N ARG A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.813A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.596A pdb=" N LYS A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLU A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 230 removed outlier: 3.636A pdb=" N PHE A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 234 through 241 removed outlier: 4.348A pdb=" N LEU A 241 " --> pdb=" O TYR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.766A pdb=" N VAL A 245 " --> pdb=" O TYR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 256 removed outlier: 3.923A pdb=" N ARG A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 removed outlier: 4.053A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.653A pdb=" N ALA A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.753A pdb=" N PHE A 297 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.912A pdb=" N GLU A 316 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.728A pdb=" N VAL F 110 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 167 through 183 Processing helix chain 'F' and resid 209 through 223 removed outlier: 4.439A pdb=" N ILE F 213 " --> pdb=" O GLY F 209 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR F 223 " --> pdb=" O ASP F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 273 through 276 Processing helix chain 'F' and resid 277 through 282 removed outlier: 4.135A pdb=" N LYS F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 295 removed outlier: 3.830A pdb=" N ARG F 295 " --> pdb=" O ASP F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 337 removed outlier: 3.837A pdb=" N GLN F 331 " --> pdb=" O ARG F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 407 Processing helix chain 'F' and resid 412 through 415 removed outlier: 3.687A pdb=" N GLU F 415 " --> pdb=" O GLN F 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 412 through 415' Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 437 through 443 Processing helix chain 'F' and resid 466 through 496 removed outlier: 4.269A pdb=" N PHE F 472 " --> pdb=" O GLU F 468 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N CYS F 481 " --> pdb=" O PHE F 477 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR F 482 " --> pdb=" O TYR F 478 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS F 483 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL F 485 " --> pdb=" O CYS F 481 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG F 486 " --> pdb=" O TYR F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 518 removed outlier: 4.348A pdb=" N LYS F 515 " --> pdb=" O GLU F 511 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP F 518 " --> pdb=" O ASP F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 535 removed outlier: 3.686A pdb=" N ARG F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 555 removed outlier: 4.015A pdb=" N ARG F 547 " --> pdb=" O GLU F 543 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 548 " --> pdb=" O ASP F 544 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS F 554 " --> pdb=" O GLU F 550 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS F 555 " --> pdb=" O SER F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 575 removed outlier: 3.725A pdb=" N ILE F 574 " --> pdb=" O ILE F 571 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN F 575 " --> pdb=" O SER F 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 571 through 575' Processing helix chain 'F' and resid 616 through 636 removed outlier: 3.740A pdb=" N ILE F 620 " --> pdb=" O ASP F 616 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR F 622 " --> pdb=" O TYR F 618 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE F 626 " --> pdb=" O TYR F 622 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP F 627 " --> pdb=" O GLU F 623 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA F 630 " --> pdb=" O ILE F 626 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA F 631 " --> pdb=" O ASP F 627 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA F 632 " --> pdb=" O THR F 628 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 664 removed outlier: 3.909A pdb=" N ARG F 664 " --> pdb=" O ILE F 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 28 removed outlier: 3.791A pdb=" N THR B 28 " --> pdb=" O TRP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 62 removed outlier: 4.025A pdb=" N GLN B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B 58 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 75 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 93 through 101 removed outlier: 3.903A pdb=" N PHE B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.866A pdb=" N SER B 105 " --> pdb=" O HIS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 removed outlier: 4.710A pdb=" N ASP B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 removed outlier: 3.543A pdb=" N LYS B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 158 removed outlier: 3.612A pdb=" N ARG B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 166 removed outlier: 3.841A pdb=" N GLY B 166 " --> pdb=" O PHE B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 167 through 176 removed outlier: 3.902A pdb=" N MET B 171 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 208 removed outlier: 4.062A pdb=" N ILE B 189 " --> pdb=" O MET B 185 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B 199 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 224 removed outlier: 4.390A pdb=" N ASP B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 230 through 243 removed outlier: 3.989A pdb=" N GLU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU B 241 " --> pdb=" O TYR B 237 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 267 removed outlier: 3.541A pdb=" N LYS B 252 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 27 removed outlier: 3.821A pdb=" N LYS E 15 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU E 25 " --> pdb=" O ARG E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.842A pdb=" N LEU E 45 " --> pdb=" O LYS E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 64 through 72 removed outlier: 4.001A pdb=" N LEU E 68 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 88 removed outlier: 3.962A pdb=" N LYS E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.608A pdb=" N VAL E 109 " --> pdb=" O PHE E 105 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL E 112 " --> pdb=" O ARG E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.814A pdb=" N LYS E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 4.195A pdb=" N MET E 132 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP E 133 " --> pdb=" O ASP E 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 128 through 133' Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 167 through 178 removed outlier: 3.783A pdb=" N ARG E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE E 173 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN E 174 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 225 Processing helix chain 'E' and resid 244 through 250 Processing helix chain 'E' and resid 273 through 282 removed outlier: 4.058A pdb=" N GLU E 277 " --> pdb=" O ASP E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.867A pdb=" N VAL E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 315 removed outlier: 4.282A pdb=" N VAL E 314 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP E 315 " --> pdb=" O TYR E 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 310 through 315' Processing helix chain 'E' and resid 326 through 341 removed outlier: 4.289A pdb=" N LEU E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE E 338 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU E 339 " --> pdb=" O GLU E 335 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 353 Processing helix chain 'E' and resid 401 through 406 removed outlier: 4.202A pdb=" N ASP E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 428 removed outlier: 4.147A pdb=" N GLU E 415 " --> pdb=" O GLY E 411 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE E 418 " --> pdb=" O VAL E 414 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER E 425 " --> pdb=" O LEU E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 443 removed outlier: 3.695A pdb=" N ARG E 438 " --> pdb=" O PRO E 434 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 439 " --> pdb=" O SER E 435 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP E 441 " --> pdb=" O VAL E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 460 removed outlier: 3.619A pdb=" N GLU E 460 " --> pdb=" O TYR E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 490 removed outlier: 3.911A pdb=" N ASN E 474 " --> pdb=" O ILE E 470 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR E 478 " --> pdb=" O ASN E 474 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR E 482 " --> pdb=" O TYR E 478 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN E 489 " --> pdb=" O VAL E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 510 Processing helix chain 'E' and resid 525 through 535 removed outlier: 3.867A pdb=" N ARG E 529 " --> pdb=" O THR E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 548 removed outlier: 3.523A pdb=" N TRP E 545 " --> pdb=" O THR E 541 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG E 546 " --> pdb=" O GLN E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 552 Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 621 through 631 Processing helix chain 'E' and resid 651 through 666 removed outlier: 3.659A pdb=" N VAL E 655 " --> pdb=" O THR E 651 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN E 656 " --> pdb=" O THR E 652 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 657 " --> pdb=" O ARG E 653 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS E 665 " --> pdb=" O TYR E 661 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY E 666 " --> pdb=" O ALA E 662 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 238 through 239 removed outlier: 7.015A pdb=" N LEU F 238 " --> pdb=" O VAL F 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 284 through 288 Processing sheet with id=AA3, first strand: chain 'F' and resid 398 through 400 Processing sheet with id=AA4, first strand: chain 'E' and resid 159 through 160 removed outlier: 3.528A pdb=" N LEU E 160 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 268 through 271 removed outlier: 4.228A pdb=" N VAL E 269 " --> pdb=" O TYR E 344 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET E 346 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE E 345 " --> pdb=" O LEU E 670 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU E 670 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AA7, first strand: chain 'E' and resid 363 through 364 removed outlier: 4.790A pdb=" N HIS E 363 " --> pdb=" O GLN E 372 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN E 372 " --> pdb=" O HIS E 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 399 through 400 removed outlier: 5.400A pdb=" N LEU E 399 " --> pdb=" O MET E 451 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 399 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4853 1.35 - 1.47: 3674 1.47 - 1.59: 6568 1.59 - 1.71: 0 1.71 - 1.83: 84 Bond restraints: 15179 Sorted by residual: bond pdb=" CB PRO E 602 " pdb=" CG PRO E 602 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.88e+00 bond pdb=" CA ILE E 588 " pdb=" CB ILE E 588 " ideal model delta sigma weight residual 1.540 1.559 -0.019 1.36e-02 5.41e+03 1.87e+00 bond pdb=" CG PRO F 343 " pdb=" CD PRO F 343 " ideal model delta sigma weight residual 1.503 1.548 -0.045 3.40e-02 8.65e+02 1.76e+00 bond pdb=" N ARG F 674 " pdb=" CA ARG F 674 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.58e+00 bond pdb=" CB GLN B 239 " pdb=" CG GLN B 239 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.38e-01 ... (remaining 15174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 20301 2.28 - 4.56: 229 4.56 - 6.85: 22 6.85 - 9.13: 8 9.13 - 11.41: 3 Bond angle restraints: 20563 Sorted by residual: angle pdb=" N ASN B 280 " pdb=" CA ASN B 280 " pdb=" C ASN B 280 " ideal model delta sigma weight residual 109.81 120.89 -11.08 2.21e+00 2.05e-01 2.51e+01 angle pdb=" C ILE F 673 " pdb=" N ARG F 674 " pdb=" CA ARG F 674 " ideal model delta sigma weight residual 121.70 128.88 -7.18 1.80e+00 3.09e-01 1.59e+01 angle pdb=" CA ARG E 135 " pdb=" CB ARG E 135 " pdb=" CG ARG E 135 " ideal model delta sigma weight residual 114.10 120.69 -6.59 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA LEU A 79 " pdb=" CB LEU A 79 " pdb=" CG LEU A 79 " ideal model delta sigma weight residual 116.30 127.71 -11.41 3.50e+00 8.16e-02 1.06e+01 angle pdb=" CG1 ILE F 584 " pdb=" CB ILE F 584 " pdb=" CG2 ILE F 584 " ideal model delta sigma weight residual 110.70 101.57 9.13 3.00e+00 1.11e-01 9.27e+00 ... (remaining 20558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.52: 8471 20.52 - 41.05: 560 41.05 - 61.57: 68 61.57 - 82.10: 3 82.10 - 102.62: 3 Dihedral angle restraints: 9105 sinusoidal: 3675 harmonic: 5430 Sorted by residual: dihedral pdb=" CA TYR F 342 " pdb=" C TYR F 342 " pdb=" N PRO F 343 " pdb=" CA PRO F 343 " ideal model delta harmonic sigma weight residual 180.00 77.38 102.62 0 5.00e+00 4.00e-02 4.21e+02 dihedral pdb=" CA ASN B 280 " pdb=" C ASN B 280 " pdb=" N PRO B 281 " pdb=" CA PRO B 281 " ideal model delta harmonic sigma weight residual 180.00 -152.08 -27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ARG A 176 " pdb=" C ARG A 176 " pdb=" N ALA A 177 " pdb=" CA ALA A 177 " ideal model delta harmonic sigma weight residual 180.00 152.41 27.59 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 9102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2044 0.074 - 0.148: 187 0.148 - 0.222: 6 0.222 - 0.296: 3 0.296 - 0.370: 1 Chirality restraints: 2241 Sorted by residual: chirality pdb=" CB THR A 180 " pdb=" CA THR A 180 " pdb=" OG1 THR A 180 " pdb=" CG2 THR A 180 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CB ILE F 584 " pdb=" CA ILE F 584 " pdb=" CG1 ILE F 584 " pdb=" CG2 ILE F 584 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB THR F 669 " pdb=" CA THR F 669 " pdb=" OG1 THR F 669 " pdb=" CG2 THR F 669 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2238 not shown) Planarity restraints: 2663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 242 " 0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO E 243 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 601 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO E 602 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 602 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 602 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 299 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO E 300 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 300 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 300 " -0.023 5.00e-02 4.00e+02 ... (remaining 2660 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 277 2.64 - 3.21: 15105 3.21 - 3.77: 23151 3.77 - 4.34: 31748 4.34 - 4.90: 48894 Nonbonded interactions: 119175 Sorted by model distance: nonbonded pdb=" OE2 GLU A 99 " pdb="MN MN A 401 " model vdw 2.078 2.320 nonbonded pdb=" OD2 ASP B 192 " pdb="MN MN B 401 " model vdw 2.103 2.320 nonbonded pdb=" OE2 GLU B 99 " pdb="MN MN B 401 " model vdw 2.117 2.320 nonbonded pdb=" OD1 ASP A 68 " pdb="MN MN A 402 " model vdw 2.135 2.320 nonbonded pdb=" OE2 GLU B 99 " pdb="MN MN B 402 " model vdw 2.146 2.320 ... (remaining 119170 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 139 or (resid 140 and (name N or name CA or name \ C or name O or name CB )) or resid 141 through 291 or resid 401 through 402)) selection = (chain 'B' and (resid 1 through 186 or (resid 187 and (name N or name CA or name \ C or name O or name CB )) or resid 188 through 402)) } 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 group one per residue 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 14.120 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 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 : 0.002 0.069 15181 Z= 0.106 Angle : 0.607 11.411 20567 Z= 0.302 Chirality : 0.044 0.370 2241 Planarity : 0.004 0.082 2663 Dihedral : 12.892 102.622 5613 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.75 % Favored : 88.70 % Rotamer: Outliers : 1.18 % Allowed : 16.65 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -2.39 (0.20), residues: 1832 helix: -0.66 (0.21), residues: 628 sheet: -3.26 (0.62), residues: 63 loop : -2.13 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 135 TYR 0.021 0.001 TYR F 671 PHE 0.016 0.001 PHE E 143 TRP 0.017 0.001 TRP B 46 HIS 0.003 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (15179) covalent geometry : angle 0.60574 / 0.30 (20563) SS BOND : bond 0.00209 / 0.10 ( 2) SS BOND : angle 2.63492 / 1.31 ( 4) hydrogen bonds : bond 0.27883 / 18.98 ( 399) hydrogen bonds : angle 9.00409 / 6.32 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.4522 (pt0) cc_final: 0.2068 (mt-10) REVERT: A 167 PHE cc_start: 0.7327 (m-80) cc_final: 0.6562 (m-80) REVERT: F 131 ILE cc_start: 0.5665 (pt) cc_final: 0.5319 (pt) REVERT: F 132 MET cc_start: 0.4958 (tmm) cc_final: 0.3535 (ptp) REVERT: F 313 MET cc_start: 0.1939 (pmm) cc_final: 0.1326 (pmm) REVERT: F 414 VAL cc_start: 0.5128 (p) cc_final: 0.4920 (p) REVERT: F 606 MET cc_start: 0.5458 (ptt) cc_final: 0.5218 (ptt) REVERT: B 185 MET cc_start: 0.7942 (pmm) cc_final: 0.7530 (pmm) REVERT: E 242 HIS cc_start: 0.5147 (OUTLIER) cc_final: 0.3629 (t-90) REVERT: E 288 PHE cc_start: 0.6469 (m-80) cc_final: 0.6169 (m-10) outliers start: 19 outliers final: 7 residues processed: 179 average time/residue: 0.1241 time to fit residues: 33.5765 Evaluate side-chains 143 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 400 ASN Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 637 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.0470 chunk 149 optimal weight: 0.8980 overall best weight: 1.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 HIS F 225 ASN ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.157340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.135720 restraints weight = 46200.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.137530 restraints weight = 34607.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.137570 restraints weight = 28208.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.137870 restraints weight = 22518.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.137997 restraints weight = 21304.904| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15181 Z= 0.170 Angle : 0.676 11.239 20567 Z= 0.347 Chirality : 0.045 0.243 2241 Planarity : 0.005 0.065 2663 Dihedral : 5.584 72.775 2055 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.74 % Favored : 87.94 % Rotamer: Outliers : 4.11 % Allowed : 17.96 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -2.61 (0.19), residues: 1832 helix: -0.92 (0.19), residues: 678 sheet: -3.79 (0.55), residues: 70 loop : -2.21 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 230 TYR 0.024 0.002 TYR F 342 PHE 0.024 0.002 PHE F 329 TRP 0.020 0.002 TRP F 521 HIS 0.006 0.001 HIS B 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (15179) covalent geometry : angle 0.67540 / 0.35 (20563) SS BOND : bond 0.00184 / 0.10 ( 2) SS BOND : angle 1.88876 / 0.92 ( 4) hydrogen bonds : bond 0.05562 / 3.70 ( 399) hydrogen bonds : angle 6.16245 / 4.43 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 152 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.7285 (t80) cc_final: 0.6637 (t80) REVERT: A 159 GLU cc_start: 0.4967 (pt0) cc_final: 0.2309 (mt-10) REVERT: A 167 PHE cc_start: 0.7488 (m-80) cc_final: 0.6329 (m-80) REVERT: F 210 VAL cc_start: 0.6712 (OUTLIER) cc_final: 0.6416 (t) REVERT: F 245 ILE cc_start: 0.7913 (mm) cc_final: 0.7666 (mm) REVERT: F 276 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.6176 (t80) REVERT: F 313 MET cc_start: 0.1774 (pmm) cc_final: 0.0747 (pmm) REVERT: F 606 MET cc_start: 0.5845 (ptt) cc_final: 0.5639 (ptt) REVERT: F 633 THR cc_start: 0.5370 (m) cc_final: 0.5165 (m) REVERT: B 138 ILE cc_start: 0.5396 (OUTLIER) cc_final: 0.5112 (mt) REVERT: B 185 MET cc_start: 0.7748 (pmm) cc_final: 0.7016 (pmm) REVERT: B 186 ILE cc_start: 0.7514 (mm) cc_final: 0.6997 (mm) REVERT: E 210 VAL cc_start: 0.6885 (OUTLIER) cc_final: 0.6568 (p) REVERT: E 242 HIS cc_start: 0.5435 (OUTLIER) cc_final: 0.3528 (t-90) REVERT: E 521 TRP cc_start: 0.3918 (OUTLIER) cc_final: 0.2258 (m100) outliers start: 66 outliers final: 34 residues processed: 203 average time/residue: 0.1102 time to fit residues: 34.9385 Evaluate side-chains 180 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 276 PHE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 286 TYR Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 446 ILE Chi-restraints excluded: chain F residue 557 ILE Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain F residue 667 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 400 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 521 TRP Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 579 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 79 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 82 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN E 174 ASN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.155920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.134434 restraints weight = 46612.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.135773 restraints weight = 35893.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.136045 restraints weight = 29936.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.136370 restraints weight = 23738.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.136447 restraints weight = 22448.222| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15181 Z= 0.168 Angle : 0.648 9.257 20567 Z= 0.335 Chirality : 0.045 0.201 2241 Planarity : 0.005 0.066 2663 Dihedral : 5.564 57.987 2050 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.41 % Favored : 88.21 % Rotamer: Outliers : 5.67 % Allowed : 18.52 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -2.68 (0.19), residues: 1832 helix: -1.10 (0.19), residues: 683 sheet: -3.86 (0.54), residues: 70 loop : -2.16 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 591 TYR 0.022 0.002 TYR E 223 PHE 0.021 0.002 PHE F 329 TRP 0.015 0.001 TRP F 521 HIS 0.007 0.001 HIS E 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (15179) covalent geometry : angle 0.64790 / 0.33 (20563) SS BOND : bond 0.00164 / 0.08 ( 2) SS BOND : angle 1.81720 / 0.88 ( 4) hydrogen bonds : bond 0.05092 / 3.41 ( 399) hydrogen bonds : angle 5.80076 / 4.18 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 157 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.7282 (t80) cc_final: 0.6453 (t80) REVERT: A 106 TYR cc_start: 0.4454 (OUTLIER) cc_final: 0.4028 (m-10) REVERT: A 159 GLU cc_start: 0.5119 (pt0) cc_final: 0.2907 (mt-10) REVERT: A 167 PHE cc_start: 0.7278 (m-80) cc_final: 0.6185 (m-80) REVERT: A 172 TYR cc_start: 0.4887 (OUTLIER) cc_final: 0.3226 (p90) REVERT: A 185 MET cc_start: 0.6084 (tmm) cc_final: 0.5719 (tmm) REVERT: A 247 LEU cc_start: 0.6648 (mt) cc_final: 0.6274 (mp) REVERT: F 132 MET cc_start: 0.5176 (ptm) cc_final: 0.4203 (ptt) REVERT: F 245 ILE cc_start: 0.7790 (mm) cc_final: 0.7540 (mm) REVERT: F 276 PHE cc_start: 0.6252 (OUTLIER) cc_final: 0.5836 (t80) REVERT: F 606 MET cc_start: 0.5420 (ptt) cc_final: 0.5148 (ptt) REVERT: B 138 ILE cc_start: 0.5388 (OUTLIER) cc_final: 0.5137 (mt) REVERT: B 185 MET cc_start: 0.7817 (pmm) cc_final: 0.7054 (pmm) REVERT: B 186 ILE cc_start: 0.7548 (mm) cc_final: 0.7031 (mm) REVERT: B 283 ILE cc_start: 0.6344 (OUTLIER) cc_final: 0.6046 (tt) REVERT: E 210 VAL cc_start: 0.6875 (OUTLIER) cc_final: 0.6630 (p) REVERT: E 242 HIS cc_start: 0.6071 (OUTLIER) cc_final: 0.3871 (t-90) REVERT: E 385 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.5676 (m-10) REVERT: E 521 TRP cc_start: 0.3644 (OUTLIER) cc_final: 0.2301 (m100) outliers start: 91 outliers final: 47 residues processed: 223 average time/residue: 0.1140 time to fit residues: 39.1823 Evaluate side-chains 201 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 145 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 276 PHE Chi-restraints excluded: chain F residue 286 TYR Chi-restraints excluded: chain F residue 316 ASN Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 446 ILE Chi-restraints excluded: chain F residue 557 ILE Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain F residue 600 TYR Chi-restraints excluded: chain F residue 642 LEU Chi-restraints excluded: chain F residue 667 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 385 TYR Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 400 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 521 TRP Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 590 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 129 optimal weight: 8.9990 chunk 144 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 0.0870 chunk 167 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 8 optimal weight: 0.0980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.159230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.138102 restraints weight = 46403.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.139350 restraints weight = 34441.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.140267 restraints weight = 28879.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.140873 restraints weight = 22360.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.141131 restraints weight = 21432.741| |-----------------------------------------------------------------------------| r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15181 Z= 0.115 Angle : 0.618 11.146 20567 Z= 0.312 Chirality : 0.043 0.230 2241 Planarity : 0.004 0.064 2663 Dihedral : 5.295 56.024 2050 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.72 % Favored : 90.01 % Rotamer: Outliers : 4.43 % Allowed : 19.64 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -2.50 (0.19), residues: 1832 helix: -0.84 (0.20), residues: 669 sheet: -3.31 (0.54), residues: 78 loop : -2.14 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 135 TYR 0.020 0.001 TYR E 618 PHE 0.015 0.001 PHE F 329 TRP 0.009 0.001 TRP E 663 HIS 0.011 0.001 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (15179) covalent geometry : angle 0.61789 / 0.31 (20563) SS BOND : bond 0.00330 / 0.16 ( 2) SS BOND : angle 1.75932 / 0.86 ( 4) hydrogen bonds : bond 0.03939 / 2.63 ( 399) hydrogen bonds : angle 5.36741 / 3.86 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 159 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.4869 (pt0) cc_final: 0.2648 (mt-10) REVERT: A 167 PHE cc_start: 0.7164 (m-80) cc_final: 0.6169 (m-80) REVERT: A 172 TYR cc_start: 0.4951 (OUTLIER) cc_final: 0.3071 (p90) REVERT: F 132 MET cc_start: 0.5225 (ptm) cc_final: 0.4102 (ptt) REVERT: F 313 MET cc_start: 0.1389 (pmm) cc_final: 0.0647 (pmm) REVERT: F 606 MET cc_start: 0.5324 (ptt) cc_final: 0.5033 (ptt) REVERT: B 138 ILE cc_start: 0.5352 (OUTLIER) cc_final: 0.5103 (mt) REVERT: B 159 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.5683 (pm20) REVERT: B 185 MET cc_start: 0.7669 (pmm) cc_final: 0.6967 (pmm) REVERT: B 186 ILE cc_start: 0.7498 (mm) cc_final: 0.6975 (mm) REVERT: E 210 VAL cc_start: 0.6712 (OUTLIER) cc_final: 0.6390 (p) REVERT: E 242 HIS cc_start: 0.5600 (OUTLIER) cc_final: 0.3801 (t-90) REVERT: E 521 TRP cc_start: 0.3893 (OUTLIER) cc_final: 0.2216 (m100) outliers start: 71 outliers final: 39 residues processed: 213 average time/residue: 0.1182 time to fit residues: 38.5310 Evaluate side-chains 191 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 286 TYR Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 446 ILE Chi-restraints excluded: chain F residue 557 ILE Chi-restraints excluded: chain F residue 642 LEU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 400 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 521 TRP Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 629 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 143 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 141 optimal weight: 0.0270 chunk 163 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN F 202 ASN ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.155033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.133665 restraints weight = 45491.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.133608 restraints weight = 35118.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.134484 restraints weight = 31996.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.134857 restraints weight = 25393.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.135046 restraints weight = 24096.881| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15181 Z= 0.173 Angle : 0.667 14.267 20567 Z= 0.341 Chirality : 0.045 0.197 2241 Planarity : 0.005 0.077 2663 Dihedral : 5.512 58.173 2046 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.68 % Favored : 87.94 % Rotamer: Outliers : 5.80 % Allowed : 20.39 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -2.70 (0.19), residues: 1832 helix: -1.03 (0.19), residues: 693 sheet: -3.74 (0.56), residues: 67 loop : -2.26 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 653 TYR 0.025 0.002 TYR E 618 PHE 0.037 0.002 PHE F 276 TRP 0.018 0.002 TRP A 32 HIS 0.008 0.001 HIS B 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (15179) covalent geometry : angle 0.66654 / 0.34 (20563) SS BOND : bond 0.00196 / 0.10 ( 2) SS BOND : angle 1.78584 / 0.85 ( 4) hydrogen bonds : bond 0.04473 / 3.00 ( 399) hydrogen bonds : angle 5.47043 / 3.94 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 150 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ILE cc_start: 0.5685 (OUTLIER) cc_final: 0.5314 (tp) REVERT: A 97 PHE cc_start: 0.7270 (t80) cc_final: 0.6226 (t80) REVERT: A 106 TYR cc_start: 0.4536 (OUTLIER) cc_final: 0.4042 (m-10) REVERT: A 159 GLU cc_start: 0.5288 (pt0) cc_final: 0.4649 (pt0) REVERT: A 167 PHE cc_start: 0.7274 (m-80) cc_final: 0.5978 (m-80) REVERT: A 185 MET cc_start: 0.6267 (tmm) cc_final: 0.5685 (tmm) REVERT: A 307 ILE cc_start: 0.6489 (OUTLIER) cc_final: 0.5956 (tt) REVERT: F 132 MET cc_start: 0.5435 (ptm) cc_final: 0.4501 (ptt) REVERT: F 276 PHE cc_start: 0.6496 (OUTLIER) cc_final: 0.5975 (t80) REVERT: F 606 MET cc_start: 0.5706 (ptt) cc_final: 0.5408 (ptt) REVERT: F 671 TYR cc_start: 0.6267 (OUTLIER) cc_final: 0.5649 (p90) REVERT: B 138 ILE cc_start: 0.5555 (OUTLIER) cc_final: 0.5330 (mt) REVERT: B 185 MET cc_start: 0.7802 (pmm) cc_final: 0.7109 (pmm) REVERT: B 186 ILE cc_start: 0.7588 (mm) cc_final: 0.7021 (mm) REVERT: E 210 VAL cc_start: 0.6983 (OUTLIER) cc_final: 0.6712 (p) REVERT: E 385 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.5944 (m-10) REVERT: E 521 TRP cc_start: 0.3813 (OUTLIER) cc_final: 0.2414 (m100) REVERT: E 653 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7354 (tpt90) outliers start: 93 outliers final: 64 residues processed: 225 average time/residue: 0.1157 time to fit residues: 39.9454 Evaluate side-chains 218 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 144 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 202 ASN Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 276 PHE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 286 TYR Chi-restraints excluded: chain F residue 316 ASN Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 557 ILE Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain F residue 600 TYR Chi-restraints excluded: chain F residue 642 LEU Chi-restraints excluded: chain F residue 667 ILE Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 385 TYR Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 400 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 521 TRP Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 629 TYR Chi-restraints excluded: chain E residue 653 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 127 optimal weight: 0.1980 chunk 31 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 115 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.157365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.136005 restraints weight = 45840.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.137359 restraints weight = 33747.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.137832 restraints weight = 28310.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.138138 restraints weight = 22285.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.138358 restraints weight = 21257.232| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15181 Z= 0.126 Angle : 0.645 11.794 20567 Z= 0.325 Chirality : 0.044 0.261 2241 Planarity : 0.004 0.059 2663 Dihedral : 5.283 50.515 2046 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.21 % Favored : 89.41 % Rotamer: Outliers : 5.36 % Allowed : 21.13 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -2.60 (0.19), residues: 1832 helix: -0.97 (0.19), residues: 699 sheet: -3.82 (0.54), residues: 67 loop : -2.18 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 653 TYR 0.030 0.001 TYR E 618 PHE 0.031 0.001 PHE F 276 TRP 0.008 0.001 TRP A 32 HIS 0.006 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15179) covalent geometry : angle 0.64464 / 0.32 (20563) SS BOND : bond 0.00199 / 0.10 ( 2) SS BOND : angle 1.66446 / 0.83 ( 4) hydrogen bonds : bond 0.03881 / 2.59 ( 399) hydrogen bonds : angle 5.28766 / 3.80 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 148 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ILE cc_start: 0.5495 (OUTLIER) cc_final: 0.5185 (tp) REVERT: A 106 TYR cc_start: 0.4751 (OUTLIER) cc_final: 0.4317 (m-10) REVERT: A 132 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6366 (tt) REVERT: A 167 PHE cc_start: 0.7047 (m-80) cc_final: 0.5851 (m-80) REVERT: A 172 TYR cc_start: 0.4900 (OUTLIER) cc_final: 0.3124 (p90) REVERT: A 185 MET cc_start: 0.6230 (tmm) cc_final: 0.5795 (tmm) REVERT: A 210 MET cc_start: 0.8487 (pmm) cc_final: 0.8263 (pmm) REVERT: A 307 ILE cc_start: 0.6450 (OUTLIER) cc_final: 0.5904 (tt) REVERT: F 132 MET cc_start: 0.5373 (ptm) cc_final: 0.4570 (ptt) REVERT: F 215 LYS cc_start: 0.6926 (pttm) cc_final: 0.6638 (ttpt) REVERT: F 276 PHE cc_start: 0.6427 (OUTLIER) cc_final: 0.5808 (t80) REVERT: F 313 MET cc_start: 0.1334 (pmm) cc_final: 0.0461 (pmm) REVERT: F 606 MET cc_start: 0.5719 (ptt) cc_final: 0.5420 (ptt) REVERT: F 671 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.5570 (p90) REVERT: B 138 ILE cc_start: 0.5504 (OUTLIER) cc_final: 0.5253 (mt) REVERT: B 185 MET cc_start: 0.7706 (pmm) cc_final: 0.7041 (pmm) REVERT: B 186 ILE cc_start: 0.7483 (mm) cc_final: 0.6904 (mm) REVERT: E 210 VAL cc_start: 0.6916 (OUTLIER) cc_final: 0.6648 (p) REVERT: E 242 HIS cc_start: 0.5709 (OUTLIER) cc_final: 0.3671 (t-90) REVERT: E 385 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.5687 (m-10) REVERT: E 521 TRP cc_start: 0.3744 (OUTLIER) cc_final: 0.2271 (m100) outliers start: 86 outliers final: 52 residues processed: 218 average time/residue: 0.1094 time to fit residues: 37.3951 Evaluate side-chains 206 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 142 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 276 PHE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 286 TYR Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 557 ILE Chi-restraints excluded: chain F residue 600 TYR Chi-restraints excluded: chain F residue 642 LEU Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 385 TYR Chi-restraints excluded: chain E residue 400 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 521 TRP Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 629 TYR Chi-restraints excluded: chain E residue 649 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 132 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.0570 chunk 60 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.158987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.137942 restraints weight = 45803.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.139233 restraints weight = 33703.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.139893 restraints weight = 27372.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.140148 restraints weight = 22073.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.140341 restraints weight = 21014.537| |-----------------------------------------------------------------------------| r_work (final): 0.4438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15181 Z= 0.115 Angle : 0.637 13.869 20567 Z= 0.316 Chirality : 0.044 0.227 2241 Planarity : 0.004 0.058 2663 Dihedral : 5.018 50.229 2046 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.43 % Favored : 89.19 % Rotamer: Outliers : 4.36 % Allowed : 22.44 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -2.48 (0.19), residues: 1832 helix: -0.80 (0.20), residues: 683 sheet: -3.22 (0.56), residues: 71 loop : -2.18 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 653 TYR 0.026 0.001 TYR E 618 PHE 0.027 0.001 PHE F 276 TRP 0.014 0.001 TRP A 32 HIS 0.005 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (15179) covalent geometry : angle 0.63648 / 0.32 (20563) SS BOND : bond 0.00162 / 0.08 ( 2) SS BOND : angle 1.71848 / 0.86 ( 4) hydrogen bonds : bond 0.03539 / 2.35 ( 399) hydrogen bonds : angle 5.09077 / 3.65 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 149 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TYR cc_start: 0.4822 (OUTLIER) cc_final: 0.4514 (m-10) REVERT: A 167 PHE cc_start: 0.7171 (m-80) cc_final: 0.5911 (m-80) REVERT: A 172 TYR cc_start: 0.4871 (OUTLIER) cc_final: 0.2969 (p90) REVERT: A 185 MET cc_start: 0.6535 (tmm) cc_final: 0.6182 (tpt) REVERT: A 307 ILE cc_start: 0.6451 (OUTLIER) cc_final: 0.5919 (tt) REVERT: F 132 MET cc_start: 0.5324 (ptm) cc_final: 0.4441 (ptt) REVERT: F 215 LYS cc_start: 0.6934 (pttm) cc_final: 0.6578 (ttpt) REVERT: F 276 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5661 (t80) REVERT: F 313 MET cc_start: 0.1301 (pmm) cc_final: 0.0522 (pmm) REVERT: F 606 MET cc_start: 0.5597 (ptt) cc_final: 0.5234 (ptt) REVERT: B 138 ILE cc_start: 0.5535 (OUTLIER) cc_final: 0.5244 (mt) REVERT: B 185 MET cc_start: 0.7669 (pmm) cc_final: 0.7000 (pmm) REVERT: B 186 ILE cc_start: 0.7596 (mm) cc_final: 0.7021 (mm) REVERT: E 210 VAL cc_start: 0.6893 (OUTLIER) cc_final: 0.6597 (p) REVERT: E 242 HIS cc_start: 0.5650 (OUTLIER) cc_final: 0.3804 (t-90) REVERT: E 521 TRP cc_start: 0.4153 (OUTLIER) cc_final: 0.2507 (m100) REVERT: E 589 GLU cc_start: 0.4924 (OUTLIER) cc_final: 0.4209 (mp0) outliers start: 70 outliers final: 45 residues processed: 207 average time/residue: 0.1176 time to fit residues: 37.2552 Evaluate side-chains 196 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 276 PHE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 286 TYR Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 557 ILE Chi-restraints excluded: chain F residue 600 TYR Chi-restraints excluded: chain F residue 642 LEU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 521 TRP Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 600 TYR Chi-restraints excluded: chain E residue 629 TYR Chi-restraints excluded: chain E residue 649 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 170 optimal weight: 0.0060 chunk 145 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 66 optimal weight: 0.0060 chunk 104 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 overall best weight: 0.7614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 192 ASN ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 GLN F 659 GLN ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.158882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.137254 restraints weight = 45169.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.138230 restraints weight = 32022.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.139143 restraints weight = 26261.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.139376 restraints weight = 21411.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.139521 restraints weight = 20649.513| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15181 Z= 0.117 Angle : 0.643 11.696 20567 Z= 0.317 Chirality : 0.044 0.262 2241 Planarity : 0.004 0.054 2663 Dihedral : 4.930 50.210 2043 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.26 % Favored : 89.36 % Rotamer: Outliers : 4.18 % Allowed : 23.19 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -2.48 (0.19), residues: 1832 helix: -0.81 (0.20), residues: 691 sheet: -3.25 (0.56), residues: 71 loop : -2.19 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 191 TYR 0.024 0.001 TYR E 618 PHE 0.026 0.001 PHE F 276 TRP 0.009 0.001 TRP A 12 HIS 0.004 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15179) covalent geometry : angle 0.64308 / 0.32 (20563) SS BOND : bond 0.00210 / 0.10 ( 2) SS BOND : angle 1.59022 / 0.78 ( 4) hydrogen bonds : bond 0.03528 / 2.35 ( 399) hydrogen bonds : angle 5.05713 / 3.62 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 149 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ILE cc_start: 0.5460 (OUTLIER) cc_final: 0.5137 (tp) REVERT: A 98 MET cc_start: 0.7131 (mmt) cc_final: 0.6575 (tpp) REVERT: A 132 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6508 (tt) REVERT: A 167 PHE cc_start: 0.7252 (m-80) cc_final: 0.6036 (m-80) REVERT: A 172 TYR cc_start: 0.5127 (OUTLIER) cc_final: 0.3203 (p90) REVERT: A 185 MET cc_start: 0.6589 (tmm) cc_final: 0.6108 (tpt) REVERT: A 307 ILE cc_start: 0.6567 (OUTLIER) cc_final: 0.6015 (tt) REVERT: F 132 MET cc_start: 0.5477 (ptm) cc_final: 0.4677 (ptt) REVERT: F 215 LYS cc_start: 0.7047 (pttm) cc_final: 0.6679 (ttpt) REVERT: F 313 MET cc_start: 0.1176 (pmm) cc_final: 0.0448 (pmm) REVERT: F 475 MET cc_start: 0.5805 (mmt) cc_final: 0.4970 (mmm) REVERT: F 606 MET cc_start: 0.5593 (ptt) cc_final: 0.5189 (ptt) REVERT: B 138 ILE cc_start: 0.5699 (OUTLIER) cc_final: 0.5386 (mt) REVERT: B 185 MET cc_start: 0.7681 (pmm) cc_final: 0.7033 (pmm) REVERT: B 186 ILE cc_start: 0.7544 (mm) cc_final: 0.6961 (mm) REVERT: E 210 VAL cc_start: 0.6950 (OUTLIER) cc_final: 0.6657 (p) REVERT: E 242 HIS cc_start: 0.5601 (OUTLIER) cc_final: 0.3686 (t-90) REVERT: E 521 TRP cc_start: 0.4235 (OUTLIER) cc_final: 0.2460 (m100) REVERT: E 589 GLU cc_start: 0.4989 (OUTLIER) cc_final: 0.4291 (mp0) outliers start: 67 outliers final: 48 residues processed: 207 average time/residue: 0.1164 time to fit residues: 37.3336 Evaluate side-chains 199 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 142 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 276 PHE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 286 TYR Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 557 ILE Chi-restraints excluded: chain F residue 600 TYR Chi-restraints excluded: chain F residue 642 LEU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 521 TRP Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 600 TYR Chi-restraints excluded: chain E residue 629 TYR Chi-restraints excluded: chain E residue 649 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 140 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 0.0570 chunk 11 optimal weight: 0.0060 chunk 127 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.156141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.135155 restraints weight = 46022.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.135876 restraints weight = 35996.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.136582 restraints weight = 31588.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.137019 restraints weight = 24703.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.137157 restraints weight = 23813.335| |-----------------------------------------------------------------------------| r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15181 Z= 0.155 Angle : 0.681 10.959 20567 Z= 0.340 Chirality : 0.045 0.255 2241 Planarity : 0.005 0.114 2663 Dihedral : 5.164 48.848 2043 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.46 % Favored : 88.16 % Rotamer: Outliers : 4.49 % Allowed : 22.94 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -2.59 (0.19), residues: 1832 helix: -0.88 (0.19), residues: 699 sheet: -3.98 (0.55), residues: 63 loop : -2.24 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 135 TYR 0.024 0.001 TYR E 618 PHE 0.029 0.002 PHE F 276 TRP 0.009 0.001 TRP A 12 HIS 0.005 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (15179) covalent geometry : angle 0.68053 / 0.34 (20563) SS BOND : bond 0.00227 / 0.12 ( 2) SS BOND : angle 1.61099 / 0.78 ( 4) hydrogen bonds : bond 0.03856 / 2.58 ( 399) hydrogen bonds : angle 5.16308 / 3.73 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 142 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6564 (tt) REVERT: A 172 TYR cc_start: 0.5219 (OUTLIER) cc_final: 0.3275 (p90) REVERT: A 307 ILE cc_start: 0.6509 (OUTLIER) cc_final: 0.5962 (tt) REVERT: F 132 MET cc_start: 0.5568 (ptm) cc_final: 0.5234 (ptm) REVERT: F 215 LYS cc_start: 0.7190 (pttm) cc_final: 0.6787 (ttpt) REVERT: F 606 MET cc_start: 0.5732 (ptt) cc_final: 0.5362 (ptt) REVERT: F 671 TYR cc_start: 0.6147 (OUTLIER) cc_final: 0.5473 (p90) REVERT: B 88 GLU cc_start: 0.7010 (pt0) cc_final: 0.6783 (pt0) REVERT: B 138 ILE cc_start: 0.5881 (OUTLIER) cc_final: 0.5553 (mt) REVERT: B 185 MET cc_start: 0.7754 (pmm) cc_final: 0.7103 (pmm) REVERT: B 186 ILE cc_start: 0.7570 (mm) cc_final: 0.7035 (mm) REVERT: B 217 LYS cc_start: 0.7069 (pptt) cc_final: 0.6763 (tptp) REVERT: E 210 VAL cc_start: 0.7121 (OUTLIER) cc_final: 0.6868 (p) REVERT: E 242 HIS cc_start: 0.5753 (OUTLIER) cc_final: 0.3636 (t-90) REVERT: E 385 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.5737 (m-10) REVERT: E 521 TRP cc_start: 0.3760 (OUTLIER) cc_final: 0.2284 (m100) REVERT: E 589 GLU cc_start: 0.5014 (OUTLIER) cc_final: 0.4387 (mp0) outliers start: 72 outliers final: 54 residues processed: 201 average time/residue: 0.1148 time to fit residues: 35.8410 Evaluate side-chains 202 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 138 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 276 PHE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 286 TYR Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 557 ILE Chi-restraints excluded: chain F residue 600 TYR Chi-restraints excluded: chain F residue 642 LEU Chi-restraints excluded: chain F residue 667 ILE Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 385 TYR Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 521 TRP Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 600 TYR Chi-restraints excluded: chain E residue 629 TYR Chi-restraints excluded: chain E residue 649 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 69 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.156830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.136011 restraints weight = 45157.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.137020 restraints weight = 35015.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.137567 restraints weight = 32463.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.138130 restraints weight = 25047.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.138336 restraints weight = 22920.923| |-----------------------------------------------------------------------------| r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15181 Z= 0.133 Angle : 0.665 10.890 20567 Z= 0.328 Chirality : 0.045 0.241 2241 Planarity : 0.004 0.114 2663 Dihedral : 5.098 48.989 2043 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.14 % Favored : 88.48 % Rotamer: Outliers : 3.87 % Allowed : 23.57 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -2.50 (0.19), residues: 1832 helix: -0.75 (0.20), residues: 675 sheet: -3.51 (0.54), residues: 71 loop : -2.21 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 135 TYR 0.024 0.001 TYR E 618 PHE 0.028 0.001 PHE F 276 TRP 0.009 0.001 TRP A 12 HIS 0.008 0.001 HIS F 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (15179) covalent geometry : angle 0.66471 / 0.33 (20563) SS BOND : bond 0.00158 / 0.08 ( 2) SS BOND : angle 1.61921 / 0.80 ( 4) hydrogen bonds : bond 0.03615 / 2.40 ( 399) hydrogen bonds : angle 5.08271 / 3.65 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 137 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6640 (tt) REVERT: A 172 TYR cc_start: 0.5213 (OUTLIER) cc_final: 0.3292 (p90) REVERT: A 307 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.5807 (tt) REVERT: F 132 MET cc_start: 0.5488 (ptm) cc_final: 0.5177 (ptm) REVERT: F 215 LYS cc_start: 0.6972 (pttm) cc_final: 0.6589 (ttpt) REVERT: F 313 MET cc_start: 0.1599 (pmm) cc_final: 0.0746 (pmm) REVERT: F 475 MET cc_start: 0.5821 (mmt) cc_final: 0.5011 (mmm) REVERT: F 606 MET cc_start: 0.5560 (ptt) cc_final: 0.5170 (ptt) REVERT: F 671 TYR cc_start: 0.6120 (OUTLIER) cc_final: 0.5239 (p90) REVERT: B 98 MET cc_start: 0.5716 (mmm) cc_final: 0.5333 (mmm) REVERT: B 138 ILE cc_start: 0.5796 (OUTLIER) cc_final: 0.5460 (mt) REVERT: B 185 MET cc_start: 0.7518 (pmm) cc_final: 0.6860 (pmm) REVERT: B 186 ILE cc_start: 0.7406 (mm) cc_final: 0.6841 (mm) REVERT: E 210 VAL cc_start: 0.7018 (OUTLIER) cc_final: 0.6747 (p) REVERT: E 242 HIS cc_start: 0.5580 (OUTLIER) cc_final: 0.3494 (t-90) REVERT: E 385 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.5639 (m-10) REVERT: E 521 TRP cc_start: 0.4074 (OUTLIER) cc_final: 0.2641 (m100) REVERT: E 589 GLU cc_start: 0.4889 (OUTLIER) cc_final: 0.4233 (mp0) outliers start: 62 outliers final: 47 residues processed: 190 average time/residue: 0.1117 time to fit residues: 33.0947 Evaluate side-chains 190 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 133 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 276 PHE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 286 TYR Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 557 ILE Chi-restraints excluded: chain F residue 600 TYR Chi-restraints excluded: chain F residue 642 LEU Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 385 TYR Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 521 TRP Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 600 TYR Chi-restraints excluded: chain E residue 629 TYR Chi-restraints excluded: chain E residue 649 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 82 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 156 optimal weight: 0.4980 chunk 114 optimal weight: 0.5980 chunk 158 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.159459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.138323 restraints weight = 45803.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.139482 restraints weight = 33025.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.140422 restraints weight = 26002.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.140510 restraints weight = 21805.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.140864 restraints weight = 20620.776| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15181 Z= 0.116 Angle : 0.660 10.653 20567 Z= 0.325 Chirality : 0.044 0.235 2241 Planarity : 0.004 0.101 2663 Dihedral : 4.985 50.129 2043 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.48 % Favored : 89.14 % Rotamer: Outliers : 3.43 % Allowed : 24.00 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -2.41 (0.19), residues: 1832 helix: -0.65 (0.20), residues: 670 sheet: -3.29 (0.57), residues: 65 loop : -2.21 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 135 TYR 0.023 0.001 TYR E 618 PHE 0.026 0.001 PHE F 276 TRP 0.010 0.001 TRP A 12 HIS 0.007 0.001 HIS F 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (15179) covalent geometry : angle 0.65923 / 0.32 (20563) SS BOND : bond 0.00157 / 0.08 ( 2) SS BOND : angle 1.65767 / 0.83 ( 4) hydrogen bonds : bond 0.03342 / 2.22 ( 399) hydrogen bonds : angle 4.96395 / 3.56 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.23 seconds wall clock time: 41 minutes 29.76 seconds (2489.76 seconds total)