Starting phenix.real_space_refine on Sat Jul 4 05:21:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eb2_31049/07_2026/7eb2_31049.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eb2_31049/07_2026/7eb2_31049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7eb2_31049/07_2026/7eb2_31049.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eb2_31049/07_2026/7eb2_31049.cif" model { file = "/net/cci-nas-00/data/ceres_data/7eb2_31049/07_2026/7eb2_31049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eb2_31049/07_2026/7eb2_31049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eb2_31049/07_2026/7eb2_31049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eb2_31049/07_2026/7eb2_31049.map" } resolution = 3.5 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= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 114 5.16 5 Cl 1 4.86 5 C 11829 2.51 5 N 3116 2.21 5 O 3434 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18497 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2820 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 347} Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "Y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "C" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5406 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 28, 'TRANS': 649} Chain breaks: 2 Chain: "D" Number of atoms: 5414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5414 Classifications: {'peptide': 680} Link IDs: {'PTRANS': 26, 'TRANS': 653} Chain breaks: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'2C0': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'FN0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.58, per 1000 atoms: 0.19 Number of scatterers: 18497 At special positions: 0 Unit cell: (142.974, 121.68, 226.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 114 16.00 F 3 9.00 O 3434 8.00 N 3116 7.00 C 11829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 159 " - pdb=" SG CYS N 229 " distance=2.20 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 135 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 648 " 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: 1.51 Conformation dependent library (CDL) restraints added in 742.5 milliseconds 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 22 sheets defined 44.8% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.587A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N HIS A 57 " --> pdb=" O MET A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 88 Processing helix chain 'A' and resid 101 through 116 Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.517A pdb=" N TYR A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 171 through 179 removed outlier: 5.490A pdb=" N THR A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.555A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.604A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.021A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.862A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.023A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'Y' and resid 7 through 23 Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 removed outlier: 3.806A pdb=" N ASP Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'N' and resid 220 through 224 Processing helix chain 'C' and resid 184 through 202 Proline residue: C 190 - end of helix removed outlier: 3.554A pdb=" N ARG C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 234 Processing helix chain 'C' and resid 246 through 257 Processing helix chain 'C' and resid 271 through 276 removed outlier: 3.542A pdb=" N ASN C 276 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 292 through 305 removed outlier: 4.107A pdb=" N THR C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 331 Processing helix chain 'C' and resid 347 through 357 Processing helix chain 'C' and resid 367 through 382 removed outlier: 4.450A pdb=" N LYS C 373 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 419 removed outlier: 3.694A pdb=" N GLU C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 454 Processing helix chain 'C' and resid 457 through 461 Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 466 through 485 removed outlier: 3.556A pdb=" N THR C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 515 removed outlier: 3.685A pdb=" N SER C 515 " --> pdb=" O ARG C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 616 Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 626 through 643 Processing helix chain 'C' and resid 644 through 649 Processing helix chain 'C' and resid 658 through 691 removed outlier: 3.692A pdb=" N VAL C 662 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N MET C 681 " --> pdb=" O GLY C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 732 removed outlier: 4.142A pdb=" N LEU C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR C 711 " --> pdb=" O PRO C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 791 Processing helix chain 'C' and resid 801 through 826 Proline residue: C 821 - end of helix removed outlier: 3.703A pdb=" N MET C 824 " --> pdb=" O ALA C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 860 Proline residue: C 855 - end of helix Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.876A pdb=" N GLY D 74 " --> pdb=" O LYS D 70 " (cutoff:3.500A) Proline residue: D 79 - end of helix Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 135 through 146 removed outlier: 3.617A pdb=" N SER D 145 " --> pdb=" O ILE D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 160 through 165 removed outlier: 3.611A pdb=" N LEU D 163 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 205 through 219 removed outlier: 4.055A pdb=" N GLY D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 245 removed outlier: 3.680A pdb=" N LYS D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 270 removed outlier: 3.844A pdb=" N ALA D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 311 Processing helix chain 'D' and resid 334 through 346 Processing helix chain 'D' and resid 354 through 375 removed outlier: 3.772A pdb=" N THR D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 404 Processing helix chain 'D' and resid 478 through 506 removed outlier: 3.911A pdb=" N ASN D 506 " --> pdb=" O PHE D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 515 removed outlier: 3.776A pdb=" N SER D 515 " --> pdb=" O LEU D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 533 Processing helix chain 'D' and resid 534 through 539 removed outlier: 3.864A pdb=" N GLY D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 539 " --> pdb=" O PHE D 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 534 through 539' Processing helix chain 'D' and resid 547 through 584 removed outlier: 3.733A pdb=" N THR D 551 " --> pdb=" O LYS D 547 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR D 554 " --> pdb=" O GLU D 550 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR D 557 " --> pdb=" O CYS D 553 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 619 removed outlier: 3.582A pdb=" N LEU D 598 " --> pdb=" O ASP D 594 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL D 599 " --> pdb=" O GLN D 595 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 600 " --> pdb=" O LYS D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 678 removed outlier: 3.998A pdb=" N TRP D 656 " --> pdb=" O HIS D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 682 removed outlier: 4.256A pdb=" N SER D 682 " --> pdb=" O ARG D 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 679 through 682' Processing helix chain 'D' and resid 688 through 713 removed outlier: 3.908A pdb=" N PHE D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 747 removed outlier: 4.418A pdb=" N VAL D 739 " --> pdb=" O THR D 735 " (cutoff:3.500A) Proline residue: D 742 - end of helix removed outlier: 3.891A pdb=" N THR D 746 " --> pdb=" O PRO D 742 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 747 " --> pdb=" O LYS D 743 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.562A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.772A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.942A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.594A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 153 removed outlier: 6.885A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.521A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.561A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.534A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.643A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.972A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'N' and resid 194 through 195 removed outlier: 5.322A pdb=" N LEU N 187 " --> pdb=" O LEU N 178 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU N 178 " --> pdb=" O LEU N 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 209 through 216 removed outlier: 8.731A pdb=" N LYS C 239 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TYR C 171 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE C 241 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE C 240 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N LEU C 265 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU C 242 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL C 264 " --> pdb=" O PHE C 284 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 336 through 343 removed outlier: 6.279A pdb=" N ILE C 309 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE C 339 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE C 361 " --> pdb=" O LYS C 308 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE C 393 " --> pdb=" O GLY C 364 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 425 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR C 537 " --> pdb=" O TYR C 552 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR C 552 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE C 539 " --> pdb=" O ILE C 550 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 517 through 520 removed outlier: 3.511A pdb=" N PHE C 518 " --> pdb=" O VAL C 525 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB8, first strand: chain 'C' and resid 735 through 740 removed outlier: 3.515A pdb=" N THR C 737 " --> pdb=" O HIS C 760 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 99 through 105 removed outlier: 5.772A pdb=" N LEU D 56 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ARG D 102 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE D 58 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR D 104 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY D 60 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N SER D 57 " --> pdb=" O MET D 129 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N PHE D 131 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N MET D 59 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 225 through 232 removed outlier: 6.891A pdb=" N VAL D 198 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLU D 230 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR D 200 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE D 232 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR D 202 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARG D 197 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LEU D 252 " --> pdb=" O ARG D 197 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY D 199 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLN D 254 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU D 201 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 315 through 319 removed outlier: 3.650A pdb=" N GLY D 440 " --> pdb=" O PHE D 428 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLN D 430 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LYS D 438 " --> pdb=" O GLN D 430 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN D 432 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU D 436 " --> pdb=" O GLN D 432 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 407 through 410 removed outlier: 3.597A pdb=" N PHE D 408 " --> pdb=" O VAL D 415 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 470 through 474 removed outlier: 6.148A pdb=" N LEU D 471 " --> pdb=" O ARG D 642 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU D 644 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN D 473 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLU D 646 " --> pdb=" O GLN D 473 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2628 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: 3.21 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3187 1.32 - 1.44: 5001 1.44 - 1.57: 10533 1.57 - 1.69: 0 1.69 - 1.82: 175 Bond restraints: 18896 Sorted by residual: bond pdb=" CA HIS D 579 " pdb=" C HIS D 579 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" C13 FN0 D 901 " pdb=" O3 FN0 D 901 " ideal model delta sigma weight residual 1.190 1.256 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C GLU A 65 " pdb=" O GLU A 65 " ideal model delta sigma weight residual 1.236 1.199 0.038 1.25e-02 6.40e+03 9.03e+00 bond pdb=" N LYS A 51 " pdb=" CA LYS A 51 " ideal model delta sigma weight residual 1.459 1.423 0.036 1.21e-02 6.83e+03 8.66e+00 bond pdb=" C3 FN0 D 901 " pdb=" C4 FN0 D 901 " ideal model delta sigma weight residual 1.526 1.468 0.058 2.00e-02 2.50e+03 8.35e+00 ... (remaining 18891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 25050 2.13 - 4.26: 471 4.26 - 6.39: 60 6.39 - 8.52: 13 8.52 - 10.64: 6 Bond angle restraints: 25600 Sorted by residual: angle pdb=" N ALA A 31 " pdb=" CA ALA A 31 " pdb=" C ALA A 31 " ideal model delta sigma weight residual 111.28 121.92 -10.64 1.09e+00 8.42e-01 9.54e+01 angle pdb=" N ARG A 32 " pdb=" CA ARG A 32 " pdb=" C ARG A 32 " ideal model delta sigma weight residual 111.28 120.47 -9.19 1.09e+00 8.42e-01 7.11e+01 angle pdb=" N LYS D 586 " pdb=" CA LYS D 586 " pdb=" C LYS D 586 " ideal model delta sigma weight residual 111.33 101.47 9.86 1.21e+00 6.83e-01 6.64e+01 angle pdb=" N LYS A 70 " pdb=" CA LYS A 70 " pdb=" C LYS A 70 " ideal model delta sigma weight residual 111.28 102.96 8.32 1.09e+00 8.42e-01 5.83e+01 angle pdb=" N ASP D 594 " pdb=" CA ASP D 594 " pdb=" C ASP D 594 " ideal model delta sigma weight residual 111.36 119.67 -8.31 1.09e+00 8.42e-01 5.82e+01 ... (remaining 25595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10588 17.85 - 35.70: 579 35.70 - 53.56: 85 53.56 - 71.41: 10 71.41 - 89.26: 18 Dihedral angle restraints: 11280 sinusoidal: 4495 harmonic: 6785 Sorted by residual: dihedral pdb=" CB CYS N 159 " pdb=" SG CYS N 159 " pdb=" SG CYS N 229 " pdb=" CB CYS N 229 " ideal model delta sinusoidal sigma weight residual 93.00 136.65 -43.65 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS C 220 " pdb=" SG CYS C 220 " pdb=" SG CYS C 246 " pdb=" CB CYS C 246 " ideal model delta sinusoidal sigma weight residual 93.00 132.51 -39.51 1 1.00e+01 1.00e-02 2.19e+01 dihedral pdb=" CA GLN D 432 " pdb=" C GLN D 432 " pdb=" N ASP D 433 " pdb=" CA ASP D 433 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 11277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2410 0.070 - 0.141: 405 0.141 - 0.211: 49 0.211 - 0.281: 8 0.281 - 0.352: 2 Chirality restraints: 2874 Sorted by residual: chirality pdb=" CA ALA A 31 " pdb=" N ALA A 31 " pdb=" C ALA A 31 " pdb=" CB ALA A 31 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ALA D 580 " pdb=" N ALA D 580 " pdb=" C ALA D 580 " pdb=" CB ALA D 580 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA ALA A 30 " pdb=" N ALA A 30 " pdb=" C ALA A 30 " pdb=" CB ALA A 30 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2871 not shown) Planarity restraints: 3237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 FN0 D 901 " 0.094 2.00e-02 2.50e+03 5.44e-02 2.96e+01 pdb=" C7 FN0 D 901 " -0.028 2.00e-02 2.50e+03 pdb=" O1 FN0 D 901 " -0.029 2.00e-02 2.50e+03 pdb=" O3 FN0 D 901 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 214 " -0.016 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C CYS A 214 " 0.059 2.00e-02 2.50e+03 pdb=" O CYS A 214 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 215 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 201 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C VAL A 201 " -0.058 2.00e-02 2.50e+03 pdb=" O VAL A 201 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY A 202 " 0.019 2.00e-02 2.50e+03 ... (remaining 3234 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 235 2.65 - 3.22: 17585 3.22 - 3.78: 27567 3.78 - 4.34: 39213 4.34 - 4.90: 64170 Nonbonded interactions: 148770 Sorted by model distance: nonbonded pdb=" O LEU A 353 " pdb=" C LYS D 513 " model vdw 2.092 3.270 nonbonded pdb=" N GLU A 63 " pdb=" OE1 GLU A 63 " model vdw 2.167 3.120 nonbonded pdb=" OG1 THR C 633 " pdb=" OG SER C 680 " model vdw 2.187 3.040 nonbonded pdb=" OE2 GLU N 6 " pdb=" N GLY N 114 " model vdw 2.190 3.120 nonbonded pdb=" O LYS A 210 " pdb=" ND1 HIS A 213 " model vdw 2.209 3.120 ... (remaining 148765 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.940 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.980 Find NCS groups from input model: 0.070 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.007 0.167 18900 Z= 0.378 Angle : 0.752 10.645 25608 Z= 0.495 Chirality : 0.053 0.352 2874 Planarity : 0.004 0.054 3237 Dihedral : 11.714 89.258 6900 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.24 (0.16), residues: 2315 helix: -0.43 (0.15), residues: 947 sheet: -0.35 (0.24), residues: 453 loop : -1.35 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.013 0.001 TYR D 314 PHE 0.015 0.001 PHE C 375 TRP 0.011 0.001 TRP B 339 HIS 0.005 0.001 HIS D 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.37 (18896) covalent geometry : angle 0.75179 / 0.49 (25600) SS BOND : bond 0.08364 / 4.40 ( 4) SS BOND : angle 1.58337 / 0.88 ( 8) hydrogen bonds : bond 0.17361 / 11.65 ( 924) hydrogen bonds : angle 6.21073 / 4.47 ( 2628) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 701 time to evaluate : 0.707 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9095 (mttt) cc_final: 0.8640 (mtmm) REVERT: A 25 GLU cc_start: 0.8502 (tt0) cc_final: 0.8203 (pt0) REVERT: A 154 TYR cc_start: 0.8094 (m-80) cc_final: 0.7824 (m-80) REVERT: A 194 LEU cc_start: 0.8162 (mp) cc_final: 0.7715 (tp) REVERT: A 198 MET cc_start: 0.8336 (ttm) cc_final: 0.8070 (ttm) REVERT: A 213 HIS cc_start: 0.7588 (p-80) cc_final: 0.7205 (p-80) REVERT: A 221 ILE cc_start: 0.7609 (mt) cc_final: 0.7155 (mm) REVERT: A 234 LEU cc_start: 0.8250 (tp) cc_final: 0.8050 (mt) REVERT: A 237 ASP cc_start: 0.8032 (t0) cc_final: 0.6503 (p0) REVERT: A 246 SER cc_start: 0.9100 (m) cc_final: 0.8844 (p) REVERT: A 247 MET cc_start: 0.8649 (mtp) cc_final: 0.7713 (mtp) REVERT: A 258 TRP cc_start: 0.7355 (m100) cc_final: 0.7081 (m100) REVERT: A 259 PHE cc_start: 0.7928 (m-80) cc_final: 0.7421 (m-80) REVERT: A 274 PHE cc_start: 0.8083 (t80) cc_final: 0.7534 (t80) REVERT: A 283 LEU cc_start: 0.9490 (mt) cc_final: 0.8935 (pp) REVERT: A 303 ILE cc_start: 0.8946 (mt) cc_final: 0.8474 (mt) REVERT: A 305 CYS cc_start: 0.8215 (m) cc_final: 0.7976 (m) REVERT: A 307 PHE cc_start: 0.8715 (m-80) cc_final: 0.8476 (m-80) REVERT: A 333 GLN cc_start: 0.8733 (mt0) cc_final: 0.8379 (mm-40) REVERT: A 334 PHE cc_start: 0.8955 (t80) cc_final: 0.8710 (t80) REVERT: A 336 PHE cc_start: 0.8050 (t80) cc_final: 0.7811 (t80) REVERT: A 337 ASP cc_start: 0.8421 (m-30) cc_final: 0.7888 (p0) REVERT: A 341 ASP cc_start: 0.8399 (m-30) cc_final: 0.7832 (m-30) REVERT: A 345 LYS cc_start: 0.8704 (mttt) cc_final: 0.8458 (mttt) REVERT: A 346 ASN cc_start: 0.8230 (m-40) cc_final: 0.7923 (t0) REVERT: B 14 LEU cc_start: 0.9172 (mt) cc_final: 0.8738 (mm) REVERT: B 15 LYS cc_start: 0.9010 (mttt) cc_final: 0.8493 (mttt) REVERT: B 19 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.8115 (mtm-85) REVERT: B 23 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8650 (ptpp) REVERT: B 32 GLN cc_start: 0.8302 (mt0) cc_final: 0.7994 (mt0) REVERT: B 81 ILE cc_start: 0.8802 (mm) cc_final: 0.8589 (tp) REVERT: B 89 LYS cc_start: 0.8978 (mttp) cc_final: 0.8752 (mttp) REVERT: B 122 SER cc_start: 0.8792 (m) cc_final: 0.8405 (p) REVERT: B 188 MET cc_start: 0.7722 (mmp) cc_final: 0.7154 (mmm) REVERT: B 209 LYS cc_start: 0.8753 (mttm) cc_final: 0.8536 (mmtp) REVERT: B 217 MET cc_start: 0.7736 (ptm) cc_final: 0.7310 (ptm) REVERT: B 219 ARG cc_start: 0.8286 (mtt-85) cc_final: 0.7821 (mmm-85) REVERT: B 256 ARG cc_start: 0.8376 (mtm180) cc_final: 0.7882 (mtm180) REVERT: B 270 ILE cc_start: 0.9382 (pt) cc_final: 0.9174 (mm) REVERT: B 298 ASP cc_start: 0.7816 (t0) cc_final: 0.6964 (p0) REVERT: Y 9 ILE cc_start: 0.6399 (mt) cc_final: 0.5817 (pt) REVERT: Y 21 MET cc_start: 0.8270 (tmm) cc_final: 0.8065 (tmm) REVERT: Y 22 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8563 (tp30) REVERT: Y 28 ILE cc_start: 0.7454 (pt) cc_final: 0.7209 (pt) REVERT: Y 44 HIS cc_start: 0.8062 (m-70) cc_final: 0.7261 (m-70) REVERT: N 38 ARG cc_start: 0.8434 (ptt180) cc_final: 0.7841 (ptm-80) REVERT: N 102 TYR cc_start: 0.8305 (p90) cc_final: 0.8014 (p90) REVERT: N 109 ASP cc_start: 0.8051 (p0) cc_final: 0.7182 (p0) REVERT: N 160 ARG cc_start: 0.8138 (mtt-85) cc_final: 0.7886 (ttm110) REVERT: C 178 MET cc_start: 0.7777 (mmt) cc_final: 0.7441 (mmm) REVERT: C 189 GLN cc_start: 0.7966 (tt0) cc_final: 0.7491 (tm-30) REVERT: C 200 ASN cc_start: 0.7850 (m-40) cc_final: 0.7478 (m-40) REVERT: C 203 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7797 (mpt-90) REVERT: C 260 TRP cc_start: 0.8188 (m-90) cc_final: 0.7788 (m-90) REVERT: C 279 ARG cc_start: 0.7962 (ttt180) cc_final: 0.7497 (mmm-85) REVERT: C 294 ASN cc_start: 0.7679 (m-40) cc_final: 0.7404 (m-40) REVERT: C 321 SER cc_start: 0.7368 (m) cc_final: 0.7052 (p) REVERT: C 327 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7316 (tm-30) REVERT: C 352 LYS cc_start: 0.8109 (ptpt) cc_final: 0.7566 (mtmm) REVERT: C 379 TYR cc_start: 0.8085 (t80) cc_final: 0.7760 (t80) REVERT: C 380 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7824 (mmmm) REVERT: C 384 PHE cc_start: 0.8717 (p90) cc_final: 0.8507 (p90) REVERT: C 415 MET cc_start: 0.7413 (ttm) cc_final: 0.6913 (ttm) REVERT: C 449 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8507 (mttp) REVERT: C 472 ASP cc_start: 0.7436 (m-30) cc_final: 0.7137 (m-30) REVERT: C 475 TRP cc_start: 0.7199 (m100) cc_final: 0.6789 (m100) REVERT: C 534 MET cc_start: 0.7472 (mtt) cc_final: 0.7064 (mtp) REVERT: C 549 LYS cc_start: 0.8734 (mttp) cc_final: 0.8370 (mtpt) REVERT: C 568 TRP cc_start: 0.8055 (m100) cc_final: 0.6981 (m100) REVERT: C 569 ILE cc_start: 0.8669 (mt) cc_final: 0.8447 (mm) REVERT: C 592 PHE cc_start: 0.7535 (t80) cc_final: 0.7266 (t80) REVERT: C 626 GLN cc_start: 0.6563 (mp10) cc_final: 0.6069 (mp10) REVERT: C 637 CYS cc_start: 0.8230 (m) cc_final: 0.7875 (m) REVERT: C 708 TRP cc_start: 0.6764 (p-90) cc_final: 0.6243 (m100) REVERT: C 745 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7546 (mm-30) REVERT: C 795 SER cc_start: 0.8810 (m) cc_final: 0.8390 (p) REVERT: C 807 MET cc_start: 0.7795 (mtm) cc_final: 0.7589 (mtm) REVERT: C 812 VAL cc_start: 0.8560 (t) cc_final: 0.8286 (p) REVERT: C 853 PHE cc_start: 0.7616 (m-80) cc_final: 0.7377 (m-10) REVERT: D 100 ASP cc_start: 0.6957 (t0) cc_final: 0.6366 (t0) REVERT: D 126 ASN cc_start: 0.6830 (p0) cc_final: 0.6025 (p0) REVERT: D 196 LYS cc_start: 0.8727 (mttt) cc_final: 0.8452 (mmtt) REVERT: D 214 ASP cc_start: 0.7924 (t0) cc_final: 0.7427 (t0) REVERT: D 220 TYR cc_start: 0.8514 (t80) cc_final: 0.8282 (t80) REVERT: D 222 GLU cc_start: 0.8062 (mp0) cc_final: 0.7635 (mp0) REVERT: D 241 LYS cc_start: 0.7572 (mtpt) cc_final: 0.7270 (mmtt) REVERT: D 270 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7889 (mm-30) REVERT: D 288 SER cc_start: 0.8749 (m) cc_final: 0.7816 (p) REVERT: D 311 MET cc_start: 0.7372 (ptp) cc_final: 0.6953 (ptp) REVERT: D 319 PHE cc_start: 0.7483 (p90) cc_final: 0.7190 (p90) REVERT: D 342 TYR cc_start: 0.7853 (t80) cc_final: 0.7623 (t80) REVERT: D 418 ARG cc_start: 0.7810 (mtp-110) cc_final: 0.7581 (mtp-110) REVERT: D 427 LYS cc_start: 0.7911 (pttt) cc_final: 0.7557 (ptmm) REVERT: D 467 LYS cc_start: 0.8358 (tppt) cc_final: 0.8118 (tppt) REVERT: D 502 PHE cc_start: 0.7570 (m-10) cc_final: 0.7084 (m-10) REVERT: D 609 LEU cc_start: 0.8098 (tt) cc_final: 0.7823 (mt) REVERT: D 630 MET cc_start: 0.4091 (tmm) cc_final: 0.3859 (tmm) REVERT: D 677 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6744 (tm-30) REVERT: D 744 LEU cc_start: 0.8786 (mp) cc_final: 0.8500 (tt) outliers start: 0 outliers final: 0 residues processed: 701 average time/residue: 0.1736 time to fit residues: 172.9877 Evaluate side-chains 537 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 340 ASN Y 11 GLN Y 44 HIS C 434 ASN C 514 ASN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS D 336 GLN D 393 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.123455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104128 restraints weight = 43252.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.107999 restraints weight = 20741.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.110555 restraints weight = 11835.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.112261 restraints weight = 7542.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.113435 restraints weight = 5206.559| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18900 Z= 0.181 Angle : 0.685 9.427 25608 Z= 0.356 Chirality : 0.045 0.174 2874 Planarity : 0.005 0.085 3237 Dihedral : 4.847 30.388 2571 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.81 % Favored : 97.11 % Rotamer: Outliers : 2.33 % Allowed : 11.62 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2315 helix: 0.69 (0.16), residues: 962 sheet: -0.09 (0.23), residues: 488 loop : -1.10 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 27 TYR 0.023 0.002 TYR D 338 PHE 0.020 0.002 PHE D 499 TRP 0.015 0.001 TRP A 211 HIS 0.010 0.001 HIS D 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (18896) covalent geometry : angle 0.68449 / 0.36 (25600) SS BOND : bond 0.00736 / 0.38 ( 4) SS BOND : angle 0.84351 / 0.45 ( 8) hydrogen bonds : bond 0.04993 / 3.32 ( 924) hydrogen bonds : angle 4.69054 / 3.38 ( 2628) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 568 time to evaluate : 0.540 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8940 (mttt) cc_final: 0.8538 (mtmm) REVERT: A 18 MET cc_start: 0.7968 (mmm) cc_final: 0.7618 (mmp) REVERT: A 24 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7945 (ttt-90) REVERT: A 29 LYS cc_start: 0.8345 (tmtt) cc_final: 0.7651 (tmtt) REVERT: A 76 ASN cc_start: 0.7354 (m-40) cc_final: 0.6973 (t0) REVERT: A 154 TYR cc_start: 0.8026 (m-80) cc_final: 0.7681 (m-80) REVERT: A 192 LYS cc_start: 0.8956 (mtmm) cc_final: 0.8256 (ptmm) REVERT: A 194 LEU cc_start: 0.8154 (mp) cc_final: 0.7828 (tp) REVERT: A 198 MET cc_start: 0.8358 (ttm) cc_final: 0.8079 (tpp) REVERT: A 213 HIS cc_start: 0.7735 (p-80) cc_final: 0.7229 (p-80) REVERT: A 246 SER cc_start: 0.9138 (m) cc_final: 0.8799 (p) REVERT: A 247 MET cc_start: 0.8370 (mtp) cc_final: 0.8005 (mtp) REVERT: A 274 PHE cc_start: 0.7899 (t80) cc_final: 0.7351 (t80) REVERT: A 283 LEU cc_start: 0.9454 (mt) cc_final: 0.8742 (pp) REVERT: A 286 CYS cc_start: 0.8316 (p) cc_final: 0.6547 (t) REVERT: A 287 TYR cc_start: 0.7746 (m-80) cc_final: 0.7355 (m-80) REVERT: A 303 ILE cc_start: 0.8937 (mt) cc_final: 0.8577 (pt) REVERT: A 304 GLN cc_start: 0.8203 (tt0) cc_final: 0.7860 (tp40) REVERT: A 333 GLN cc_start: 0.8669 (mt0) cc_final: 0.8386 (mm-40) REVERT: A 334 PHE cc_start: 0.9003 (t80) cc_final: 0.8475 (t80) REVERT: A 336 PHE cc_start: 0.8386 (t80) cc_final: 0.7272 (t80) REVERT: A 337 ASP cc_start: 0.8367 (m-30) cc_final: 0.7771 (p0) REVERT: A 341 ASP cc_start: 0.8324 (m-30) cc_final: 0.8038 (m-30) REVERT: A 345 LYS cc_start: 0.8796 (mttt) cc_final: 0.8595 (ptpp) REVERT: A 346 ASN cc_start: 0.8150 (m-40) cc_final: 0.7880 (m-40) REVERT: B 9 GLN cc_start: 0.8841 (mt0) cc_final: 0.8485 (mt0) REVERT: B 12 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8506 (pp20) REVERT: B 15 LYS cc_start: 0.8955 (mttt) cc_final: 0.8574 (mttt) REVERT: B 19 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.8189 (mtm-85) REVERT: B 23 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8820 (ptpt) REVERT: B 32 GLN cc_start: 0.8289 (mt0) cc_final: 0.8081 (mt0) REVERT: B 101 MET cc_start: 0.8085 (mmm) cc_final: 0.7882 (tpp) REVERT: B 122 SER cc_start: 0.8800 (m) cc_final: 0.8409 (p) REVERT: B 156 GLN cc_start: 0.6474 (mp-120) cc_final: 0.6201 (mp10) REVERT: B 172 GLU cc_start: 0.8203 (tp30) cc_final: 0.7988 (tp30) REVERT: B 298 ASP cc_start: 0.7743 (t0) cc_final: 0.7432 (t70) REVERT: Y 9 ILE cc_start: 0.6602 (mt) cc_final: 0.5687 (mt) REVERT: Y 13 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.8203 (ptp90) REVERT: Y 14 LYS cc_start: 0.8731 (mppt) cc_final: 0.8412 (mppt) REVERT: Y 25 ILE cc_start: 0.8500 (tt) cc_final: 0.8190 (tt) REVERT: Y 27 ARG cc_start: 0.6454 (mtt90) cc_final: 0.6174 (mtt90) REVERT: Y 32 LYS cc_start: 0.8332 (mmtt) cc_final: 0.7921 (mmtt) REVERT: N 96 CYS cc_start: 0.7198 (p) cc_final: 0.6169 (p) REVERT: N 109 ASP cc_start: 0.8156 (p0) cc_final: 0.7795 (p0) REVERT: N 110 PHE cc_start: 0.8623 (t80) cc_final: 0.8375 (t80) REVERT: N 244 LYS cc_start: 0.8700 (tttt) cc_final: 0.8492 (tttt) REVERT: C 200 ASN cc_start: 0.7856 (m-40) cc_final: 0.7510 (m-40) REVERT: C 279 ARG cc_start: 0.8122 (ttt180) cc_final: 0.7712 (mmm-85) REVERT: C 321 SER cc_start: 0.7352 (m) cc_final: 0.6958 (p) REVERT: C 327 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7436 (tm-30) REVERT: C 379 TYR cc_start: 0.7972 (t80) cc_final: 0.7566 (t80) REVERT: C 380 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7875 (mmmm) REVERT: C 384 PHE cc_start: 0.8748 (p90) cc_final: 0.8538 (p90) REVERT: C 415 MET cc_start: 0.7365 (ttm) cc_final: 0.7057 (ttm) REVERT: C 448 GLU cc_start: 0.8495 (pt0) cc_final: 0.8149 (pt0) REVERT: C 454 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8647 (mm) REVERT: C 456 ARG cc_start: 0.7679 (mtm180) cc_final: 0.7350 (mtm110) REVERT: C 469 LEU cc_start: 0.7137 (mt) cc_final: 0.6368 (mm) REVERT: C 534 MET cc_start: 0.7752 (mtt) cc_final: 0.7410 (mtp) REVERT: C 548 LYS cc_start: 0.8400 (mmmt) cc_final: 0.8082 (mmmt) REVERT: C 567 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7767 (ttpp) REVERT: C 568 TRP cc_start: 0.7896 (m100) cc_final: 0.7386 (m100) REVERT: C 708 TRP cc_start: 0.6798 (p-90) cc_final: 0.6295 (m100) REVERT: C 740 THR cc_start: 0.8150 (p) cc_final: 0.7715 (p) REVERT: C 795 SER cc_start: 0.8687 (m) cc_final: 0.8304 (p) REVERT: C 812 VAL cc_start: 0.8529 (t) cc_final: 0.8260 (p) REVERT: C 814 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7981 (p) REVERT: C 853 PHE cc_start: 0.7616 (m-80) cc_final: 0.7387 (m-10) REVERT: D 83 LEU cc_start: 0.8450 (mt) cc_final: 0.7703 (tp) REVERT: D 94 LEU cc_start: 0.8148 (mm) cc_final: 0.7898 (pt) REVERT: D 100 ASP cc_start: 0.7045 (t0) cc_final: 0.6756 (t0) REVERT: D 107 GLU cc_start: 0.7152 (mp0) cc_final: 0.6765 (mp0) REVERT: D 112 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7735 (mtpt) REVERT: D 126 ASN cc_start: 0.7239 (p0) cc_final: 0.6473 (p0) REVERT: D 214 ASP cc_start: 0.7737 (t0) cc_final: 0.7106 (t0) REVERT: D 222 GLU cc_start: 0.7930 (mp0) cc_final: 0.7612 (mp0) REVERT: D 268 TYR cc_start: 0.8107 (t80) cc_final: 0.7649 (t80) REVERT: D 272 MET cc_start: 0.7864 (ttt) cc_final: 0.7616 (ttt) REVERT: D 276 LYS cc_start: 0.8581 (ptmm) cc_final: 0.8301 (ptmm) REVERT: D 288 SER cc_start: 0.8943 (m) cc_final: 0.8239 (p) REVERT: D 311 MET cc_start: 0.7451 (ptp) cc_final: 0.7100 (ptp) REVERT: D 320 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7342 (mt-10) REVERT: D 338 TYR cc_start: 0.7599 (t80) cc_final: 0.7225 (t80) REVERT: D 342 TYR cc_start: 0.8070 (t80) cc_final: 0.7296 (t80) REVERT: D 427 LYS cc_start: 0.8008 (pttt) cc_final: 0.7583 (ptmm) REVERT: D 476 LYS cc_start: 0.8229 (ptmm) cc_final: 0.7978 (ptmm) REVERT: D 609 LEU cc_start: 0.8107 (tt) cc_final: 0.7898 (mt) REVERT: D 630 MET cc_start: 0.4539 (tmm) cc_final: 0.4157 (tmm) REVERT: D 697 TYR cc_start: 0.8051 (t80) cc_final: 0.7769 (t80) REVERT: D 715 ASP cc_start: 0.8186 (p0) cc_final: 0.7972 (p0) REVERT: D 744 LEU cc_start: 0.8813 (mp) cc_final: 0.8214 (tt) outliers start: 47 outliers final: 25 residues processed: 591 average time/residue: 0.1514 time to fit residues: 128.7508 Evaluate side-chains 543 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 516 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 728 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.0270 chunk 76 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 214 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 165 optimal weight: 0.1980 chunk 143 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 220 GLN Y 11 GLN ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.123230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104245 restraints weight = 43363.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.108116 restraints weight = 20657.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.110614 restraints weight = 11701.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.112334 restraints weight = 7439.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.113423 restraints weight = 5105.024| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18900 Z= 0.133 Angle : 0.663 10.835 25608 Z= 0.338 Chirality : 0.044 0.236 2874 Planarity : 0.004 0.055 3237 Dihedral : 4.617 39.145 2571 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.80 % Rotamer: Outliers : 2.38 % Allowed : 15.25 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.17), residues: 2315 helix: 0.99 (0.16), residues: 966 sheet: 0.11 (0.23), residues: 484 loop : -1.15 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 24 TYR 0.020 0.001 TYR D 118 PHE 0.040 0.001 PHE A 307 TRP 0.027 0.001 TRP D 656 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (18896) covalent geometry : angle 0.66212 / 0.34 (25600) SS BOND : bond 0.00387 / 0.20 ( 4) SS BOND : angle 1.59680 / 0.72 ( 8) hydrogen bonds : bond 0.04364 / 2.91 ( 924) hydrogen bonds : angle 4.43305 / 3.20 ( 2628) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 528 time to evaluate : 0.702 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8632 (m-30) cc_final: 0.8203 (m-30) REVERT: A 10 LYS cc_start: 0.9007 (mttt) cc_final: 0.8517 (mtmm) REVERT: A 22 ASN cc_start: 0.8563 (m-40) cc_final: 0.8034 (m-40) REVERT: A 29 LYS cc_start: 0.8435 (tmtt) cc_final: 0.8164 (tptp) REVERT: A 32 ARG cc_start: 0.7436 (mpt-90) cc_final: 0.7055 (mpt-90) REVERT: A 213 HIS cc_start: 0.7570 (p-80) cc_final: 0.7257 (p-80) REVERT: A 236 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: A 237 ASP cc_start: 0.8338 (m-30) cc_final: 0.7304 (p0) REVERT: A 240 MET cc_start: 0.7601 (ttt) cc_final: 0.6939 (ttt) REVERT: A 246 SER cc_start: 0.9162 (m) cc_final: 0.8713 (p) REVERT: A 249 LEU cc_start: 0.9274 (tt) cc_final: 0.9034 (pp) REVERT: A 274 PHE cc_start: 0.7777 (t80) cc_final: 0.7186 (t80) REVERT: A 283 LEU cc_start: 0.9458 (mt) cc_final: 0.8878 (pp) REVERT: A 303 ILE cc_start: 0.9013 (mt) cc_final: 0.8626 (mt) REVERT: A 307 PHE cc_start: 0.8502 (m-80) cc_final: 0.8234 (m-80) REVERT: A 323 PHE cc_start: 0.7888 (m-10) cc_final: 0.7650 (m-10) REVERT: A 334 PHE cc_start: 0.8863 (t80) cc_final: 0.8557 (t80) REVERT: A 336 PHE cc_start: 0.8299 (t80) cc_final: 0.8055 (t80) REVERT: A 337 ASP cc_start: 0.8364 (m-30) cc_final: 0.7854 (p0) REVERT: A 346 ASN cc_start: 0.8122 (m-40) cc_final: 0.7881 (m-40) REVERT: B 15 LYS cc_start: 0.8975 (mttt) cc_final: 0.8557 (mttt) REVERT: B 19 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.8259 (mtm-85) REVERT: B 23 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8782 (mttt) REVERT: B 42 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7517 (ttp80) REVERT: B 52 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7687 (ptp90) REVERT: B 61 MET cc_start: 0.8078 (tmm) cc_final: 0.7575 (ppp) REVERT: B 81 ILE cc_start: 0.8967 (mt) cc_final: 0.8725 (tp) REVERT: B 122 SER cc_start: 0.8783 (m) cc_final: 0.8409 (p) REVERT: B 172 GLU cc_start: 0.8145 (tp30) cc_final: 0.7870 (tp30) REVERT: B 289 TYR cc_start: 0.6792 (m-80) cc_final: 0.6108 (m-80) REVERT: B 298 ASP cc_start: 0.7756 (t0) cc_final: 0.7405 (t70) REVERT: Y 14 LYS cc_start: 0.8762 (mppt) cc_final: 0.8549 (mppt) REVERT: Y 32 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7918 (mmtt) REVERT: N 38 ARG cc_start: 0.7902 (ptt180) cc_final: 0.7619 (ptm-80) REVERT: N 96 CYS cc_start: 0.7464 (p) cc_final: 0.6895 (p) REVERT: N 110 PHE cc_start: 0.8717 (t80) cc_final: 0.8473 (t80) REVERT: N 244 LYS cc_start: 0.8691 (tttt) cc_final: 0.8477 (tttt) REVERT: C 279 ARG cc_start: 0.8042 (ttt180) cc_final: 0.7723 (mmm-85) REVERT: C 321 SER cc_start: 0.7288 (m) cc_final: 0.6859 (p) REVERT: C 327 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7543 (tm-30) REVERT: C 379 TYR cc_start: 0.8021 (t80) cc_final: 0.7515 (t80) REVERT: C 380 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7905 (mmtp) REVERT: C 384 PHE cc_start: 0.8743 (p90) cc_final: 0.8470 (p90) REVERT: C 415 MET cc_start: 0.7402 (ttm) cc_final: 0.7085 (ttm) REVERT: C 448 GLU cc_start: 0.8528 (pt0) cc_final: 0.8277 (pt0) REVERT: C 452 LYS cc_start: 0.9159 (mtpp) cc_final: 0.8728 (mtmm) REVERT: C 454 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8611 (mm) REVERT: C 456 ARG cc_start: 0.7725 (mtm180) cc_final: 0.7344 (mtm110) REVERT: C 459 GLU cc_start: 0.8500 (pm20) cc_final: 0.7888 (mp0) REVERT: C 548 LYS cc_start: 0.8368 (mmmt) cc_final: 0.8083 (mmmt) REVERT: C 557 LYS cc_start: 0.8235 (mtpt) cc_final: 0.8020 (mtmm) REVERT: C 567 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7807 (ttpp) REVERT: C 592 PHE cc_start: 0.7498 (t80) cc_final: 0.7260 (t80) REVERT: C 708 TRP cc_start: 0.6797 (p-90) cc_final: 0.6315 (m100) REVERT: C 795 SER cc_start: 0.8706 (m) cc_final: 0.8329 (p) REVERT: C 807 MET cc_start: 0.7580 (mtm) cc_final: 0.7031 (mtm) REVERT: C 812 VAL cc_start: 0.8447 (t) cc_final: 0.8216 (p) REVERT: C 843 PHE cc_start: 0.7956 (m-10) cc_final: 0.7738 (m-10) REVERT: C 847 ILE cc_start: 0.8608 (mm) cc_final: 0.8393 (mt) REVERT: C 853 PHE cc_start: 0.7594 (m-80) cc_final: 0.7393 (m-10) REVERT: D 62 MET cc_start: 0.8195 (ptp) cc_final: 0.7862 (tmm) REVERT: D 95 ARG cc_start: 0.7649 (tpp80) cc_final: 0.7389 (mmm160) REVERT: D 107 GLU cc_start: 0.7192 (mp0) cc_final: 0.6832 (mp0) REVERT: D 112 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7964 (mtpt) REVERT: D 126 ASN cc_start: 0.7237 (p0) cc_final: 0.6445 (p0) REVERT: D 144 GLU cc_start: 0.7289 (pt0) cc_final: 0.6952 (tm-30) REVERT: D 214 ASP cc_start: 0.7677 (t0) cc_final: 0.6980 (t0) REVERT: D 222 GLU cc_start: 0.7921 (mp0) cc_final: 0.7643 (mp0) REVERT: D 223 ASP cc_start: 0.7825 (p0) cc_final: 0.7467 (p0) REVERT: D 226 ILE cc_start: 0.8557 (mt) cc_final: 0.8216 (mm) REVERT: D 241 LYS cc_start: 0.7798 (mttt) cc_final: 0.7564 (mmtm) REVERT: D 268 TYR cc_start: 0.8084 (t80) cc_final: 0.7648 (t80) REVERT: D 272 MET cc_start: 0.7852 (ttt) cc_final: 0.7649 (ttt) REVERT: D 276 LYS cc_start: 0.8603 (ptmm) cc_final: 0.8295 (ptmm) REVERT: D 290 TRP cc_start: 0.8420 (p90) cc_final: 0.8027 (p90) REVERT: D 311 MET cc_start: 0.7397 (ptp) cc_final: 0.6991 (ptp) REVERT: D 353 LYS cc_start: 0.8932 (mmtm) cc_final: 0.8637 (mmmm) REVERT: D 397 ARG cc_start: 0.7975 (mmm160) cc_final: 0.7452 (mmm160) REVERT: D 421 GLU cc_start: 0.7206 (tp30) cc_final: 0.6928 (tp30) REVERT: D 427 LYS cc_start: 0.7996 (pttt) cc_final: 0.7727 (ptmm) REVERT: D 678 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7747 (t) REVERT: D 715 ASP cc_start: 0.8165 (p0) cc_final: 0.7900 (p0) outliers start: 48 outliers final: 21 residues processed: 553 average time/residue: 0.1611 time to fit residues: 128.5214 Evaluate side-chains 518 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 494 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 703 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN B 156 GLN B 176 GLN B 220 GLN B 268 ASN B 340 ASN Y 11 GLN D 344 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.120417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.101359 restraints weight = 43339.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.105156 restraints weight = 20789.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.107625 restraints weight = 11837.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.109296 restraints weight = 7557.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.110446 restraints weight = 5199.580| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18900 Z= 0.167 Angle : 0.684 9.962 25608 Z= 0.348 Chirality : 0.045 0.178 2874 Planarity : 0.004 0.046 3237 Dihedral : 4.772 40.663 2571 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.63 % Rotamer: Outliers : 3.38 % Allowed : 16.84 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2315 helix: 0.98 (0.16), residues: 970 sheet: 0.33 (0.25), residues: 457 loop : -1.07 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 21 TYR 0.020 0.001 TYR D 342 PHE 0.036 0.001 PHE D 499 TRP 0.044 0.002 TRP C 562 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (18896) covalent geometry : angle 0.68337 / 0.35 (25600) SS BOND : bond 0.00522 / 0.26 ( 4) SS BOND : angle 1.33169 / 0.61 ( 8) hydrogen bonds : bond 0.04419 / 2.95 ( 924) hydrogen bonds : angle 4.36925 / 3.15 ( 2628) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 514 time to evaluate : 0.732 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: 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: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8623 (m-30) cc_final: 0.8188 (m-30) REVERT: A 10 LYS cc_start: 0.8961 (mttt) cc_final: 0.8463 (mtmm) REVERT: A 18 MET cc_start: 0.7898 (mmp) cc_final: 0.7689 (mmp) REVERT: A 21 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7662 (ttp80) REVERT: A 29 LYS cc_start: 0.8500 (tmtt) cc_final: 0.7968 (tmtt) REVERT: A 32 ARG cc_start: 0.7450 (mpt-90) cc_final: 0.6979 (mpt-90) REVERT: A 158 ASP cc_start: 0.7079 (t0) cc_final: 0.6853 (t0) REVERT: A 213 HIS cc_start: 0.7642 (p-80) cc_final: 0.7362 (p-80) REVERT: A 236 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8318 (pm20) REVERT: A 237 ASP cc_start: 0.8274 (m-30) cc_final: 0.7242 (p0) REVERT: A 240 MET cc_start: 0.7782 (ttt) cc_final: 0.7129 (ttt) REVERT: A 246 SER cc_start: 0.9161 (m) cc_final: 0.8710 (p) REVERT: A 249 LEU cc_start: 0.9275 (tt) cc_final: 0.8975 (pp) REVERT: A 274 PHE cc_start: 0.7745 (t80) cc_final: 0.7172 (t80) REVERT: A 283 LEU cc_start: 0.9475 (mt) cc_final: 0.8944 (pp) REVERT: A 303 ILE cc_start: 0.8823 (mt) cc_final: 0.8443 (pt) REVERT: A 313 ARG cc_start: 0.8527 (ttp-170) cc_final: 0.8280 (ttp-170) REVERT: A 323 PHE cc_start: 0.7724 (m-10) cc_final: 0.7193 (m-10) REVERT: A 328 ASP cc_start: 0.6325 (t0) cc_final: 0.4823 (m-30) REVERT: A 334 PHE cc_start: 0.8797 (t80) cc_final: 0.8373 (t80) REVERT: A 337 ASP cc_start: 0.8214 (m-30) cc_final: 0.7988 (p0) REVERT: A 345 LYS cc_start: 0.8963 (ptpp) cc_final: 0.8405 (pttm) REVERT: A 346 ASN cc_start: 0.8124 (m-40) cc_final: 0.7819 (m-40) REVERT: B 9 GLN cc_start: 0.8775 (mt0) cc_final: 0.8408 (pt0) REVERT: B 12 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8465 (pp20) REVERT: B 15 LYS cc_start: 0.8999 (mttt) cc_final: 0.8596 (mttt) REVERT: B 42 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7490 (ttp80) REVERT: B 45 MET cc_start: 0.7687 (tpp) cc_final: 0.7443 (tpp) REVERT: B 52 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7794 (ptp90) REVERT: B 61 MET cc_start: 0.8099 (tmm) cc_final: 0.7591 (ppp) REVERT: B 81 ILE cc_start: 0.8971 (mt) cc_final: 0.8761 (tp) REVERT: B 122 SER cc_start: 0.8809 (m) cc_final: 0.8401 (p) REVERT: B 172 GLU cc_start: 0.8128 (tp30) cc_final: 0.7825 (tp30) REVERT: B 175 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8356 (tm-30) REVERT: B 289 TYR cc_start: 0.7068 (m-80) cc_final: 0.6260 (m-80) REVERT: B 298 ASP cc_start: 0.7737 (t0) cc_final: 0.7463 (t70) REVERT: Y 14 LYS cc_start: 0.8824 (mppt) cc_final: 0.8419 (mmtm) REVERT: Y 32 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8255 (mmtt) REVERT: N 38 ARG cc_start: 0.8064 (ptt180) cc_final: 0.7733 (ptm-80) REVERT: N 96 CYS cc_start: 0.7463 (p) cc_final: 0.6993 (p) REVERT: N 110 PHE cc_start: 0.8729 (t80) cc_final: 0.8428 (t80) REVERT: N 186 GLN cc_start: 0.8152 (mp10) cc_final: 0.7934 (mp10) REVERT: N 219 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8591 (tp) REVERT: N 230 MET cc_start: 0.7344 (ttp) cc_final: 0.7104 (ttp) REVERT: N 244 LYS cc_start: 0.8737 (tttt) cc_final: 0.8489 (tttt) REVERT: C 279 ARG cc_start: 0.8030 (ttt180) cc_final: 0.7781 (mmm-85) REVERT: C 321 SER cc_start: 0.7318 (m) cc_final: 0.6893 (p) REVERT: C 327 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7606 (tm-30) REVERT: C 379 TYR cc_start: 0.8016 (t80) cc_final: 0.7517 (t80) REVERT: C 380 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7874 (mmmm) REVERT: C 384 PHE cc_start: 0.8769 (p90) cc_final: 0.8444 (p90) REVERT: C 399 ASN cc_start: 0.8142 (p0) cc_final: 0.7724 (p0) REVERT: C 415 MET cc_start: 0.7306 (ttm) cc_final: 0.7063 (ttm) REVERT: C 454 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8610 (mm) REVERT: C 459 GLU cc_start: 0.8223 (pm20) cc_final: 0.6917 (mp0) REVERT: C 548 LYS cc_start: 0.8451 (mmmt) cc_final: 0.8162 (mmmt) REVERT: C 567 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7901 (ttpp) REVERT: C 592 PHE cc_start: 0.7633 (t80) cc_final: 0.7398 (t80) REVERT: C 593 ILE cc_start: 0.8088 (pt) cc_final: 0.7881 (pt) REVERT: C 708 TRP cc_start: 0.6887 (p-90) cc_final: 0.6427 (m100) REVERT: C 795 SER cc_start: 0.8637 (m) cc_final: 0.8227 (p) REVERT: C 807 MET cc_start: 0.7562 (mtm) cc_final: 0.7010 (mtm) REVERT: C 812 VAL cc_start: 0.8457 (t) cc_final: 0.8182 (p) REVERT: D 82 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7876 (pt0) REVERT: D 95 ARG cc_start: 0.7670 (tpp80) cc_final: 0.7462 (mmm160) REVERT: D 104 TYR cc_start: 0.8098 (m-80) cc_final: 0.7885 (m-80) REVERT: D 107 GLU cc_start: 0.7307 (mp0) cc_final: 0.6889 (mp0) REVERT: D 112 LYS cc_start: 0.8242 (mtpp) cc_final: 0.7988 (mtpt) REVERT: D 126 ASN cc_start: 0.7191 (p0) cc_final: 0.6444 (p0) REVERT: D 144 GLU cc_start: 0.7309 (pt0) cc_final: 0.6989 (tm-30) REVERT: D 214 ASP cc_start: 0.7660 (t0) cc_final: 0.7017 (t0) REVERT: D 222 GLU cc_start: 0.7902 (mp0) cc_final: 0.7670 (mp0) REVERT: D 223 ASP cc_start: 0.7822 (p0) cc_final: 0.7457 (p0) REVERT: D 272 MET cc_start: 0.7912 (ttt) cc_final: 0.7664 (ttt) REVERT: D 311 MET cc_start: 0.7377 (ptp) cc_final: 0.7025 (ptp) REVERT: D 337 GLN cc_start: 0.7361 (mm-40) cc_final: 0.6860 (tp40) REVERT: D 340 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7189 (ttp-110) REVERT: D 342 TYR cc_start: 0.7981 (t80) cc_final: 0.7716 (t80) REVERT: D 353 LYS cc_start: 0.8947 (mmtm) cc_final: 0.8651 (mmmm) REVERT: D 355 HIS cc_start: 0.7759 (p-80) cc_final: 0.7307 (p90) REVERT: D 397 ARG cc_start: 0.7924 (mmm160) cc_final: 0.7268 (mmm160) REVERT: D 416 VAL cc_start: 0.8515 (t) cc_final: 0.8202 (m) REVERT: D 430 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7776 (tm-30) REVERT: D 432 GLN cc_start: 0.8610 (mt0) cc_final: 0.8372 (mm-40) REVERT: D 715 ASP cc_start: 0.8122 (p0) cc_final: 0.7757 (p0) outliers start: 68 outliers final: 39 residues processed: 550 average time/residue: 0.1659 time to fit residues: 130.9817 Evaluate side-chains 527 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 485 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain Y residue 44 HIS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 553 CYS Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 728 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 156 GLN B 220 GLN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 HIS D 687 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.117480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.098219 restraints weight = 43076.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.101946 restraints weight = 20951.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.104393 restraints weight = 12120.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.106042 restraints weight = 7800.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.107200 restraints weight = 5419.100| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18900 Z= 0.186 Angle : 0.711 9.594 25608 Z= 0.364 Chirality : 0.046 0.192 2874 Planarity : 0.004 0.089 3237 Dihedral : 4.898 40.179 2571 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 3.48 % Allowed : 18.28 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2315 helix: 0.95 (0.16), residues: 971 sheet: 0.37 (0.24), residues: 460 loop : -1.08 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Y 27 TYR 0.028 0.002 TYR D 338 PHE 0.062 0.002 PHE D 499 TRP 0.035 0.002 TRP A 258 HIS 0.006 0.001 HIS C 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (18896) covalent geometry : angle 0.71051 / 0.36 (25600) SS BOND : bond 0.00495 / 0.26 ( 4) SS BOND : angle 1.29356 / 0.60 ( 8) hydrogen bonds : bond 0.04491 / 3.01 ( 924) hydrogen bonds : angle 4.40270 / 3.15 ( 2628) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 518 time to evaluate : 0.725 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: 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: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8616 (m-30) cc_final: 0.8152 (m-30) REVERT: A 10 LYS cc_start: 0.8926 (mttt) cc_final: 0.8426 (mtmm) REVERT: A 29 LYS cc_start: 0.8546 (tmtt) cc_final: 0.7913 (tmtt) REVERT: A 32 ARG cc_start: 0.7461 (mpt-90) cc_final: 0.6989 (mpt-90) REVERT: A 88 MET cc_start: 0.1487 (OUTLIER) cc_final: 0.1143 (ttt) REVERT: A 142 ARG cc_start: 0.6291 (mtm180) cc_final: 0.6072 (mtt180) REVERT: A 158 ASP cc_start: 0.7140 (t0) cc_final: 0.6883 (t0) REVERT: A 193 ASP cc_start: 0.7785 (p0) cc_final: 0.7584 (p0) REVERT: A 213 HIS cc_start: 0.7713 (p-80) cc_final: 0.7411 (p-80) REVERT: A 236 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8570 (pm20) REVERT: A 237 ASP cc_start: 0.8309 (m-30) cc_final: 0.7229 (p0) REVERT: A 240 MET cc_start: 0.7888 (ttt) cc_final: 0.7236 (ttt) REVERT: A 243 MET cc_start: 0.8450 (ppp) cc_final: 0.7558 (ppp) REVERT: A 246 SER cc_start: 0.9153 (m) cc_final: 0.8631 (p) REVERT: A 247 MET cc_start: 0.8549 (mtp) cc_final: 0.7786 (mpp) REVERT: A 249 LEU cc_start: 0.9293 (tt) cc_final: 0.9010 (pp) REVERT: A 274 PHE cc_start: 0.7846 (t80) cc_final: 0.7306 (t80) REVERT: A 283 LEU cc_start: 0.9480 (mt) cc_final: 0.9017 (pp) REVERT: A 307 PHE cc_start: 0.8377 (m-80) cc_final: 0.8041 (m-80) REVERT: A 313 ARG cc_start: 0.8540 (ttp-170) cc_final: 0.8191 (tmm-80) REVERT: A 328 ASP cc_start: 0.6634 (t0) cc_final: 0.4432 (m-30) REVERT: A 334 PHE cc_start: 0.8790 (t80) cc_final: 0.8541 (t80) REVERT: A 337 ASP cc_start: 0.8209 (m-30) cc_final: 0.7865 (m-30) REVERT: A 345 LYS cc_start: 0.8959 (ptpp) cc_final: 0.8495 (pttm) REVERT: A 346 ASN cc_start: 0.8109 (m-40) cc_final: 0.7799 (m-40) REVERT: B 15 LYS cc_start: 0.9005 (mttt) cc_final: 0.8598 (mttt) REVERT: B 19 ARG cc_start: 0.8418 (mtm-85) cc_final: 0.8167 (mtm-85) REVERT: B 45 MET cc_start: 0.7868 (tpp) cc_final: 0.7431 (mmm) REVERT: B 52 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7945 (ptp90) REVERT: B 61 MET cc_start: 0.8155 (tmm) cc_final: 0.7651 (ppp) REVERT: B 81 ILE cc_start: 0.8985 (mt) cc_final: 0.8773 (tp) REVERT: B 122 SER cc_start: 0.8727 (m) cc_final: 0.8425 (p) REVERT: B 129 ARG cc_start: 0.8028 (ptm160) cc_final: 0.7818 (ptm-80) REVERT: B 135 VAL cc_start: 0.8835 (t) cc_final: 0.8633 (p) REVERT: B 156 GLN cc_start: 0.6931 (mm110) cc_final: 0.6588 (mp10) REVERT: B 172 GLU cc_start: 0.8192 (tp30) cc_final: 0.7874 (tp30) REVERT: B 289 TYR cc_start: 0.7105 (m-80) cc_final: 0.6355 (m-80) REVERT: B 298 ASP cc_start: 0.7728 (t0) cc_final: 0.7438 (t70) REVERT: Y 32 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8323 (mmtt) REVERT: N 6 GLU cc_start: 0.7008 (pt0) cc_final: 0.6149 (mt-10) REVERT: N 38 ARG cc_start: 0.8067 (ptt180) cc_final: 0.7774 (ptm-80) REVERT: N 110 PHE cc_start: 0.8802 (t80) cc_final: 0.8504 (t80) REVERT: N 219 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8574 (tp) REVERT: N 220 GLU cc_start: 0.7863 (mp0) cc_final: 0.7575 (mp0) REVERT: N 230 MET cc_start: 0.7593 (ttp) cc_final: 0.7293 (tmm) REVERT: N 244 LYS cc_start: 0.8777 (tttt) cc_final: 0.8492 (tttt) REVERT: C 193 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8222 (mm-30) REVERT: C 279 ARG cc_start: 0.8014 (ttt180) cc_final: 0.7810 (mmm-85) REVERT: C 321 SER cc_start: 0.7335 (m) cc_final: 0.6880 (p) REVERT: C 327 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 379 TYR cc_start: 0.8090 (t80) cc_final: 0.7616 (t80) REVERT: C 384 PHE cc_start: 0.8805 (p90) cc_final: 0.8474 (p90) REVERT: C 399 ASN cc_start: 0.8226 (p0) cc_final: 0.7835 (p0) REVERT: C 415 MET cc_start: 0.7448 (ttm) cc_final: 0.7199 (ttm) REVERT: C 449 LYS cc_start: 0.8978 (mtmt) cc_final: 0.8646 (ttmm) REVERT: C 454 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8585 (mm) REVERT: C 457 HIS cc_start: 0.7374 (t-90) cc_final: 0.6939 (t70) REVERT: C 459 GLU cc_start: 0.7889 (pm20) cc_final: 0.6413 (pm20) REVERT: C 548 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8215 (mmmt) REVERT: C 592 PHE cc_start: 0.7797 (t80) cc_final: 0.7551 (t80) REVERT: C 593 ILE cc_start: 0.8110 (pt) cc_final: 0.7905 (pt) REVERT: C 708 TRP cc_start: 0.6894 (p-90) cc_final: 0.6395 (m100) REVERT: C 743 LYS cc_start: 0.8360 (tmtt) cc_final: 0.8118 (tmtt) REVERT: C 795 SER cc_start: 0.8674 (m) cc_final: 0.8349 (p) REVERT: C 807 MET cc_start: 0.7593 (mtm) cc_final: 0.7031 (mtm) REVERT: C 812 VAL cc_start: 0.8468 (t) cc_final: 0.8200 (p) REVERT: D 62 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7672 (tmm) REVERT: D 95 ARG cc_start: 0.7743 (tpp80) cc_final: 0.7392 (mmm-85) REVERT: D 104 TYR cc_start: 0.8244 (m-80) cc_final: 0.7983 (m-80) REVERT: D 107 GLU cc_start: 0.7245 (mp0) cc_final: 0.6743 (mp0) REVERT: D 112 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7931 (mtpt) REVERT: D 126 ASN cc_start: 0.7187 (p0) cc_final: 0.6518 (p0) REVERT: D 144 GLU cc_start: 0.7337 (pt0) cc_final: 0.7028 (tm-30) REVERT: D 214 ASP cc_start: 0.7665 (t0) cc_final: 0.6993 (t0) REVERT: D 222 GLU cc_start: 0.7932 (mp0) cc_final: 0.7689 (mp0) REVERT: D 223 ASP cc_start: 0.7872 (p0) cc_final: 0.7499 (p0) REVERT: D 269 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7713 (pp20) REVERT: D 272 MET cc_start: 0.8065 (ttt) cc_final: 0.7841 (ttt) REVERT: D 276 LYS cc_start: 0.8553 (ptmm) cc_final: 0.8344 (ptmm) REVERT: D 311 MET cc_start: 0.7470 (ptp) cc_final: 0.7091 (ptp) REVERT: D 342 TYR cc_start: 0.7988 (t80) cc_final: 0.7727 (t80) REVERT: D 353 LYS cc_start: 0.8987 (mmtm) cc_final: 0.8715 (mmmm) REVERT: D 355 HIS cc_start: 0.7734 (p-80) cc_final: 0.7288 (p90) REVERT: D 397 ARG cc_start: 0.8017 (mmm160) cc_final: 0.7236 (mmm160) REVERT: D 416 VAL cc_start: 0.8569 (t) cc_final: 0.8266 (m) REVERT: D 427 LYS cc_start: 0.8108 (pttt) cc_final: 0.7766 (ptmm) REVERT: D 467 LYS cc_start: 0.8395 (tppt) cc_final: 0.8157 (tppt) REVERT: D 556 ARG cc_start: 0.6971 (ttp80) cc_final: 0.6569 (tmm-80) REVERT: D 626 GLU cc_start: 0.7441 (pt0) cc_final: 0.7194 (pp20) REVERT: D 715 ASP cc_start: 0.8127 (p0) cc_final: 0.7767 (p0) outliers start: 70 outliers final: 44 residues processed: 553 average time/residue: 0.1539 time to fit residues: 122.8614 Evaluate side-chains 550 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 501 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain Y residue 9 ILE Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 44 HIS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 553 CYS Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 728 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 145 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 304 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 687 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.117063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.098276 restraints weight = 43257.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.101931 restraints weight = 20921.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104271 restraints weight = 11952.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105849 restraints weight = 7658.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.106994 restraints weight = 5341.886| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 18900 Z= 0.192 Angle : 0.742 10.333 25608 Z= 0.377 Chirality : 0.046 0.336 2874 Planarity : 0.005 0.096 3237 Dihedral : 4.787 39.763 2571 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 3.58 % Allowed : 19.47 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2315 helix: 0.94 (0.16), residues: 967 sheet: 0.39 (0.25), residues: 461 loop : -1.10 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Y 27 TYR 0.029 0.002 TYR A 302 PHE 0.048 0.002 PHE A 307 TRP 0.048 0.002 TRP A 258 HIS 0.006 0.001 HIS C 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (18896) covalent geometry : angle 0.74148 / 0.38 (25600) SS BOND : bond 0.00608 / 0.31 ( 4) SS BOND : angle 1.40047 / 0.65 ( 8) hydrogen bonds : bond 0.04545 / 3.03 ( 924) hydrogen bonds : angle 4.37029 / 3.13 ( 2628) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 518 time to evaluate : 0.574 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: 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 9 ASP cc_start: 0.8629 (m-30) cc_final: 0.8160 (m-30) REVERT: A 10 LYS cc_start: 0.8961 (mttt) cc_final: 0.8429 (mtmm) REVERT: A 21 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7642 (ttp80) REVERT: A 29 LYS cc_start: 0.8553 (tmtt) cc_final: 0.7933 (tmtt) REVERT: A 32 ARG cc_start: 0.7421 (mpt-90) cc_final: 0.7020 (mpt-90) REVERT: A 88 MET cc_start: 0.1355 (OUTLIER) cc_final: 0.1048 (ttt) REVERT: A 142 ARG cc_start: 0.6403 (mtm180) cc_final: 0.6194 (mtt180) REVERT: A 158 ASP cc_start: 0.7310 (t0) cc_final: 0.7038 (t0) REVERT: A 189 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.5694 (t80) REVERT: A 197 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7562 (mmtt) REVERT: A 236 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8567 (pm20) REVERT: A 237 ASP cc_start: 0.8343 (m-30) cc_final: 0.7279 (p0) REVERT: A 240 MET cc_start: 0.7888 (ttt) cc_final: 0.7226 (ttt) REVERT: A 243 MET cc_start: 0.8443 (ppp) cc_final: 0.7480 (ppp) REVERT: A 246 SER cc_start: 0.9163 (m) cc_final: 0.8627 (p) REVERT: A 247 MET cc_start: 0.8545 (mtp) cc_final: 0.7799 (mpp) REVERT: A 249 LEU cc_start: 0.9277 (tt) cc_final: 0.8997 (pp) REVERT: A 274 PHE cc_start: 0.7837 (t80) cc_final: 0.7342 (t80) REVERT: A 283 LEU cc_start: 0.9437 (mt) cc_final: 0.9049 (pp) REVERT: A 307 PHE cc_start: 0.8472 (m-80) cc_final: 0.8065 (m-80) REVERT: A 313 ARG cc_start: 0.8598 (ttp-170) cc_final: 0.8127 (ttp-170) REVERT: A 328 ASP cc_start: 0.6224 (t0) cc_final: 0.4675 (m-30) REVERT: A 334 PHE cc_start: 0.8757 (t80) cc_final: 0.8352 (t80) REVERT: A 337 ASP cc_start: 0.8208 (m-30) cc_final: 0.7768 (m-30) REVERT: A 345 LYS cc_start: 0.8963 (ptpp) cc_final: 0.8520 (pttm) REVERT: A 346 ASN cc_start: 0.8084 (m-40) cc_final: 0.7784 (m-40) REVERT: B 12 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8445 (pp20) REVERT: B 15 LYS cc_start: 0.9016 (mttt) cc_final: 0.8606 (mttt) REVERT: B 19 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8151 (mtm-85) REVERT: B 45 MET cc_start: 0.7905 (tpp) cc_final: 0.7626 (mmm) REVERT: B 52 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7733 (ptp90) REVERT: B 61 MET cc_start: 0.8161 (tmm) cc_final: 0.7663 (ppp) REVERT: B 122 SER cc_start: 0.8649 (m) cc_final: 0.8369 (p) REVERT: B 135 VAL cc_start: 0.8922 (t) cc_final: 0.8649 (p) REVERT: B 156 GLN cc_start: 0.7089 (mm110) cc_final: 0.6805 (mp10) REVERT: B 172 GLU cc_start: 0.8209 (tp30) cc_final: 0.7924 (tp30) REVERT: B 220 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7302 (mm-40) REVERT: B 226 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7632 (mp0) REVERT: B 251 ARG cc_start: 0.7542 (mtt-85) cc_final: 0.6877 (mtt90) REVERT: B 260 GLU cc_start: 0.7482 (tp30) cc_final: 0.7125 (tp30) REVERT: B 289 TYR cc_start: 0.7056 (m-80) cc_final: 0.6258 (m-80) REVERT: B 298 ASP cc_start: 0.7746 (t0) cc_final: 0.7457 (t70) REVERT: Y 14 LYS cc_start: 0.8586 (mppt) cc_final: 0.8326 (mmtm) REVERT: Y 18 GLN cc_start: 0.8742 (tp40) cc_final: 0.7675 (pp30) REVERT: Y 22 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7816 (mm-30) REVERT: Y 32 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8343 (mmtt) REVERT: N 6 GLU cc_start: 0.6972 (pt0) cc_final: 0.6070 (mt-10) REVERT: N 38 ARG cc_start: 0.8087 (ptt180) cc_final: 0.7817 (ptm-80) REVERT: N 110 PHE cc_start: 0.8813 (t80) cc_final: 0.8432 (t80) REVERT: N 140 MET cc_start: 0.7225 (mmm) cc_final: 0.7006 (mmm) REVERT: N 220 GLU cc_start: 0.7935 (mp0) cc_final: 0.7659 (mp0) REVERT: N 230 MET cc_start: 0.7627 (ttp) cc_final: 0.7377 (tmm) REVERT: N 244 LYS cc_start: 0.8792 (tttt) cc_final: 0.8471 (tttt) REVERT: C 178 MET cc_start: 0.8482 (mmm) cc_final: 0.8230 (mmm) REVERT: C 193 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8159 (mm-30) REVERT: C 321 SER cc_start: 0.7336 (m) cc_final: 0.6882 (p) REVERT: C 327 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 384 PHE cc_start: 0.8824 (p90) cc_final: 0.8480 (p90) REVERT: C 399 ASN cc_start: 0.8315 (p0) cc_final: 0.7953 (p0) REVERT: C 449 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8665 (ttmm) REVERT: C 454 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8507 (mm) REVERT: C 497 ASP cc_start: 0.7409 (p0) cc_final: 0.6864 (t0) REVERT: C 548 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8278 (mmmt) REVERT: C 592 PHE cc_start: 0.7774 (t80) cc_final: 0.7548 (t80) REVERT: C 598 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8712 (tp) REVERT: C 708 TRP cc_start: 0.6868 (p-90) cc_final: 0.6443 (m100) REVERT: C 743 LYS cc_start: 0.8357 (tmtt) cc_final: 0.8122 (tmtt) REVERT: C 795 SER cc_start: 0.8678 (m) cc_final: 0.8313 (p) REVERT: C 807 MET cc_start: 0.7561 (mtm) cc_final: 0.7017 (mtm) REVERT: C 812 VAL cc_start: 0.8476 (t) cc_final: 0.8219 (p) REVERT: D 62 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7598 (tmm) REVERT: D 92 SER cc_start: 0.8817 (t) cc_final: 0.8446 (p) REVERT: D 95 ARG cc_start: 0.7727 (tpp80) cc_final: 0.7373 (mmm-85) REVERT: D 104 TYR cc_start: 0.8275 (m-80) cc_final: 0.7973 (m-80) REVERT: D 107 GLU cc_start: 0.7234 (mp0) cc_final: 0.6028 (mp0) REVERT: D 112 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7860 (ttpt) REVERT: D 126 ASN cc_start: 0.7167 (p0) cc_final: 0.6520 (p0) REVERT: D 144 GLU cc_start: 0.7245 (pt0) cc_final: 0.6960 (tm-30) REVERT: D 214 ASP cc_start: 0.7647 (t0) cc_final: 0.6977 (t0) REVERT: D 222 GLU cc_start: 0.7935 (mp0) cc_final: 0.7705 (mp0) REVERT: D 223 ASP cc_start: 0.7913 (p0) cc_final: 0.7583 (p0) REVERT: D 269 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7833 (pp20) REVERT: D 272 MET cc_start: 0.8043 (ttt) cc_final: 0.7812 (ttt) REVERT: D 276 LYS cc_start: 0.8506 (ptmm) cc_final: 0.8064 (ptmm) REVERT: D 311 MET cc_start: 0.7529 (ptp) cc_final: 0.7213 (ptp) REVERT: D 342 TYR cc_start: 0.7936 (t80) cc_final: 0.7652 (t80) REVERT: D 353 LYS cc_start: 0.8994 (mmtm) cc_final: 0.8735 (mmmm) REVERT: D 355 HIS cc_start: 0.7635 (p-80) cc_final: 0.7406 (p-80) REVERT: D 397 ARG cc_start: 0.7998 (mmm160) cc_final: 0.7189 (mmm160) REVERT: D 416 VAL cc_start: 0.8623 (t) cc_final: 0.8327 (m) REVERT: D 427 LYS cc_start: 0.8142 (pttt) cc_final: 0.7842 (ptmm) REVERT: D 450 GLU cc_start: 0.8004 (mp0) cc_final: 0.7761 (mp0) REVERT: D 626 GLU cc_start: 0.7441 (pt0) cc_final: 0.7156 (pp20) REVERT: D 649 GLU cc_start: 0.6966 (mp0) cc_final: 0.6747 (mp0) REVERT: D 715 ASP cc_start: 0.8116 (p0) cc_final: 0.7875 (p0) outliers start: 72 outliers final: 48 residues processed: 553 average time/residue: 0.1515 time to fit residues: 120.7553 Evaluate side-chains 549 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 494 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain Y residue 9 ILE Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 625 SER Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 553 CYS Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 216 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 120 optimal weight: 0.0370 chunk 204 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 304 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.118075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.098880 restraints weight = 43641.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.102695 restraints weight = 20983.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.105153 restraints weight = 11992.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.106790 restraints weight = 7658.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.107941 restraints weight = 5299.521| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18900 Z= 0.144 Angle : 0.741 12.311 25608 Z= 0.374 Chirality : 0.045 0.311 2874 Planarity : 0.004 0.099 3237 Dihedral : 4.731 40.494 2571 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 3.53 % Allowed : 20.72 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2315 helix: 0.98 (0.16), residues: 977 sheet: 0.40 (0.24), residues: 462 loop : -1.06 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 356 TYR 0.026 0.001 TYR D 338 PHE 0.053 0.002 PHE A 307 TRP 0.015 0.001 TRP C 562 HIS 0.004 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (18896) covalent geometry : angle 0.74095 / 0.37 (25600) SS BOND : bond 0.00503 / 0.26 ( 4) SS BOND : angle 1.10458 / 0.52 ( 8) hydrogen bonds : bond 0.04282 / 2.87 ( 924) hydrogen bonds : angle 4.28387 / 3.06 ( 2628) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 513 time to evaluate : 0.658 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: 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 9 ASP cc_start: 0.8629 (m-30) cc_final: 0.8150 (m-30) REVERT: A 10 LYS cc_start: 0.8930 (mttt) cc_final: 0.8395 (mtmm) REVERT: A 29 LYS cc_start: 0.8568 (tmtt) cc_final: 0.7976 (tmtt) REVERT: A 32 ARG cc_start: 0.7394 (mpt-90) cc_final: 0.6988 (mpt-90) REVERT: A 88 MET cc_start: 0.1302 (OUTLIER) cc_final: 0.1011 (ttt) REVERT: A 158 ASP cc_start: 0.7262 (t0) cc_final: 0.7005 (t0) REVERT: A 189 PHE cc_start: 0.6348 (OUTLIER) cc_final: 0.5728 (t80) REVERT: A 190 THR cc_start: 0.8182 (p) cc_final: 0.7947 (t) REVERT: A 197 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7500 (mmtt) REVERT: A 213 HIS cc_start: 0.8189 (p-80) cc_final: 0.7883 (p-80) REVERT: A 236 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8657 (pm20) REVERT: A 237 ASP cc_start: 0.8368 (m-30) cc_final: 0.7271 (p0) REVERT: A 240 MET cc_start: 0.7903 (ttt) cc_final: 0.7240 (ttt) REVERT: A 246 SER cc_start: 0.9142 (m) cc_final: 0.8825 (p) REVERT: A 274 PHE cc_start: 0.7810 (t80) cc_final: 0.7331 (t80) REVERT: A 283 LEU cc_start: 0.9432 (mt) cc_final: 0.9075 (pp) REVERT: A 307 PHE cc_start: 0.8368 (m-80) cc_final: 0.8002 (m-80) REVERT: A 313 ARG cc_start: 0.8564 (ttp-170) cc_final: 0.8205 (ttp-170) REVERT: A 328 ASP cc_start: 0.6445 (t0) cc_final: 0.4851 (m-30) REVERT: A 337 ASP cc_start: 0.8230 (m-30) cc_final: 0.7847 (m-30) REVERT: A 341 ASP cc_start: 0.8263 (m-30) cc_final: 0.7925 (p0) REVERT: A 345 LYS cc_start: 0.8963 (ptpp) cc_final: 0.8486 (pttm) REVERT: A 346 ASN cc_start: 0.8094 (m-40) cc_final: 0.7782 (m-40) REVERT: B 12 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8504 (pp20) REVERT: B 15 LYS cc_start: 0.9020 (mttt) cc_final: 0.8603 (mttt) REVERT: B 19 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.8122 (mtm-85) REVERT: B 42 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7928 (ttp80) REVERT: B 45 MET cc_start: 0.7846 (tpp) cc_final: 0.7552 (mmm) REVERT: B 52 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7712 (ptp90) REVERT: B 96 ARG cc_start: 0.6359 (mmp80) cc_final: 0.5998 (mmp80) REVERT: B 122 SER cc_start: 0.8647 (m) cc_final: 0.8394 (p) REVERT: B 135 VAL cc_start: 0.8912 (t) cc_final: 0.8636 (p) REVERT: B 156 GLN cc_start: 0.7154 (mm110) cc_final: 0.6902 (mp10) REVERT: B 170 ASP cc_start: 0.8192 (t0) cc_final: 0.7631 (p0) REVERT: B 172 GLU cc_start: 0.8168 (tp30) cc_final: 0.7621 (tp30) REVERT: B 220 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7364 (mm110) REVERT: B 226 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7596 (mp0) REVERT: B 251 ARG cc_start: 0.7467 (mtt-85) cc_final: 0.6854 (mtt90) REVERT: B 254 ASP cc_start: 0.7202 (t70) cc_final: 0.6934 (t0) REVERT: B 260 GLU cc_start: 0.7378 (tp30) cc_final: 0.7107 (tp30) REVERT: B 289 TYR cc_start: 0.6987 (m-80) cc_final: 0.6198 (m-80) REVERT: B 298 ASP cc_start: 0.7738 (t0) cc_final: 0.7534 (t0) REVERT: Y 32 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8439 (mmtt) REVERT: N 6 GLU cc_start: 0.6916 (pt0) cc_final: 0.6122 (mt-10) REVERT: N 38 ARG cc_start: 0.8057 (ptt180) cc_final: 0.7845 (ptm-80) REVERT: N 100 ILE cc_start: 0.9047 (tp) cc_final: 0.8782 (tt) REVERT: N 110 PHE cc_start: 0.8767 (t80) cc_final: 0.8406 (t80) REVERT: N 220 GLU cc_start: 0.7909 (mp0) cc_final: 0.7639 (mp0) REVERT: N 230 MET cc_start: 0.7601 (ttp) cc_final: 0.7348 (tmm) REVERT: N 244 LYS cc_start: 0.8798 (tttt) cc_final: 0.8485 (tttt) REVERT: C 178 MET cc_start: 0.8487 (mmm) cc_final: 0.8146 (mmm) REVERT: C 193 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8196 (mm-30) REVERT: C 279 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7760 (ttm-80) REVERT: C 321 SER cc_start: 0.7286 (m) cc_final: 0.6841 (p) REVERT: C 327 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7562 (tm-30) REVERT: C 356 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7512 (ttp80) REVERT: C 384 PHE cc_start: 0.8788 (p90) cc_final: 0.8426 (p90) REVERT: C 399 ASN cc_start: 0.8304 (p0) cc_final: 0.7714 (p0) REVERT: C 415 MET cc_start: 0.7502 (ttm) cc_final: 0.7259 (tpt) REVERT: C 449 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8674 (ttmm) REVERT: C 454 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8485 (mm) REVERT: C 457 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.7053 (t70) REVERT: C 497 ASP cc_start: 0.7394 (p0) cc_final: 0.6827 (t0) REVERT: C 549 LYS cc_start: 0.8803 (mttp) cc_final: 0.8483 (mtmt) REVERT: C 593 ILE cc_start: 0.8147 (pt) cc_final: 0.7913 (pt) REVERT: C 598 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8717 (tp) REVERT: C 708 TRP cc_start: 0.6843 (p-90) cc_final: 0.6463 (m100) REVERT: C 743 LYS cc_start: 0.8397 (tmtt) cc_final: 0.8190 (tmtt) REVERT: C 795 SER cc_start: 0.8725 (m) cc_final: 0.8375 (p) REVERT: C 807 MET cc_start: 0.7539 (mtm) cc_final: 0.7035 (mtm) REVERT: C 812 VAL cc_start: 0.8417 (t) cc_final: 0.8158 (p) REVERT: D 62 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7534 (tmm) REVERT: D 92 SER cc_start: 0.8794 (t) cc_final: 0.8419 (p) REVERT: D 95 ARG cc_start: 0.7739 (tpp80) cc_final: 0.7416 (mmm-85) REVERT: D 104 TYR cc_start: 0.8261 (m-80) cc_final: 0.7880 (m-80) REVERT: D 107 GLU cc_start: 0.7222 (mp0) cc_final: 0.6746 (mp0) REVERT: D 144 GLU cc_start: 0.7222 (pt0) cc_final: 0.6825 (tm-30) REVERT: D 214 ASP cc_start: 0.7622 (t0) cc_final: 0.6860 (t0) REVERT: D 222 GLU cc_start: 0.7930 (mp0) cc_final: 0.7699 (mp0) REVERT: D 223 ASP cc_start: 0.7908 (p0) cc_final: 0.7566 (p0) REVERT: D 230 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6627 (mm-30) REVERT: D 269 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7722 (pp20) REVERT: D 272 MET cc_start: 0.8011 (ttt) cc_final: 0.7755 (ttt) REVERT: D 311 MET cc_start: 0.7571 (ptp) cc_final: 0.7234 (ptp) REVERT: D 322 LEU cc_start: 0.8379 (mt) cc_final: 0.8165 (mp) REVERT: D 342 TYR cc_start: 0.7953 (t80) cc_final: 0.7720 (t80) REVERT: D 353 LYS cc_start: 0.9016 (mmtm) cc_final: 0.8787 (mmmt) REVERT: D 355 HIS cc_start: 0.7674 (p-80) cc_final: 0.7234 (p90) REVERT: D 397 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7074 (mmm160) REVERT: D 416 VAL cc_start: 0.8564 (t) cc_final: 0.8245 (m) REVERT: D 450 GLU cc_start: 0.7964 (mp0) cc_final: 0.7701 (mp0) REVERT: D 626 GLU cc_start: 0.7399 (pt0) cc_final: 0.7121 (pp20) REVERT: D 702 MET cc_start: 0.8556 (mmp) cc_final: 0.8243 (mmm) REVERT: D 715 ASP cc_start: 0.8114 (p0) cc_final: 0.7841 (p0) outliers start: 71 outliers final: 44 residues processed: 550 average time/residue: 0.1549 time to fit residues: 123.0647 Evaluate side-chains 552 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 500 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 625 SER Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 553 CYS Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 661 TYR Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 186 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 213 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 177 optimal weight: 0.3980 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN B 175 GLN Y 11 GLN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 687 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.118348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.099093 restraints weight = 43040.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.102890 restraints weight = 20846.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.105413 restraints weight = 11947.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.107064 restraints weight = 7632.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.108114 restraints weight = 5308.244| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18900 Z= 0.145 Angle : 0.777 13.426 25608 Z= 0.390 Chirality : 0.046 0.456 2874 Planarity : 0.004 0.051 3237 Dihedral : 4.581 40.674 2571 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 3.23 % Allowed : 21.61 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2315 helix: 0.98 (0.16), residues: 976 sheet: 0.40 (0.24), residues: 466 loop : -1.02 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG Y 13 TYR 0.026 0.001 TYR D 338 PHE 0.051 0.002 PHE A 307 TRP 0.018 0.001 TRP B 99 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (18896) covalent geometry : angle 0.77725 / 0.39 (25600) SS BOND : bond 0.00548 / 0.27 ( 4) SS BOND : angle 1.24175 / 0.57 ( 8) hydrogen bonds : bond 0.04189 / 2.83 ( 924) hydrogen bonds : angle 4.27695 / 3.07 ( 2628) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 507 time to evaluate : 0.720 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8637 (m-30) cc_final: 0.8174 (m-30) REVERT: A 10 LYS cc_start: 0.8925 (mttt) cc_final: 0.8665 (mttp) REVERT: A 29 LYS cc_start: 0.8573 (tmtt) cc_final: 0.7957 (tmtt) REVERT: A 32 ARG cc_start: 0.7413 (mpt-90) cc_final: 0.6963 (mpt-90) REVERT: A 88 MET cc_start: 0.1605 (OUTLIER) cc_final: 0.1242 (ttt) REVERT: A 189 PHE cc_start: 0.6256 (OUTLIER) cc_final: 0.5782 (t80) REVERT: A 190 THR cc_start: 0.8170 (p) cc_final: 0.7946 (t) REVERT: A 197 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7444 (mmtt) REVERT: A 213 HIS cc_start: 0.8211 (p-80) cc_final: 0.7943 (p-80) REVERT: A 236 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8788 (pm20) REVERT: A 237 ASP cc_start: 0.8325 (m-30) cc_final: 0.7152 (p0) REVERT: A 240 MET cc_start: 0.7879 (ttt) cc_final: 0.7200 (ttt) REVERT: A 246 SER cc_start: 0.9123 (m) cc_final: 0.8821 (p) REVERT: A 266 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7268 (pp) REVERT: A 274 PHE cc_start: 0.7843 (t80) cc_final: 0.7375 (t80) REVERT: A 283 LEU cc_start: 0.9433 (mt) cc_final: 0.9065 (pp) REVERT: A 307 PHE cc_start: 0.8337 (m-80) cc_final: 0.7951 (m-80) REVERT: A 334 PHE cc_start: 0.8843 (t80) cc_final: 0.8501 (t80) REVERT: A 337 ASP cc_start: 0.8239 (m-30) cc_final: 0.7850 (m-30) REVERT: A 341 ASP cc_start: 0.8319 (m-30) cc_final: 0.7984 (p0) REVERT: A 345 LYS cc_start: 0.8952 (ptpp) cc_final: 0.8454 (pttm) REVERT: A 346 ASN cc_start: 0.8103 (m-40) cc_final: 0.7799 (m-40) REVERT: B 8 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7888 (ttp80) REVERT: B 12 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8462 (pp20) REVERT: B 15 LYS cc_start: 0.9040 (mttt) cc_final: 0.8677 (mttt) REVERT: B 23 LYS cc_start: 0.9077 (mtmt) cc_final: 0.8650 (mttm) REVERT: B 42 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7611 (ttp80) REVERT: B 45 MET cc_start: 0.7816 (tpp) cc_final: 0.7521 (mmm) REVERT: B 52 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7701 (ptp90) REVERT: B 96 ARG cc_start: 0.6441 (mmp80) cc_final: 0.6053 (mmp80) REVERT: B 122 SER cc_start: 0.8640 (m) cc_final: 0.8386 (p) REVERT: B 135 VAL cc_start: 0.8919 (t) cc_final: 0.8612 (p) REVERT: B 156 GLN cc_start: 0.7203 (mm110) cc_final: 0.6963 (mp10) REVERT: B 170 ASP cc_start: 0.8140 (t0) cc_final: 0.7646 (p0) REVERT: B 172 GLU cc_start: 0.8146 (tp30) cc_final: 0.7601 (tp30) REVERT: B 226 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7753 (mp0) REVERT: B 251 ARG cc_start: 0.7541 (mtt-85) cc_final: 0.7267 (mtt90) REVERT: B 254 ASP cc_start: 0.7174 (t70) cc_final: 0.6891 (t0) REVERT: B 289 TYR cc_start: 0.6998 (m-80) cc_final: 0.6241 (m-80) REVERT: B 298 ASP cc_start: 0.7652 (t0) cc_final: 0.7444 (t0) REVERT: Y 32 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8401 (mmtt) REVERT: N 6 GLU cc_start: 0.6907 (pt0) cc_final: 0.6133 (mt-10) REVERT: N 94 TYR cc_start: 0.7972 (m-80) cc_final: 0.7681 (m-10) REVERT: N 109 ASP cc_start: 0.8166 (p0) cc_final: 0.7917 (p0) REVERT: N 110 PHE cc_start: 0.8759 (t80) cc_final: 0.8436 (t80) REVERT: N 220 GLU cc_start: 0.8034 (mp0) cc_final: 0.7797 (mp0) REVERT: N 230 MET cc_start: 0.7644 (ttp) cc_final: 0.7382 (tmm) REVERT: N 244 LYS cc_start: 0.8790 (tttt) cc_final: 0.8491 (tttt) REVERT: C 178 MET cc_start: 0.8545 (mmm) cc_final: 0.8208 (mmm) REVERT: C 279 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7785 (ttm-80) REVERT: C 321 SER cc_start: 0.7274 (m) cc_final: 0.6842 (p) REVERT: C 327 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7626 (tm-30) REVERT: C 356 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7586 (tmm160) REVERT: C 357 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7550 (tp40) REVERT: C 375 PHE cc_start: 0.8591 (m-80) cc_final: 0.8178 (m-80) REVERT: C 384 PHE cc_start: 0.8787 (p90) cc_final: 0.8434 (p90) REVERT: C 399 ASN cc_start: 0.8297 (p0) cc_final: 0.7707 (p0) REVERT: C 415 MET cc_start: 0.7367 (ttm) cc_final: 0.7160 (ttm) REVERT: C 449 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8680 (ttmm) REVERT: C 454 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8476 (mm) REVERT: C 457 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.7043 (t70) REVERT: C 497 ASP cc_start: 0.7448 (p0) cc_final: 0.6852 (t0) REVERT: C 567 LYS cc_start: 0.8399 (ttpp) cc_final: 0.8029 (ttpp) REVERT: C 598 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8745 (tp) REVERT: C 708 TRP cc_start: 0.6820 (p-90) cc_final: 0.6467 (m100) REVERT: C 743 LYS cc_start: 0.8397 (tmtt) cc_final: 0.8169 (tmtt) REVERT: C 795 SER cc_start: 0.8691 (m) cc_final: 0.8351 (p) REVERT: C 807 MET cc_start: 0.7534 (mtm) cc_final: 0.7027 (mtm) REVERT: C 812 VAL cc_start: 0.8443 (t) cc_final: 0.8189 (p) REVERT: D 92 SER cc_start: 0.8710 (t) cc_final: 0.8341 (p) REVERT: D 95 ARG cc_start: 0.7784 (tpp80) cc_final: 0.7453 (mmm-85) REVERT: D 107 GLU cc_start: 0.7100 (mp0) cc_final: 0.6451 (mp0) REVERT: D 112 LYS cc_start: 0.8032 (ttpt) cc_final: 0.7315 (ttpt) REVERT: D 144 GLU cc_start: 0.7203 (pt0) cc_final: 0.6839 (tm-30) REVERT: D 214 ASP cc_start: 0.7598 (t0) cc_final: 0.6858 (t0) REVERT: D 222 GLU cc_start: 0.7937 (mp0) cc_final: 0.7721 (mp0) REVERT: D 223 ASP cc_start: 0.7918 (p0) cc_final: 0.7563 (p0) REVERT: D 230 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6689 (mm-30) REVERT: D 272 MET cc_start: 0.8024 (ttt) cc_final: 0.7778 (ttt) REVERT: D 311 MET cc_start: 0.7556 (ptp) cc_final: 0.7205 (ptp) REVERT: D 353 LYS cc_start: 0.8993 (mmtm) cc_final: 0.8773 (mmmt) REVERT: D 355 HIS cc_start: 0.7644 (p-80) cc_final: 0.7248 (p90) REVERT: D 374 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7946 (pp20) REVERT: D 397 ARG cc_start: 0.7932 (mmm160) cc_final: 0.7278 (mmm160) REVERT: D 416 VAL cc_start: 0.8543 (t) cc_final: 0.8225 (m) REVERT: D 423 MET cc_start: 0.7039 (mmm) cc_final: 0.6799 (mmm) REVERT: D 427 LYS cc_start: 0.8050 (pttt) cc_final: 0.7759 (ptmm) REVERT: D 450 GLU cc_start: 0.7941 (mp0) cc_final: 0.7672 (mp0) REVERT: D 626 GLU cc_start: 0.7405 (pt0) cc_final: 0.7122 (pp20) REVERT: D 649 GLU cc_start: 0.6956 (mp0) cc_final: 0.6750 (mp0) REVERT: D 702 MET cc_start: 0.8573 (mmp) cc_final: 0.8278 (mmm) REVERT: D 715 ASP cc_start: 0.8075 (p0) cc_final: 0.7798 (p0) outliers start: 65 outliers final: 44 residues processed: 534 average time/residue: 0.1497 time to fit residues: 115.8309 Evaluate side-chains 553 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 502 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 625 SER Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 661 TYR Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 710 SER Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 124 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 228 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.116859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.097633 restraints weight = 43223.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.101412 restraints weight = 20931.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.103816 restraints weight = 11993.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.105481 restraints weight = 7697.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.106612 restraints weight = 5331.006| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18900 Z= 0.171 Angle : 0.803 13.938 25608 Z= 0.405 Chirality : 0.047 0.419 2874 Planarity : 0.004 0.062 3237 Dihedral : 4.630 39.625 2571 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 3.13 % Allowed : 21.86 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2315 helix: 0.95 (0.16), residues: 967 sheet: 0.44 (0.24), residues: 464 loop : -1.00 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 8 TYR 0.026 0.001 TYR D 338 PHE 0.048 0.002 PHE A 307 TRP 0.017 0.001 TRP B 99 HIS 0.005 0.001 HIS D 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (18896) covalent geometry : angle 0.80317 / 0.40 (25600) SS BOND : bond 0.00541 / 0.27 ( 4) SS BOND : angle 1.32891 / 0.61 ( 8) hydrogen bonds : bond 0.04364 / 2.93 ( 924) hydrogen bonds : angle 4.35628 / 3.11 ( 2628) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 501 time to evaluate : 0.679 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: 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: 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 9 ASP cc_start: 0.8641 (m-30) cc_final: 0.8168 (m-30) REVERT: A 10 LYS cc_start: 0.8925 (mttt) cc_final: 0.8389 (mtmm) REVERT: A 29 LYS cc_start: 0.8601 (tmtt) cc_final: 0.7969 (tmtt) REVERT: A 32 ARG cc_start: 0.7434 (mpt-90) cc_final: 0.6962 (mpt-90) REVERT: A 88 MET cc_start: 0.2035 (OUTLIER) cc_final: 0.1553 (ttt) REVERT: A 105 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7586 (mmm-85) REVERT: A 189 PHE cc_start: 0.6260 (OUTLIER) cc_final: 0.5851 (t80) REVERT: A 194 LEU cc_start: 0.8443 (tp) cc_final: 0.7914 (tp) REVERT: A 213 HIS cc_start: 0.8310 (p-80) cc_final: 0.8011 (p-80) REVERT: A 236 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8716 (pm20) REVERT: A 237 ASP cc_start: 0.8369 (m-30) cc_final: 0.7167 (p0) REVERT: A 240 MET cc_start: 0.7896 (ttt) cc_final: 0.7209 (ttt) REVERT: A 246 SER cc_start: 0.9139 (m) cc_final: 0.8830 (p) REVERT: A 266 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7276 (pp) REVERT: A 274 PHE cc_start: 0.7888 (t80) cc_final: 0.7446 (t80) REVERT: A 283 LEU cc_start: 0.9415 (mt) cc_final: 0.9054 (pp) REVERT: A 306 GLN cc_start: 0.8749 (pm20) cc_final: 0.8481 (pm20) REVERT: A 307 PHE cc_start: 0.8395 (m-80) cc_final: 0.7980 (m-80) REVERT: A 313 ARG cc_start: 0.8484 (ttp-170) cc_final: 0.8100 (tmm-80) REVERT: A 334 PHE cc_start: 0.8847 (t80) cc_final: 0.8549 (t80) REVERT: A 337 ASP cc_start: 0.8232 (m-30) cc_final: 0.7874 (m-30) REVERT: A 341 ASP cc_start: 0.8282 (m-30) cc_final: 0.7921 (p0) REVERT: A 345 LYS cc_start: 0.8958 (ptpp) cc_final: 0.8492 (pttm) REVERT: A 346 ASN cc_start: 0.8115 (m-40) cc_final: 0.7817 (m-40) REVERT: B 23 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8654 (mttt) REVERT: B 42 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7613 (ttp80) REVERT: B 45 MET cc_start: 0.7846 (tpp) cc_final: 0.7582 (mmm) REVERT: B 52 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7718 (ptp90) REVERT: B 61 MET cc_start: 0.8216 (tmm) cc_final: 0.7774 (ppp) REVERT: B 96 ARG cc_start: 0.6490 (mmp80) cc_final: 0.6150 (mmp80) REVERT: B 122 SER cc_start: 0.8584 (m) cc_final: 0.8295 (p) REVERT: B 135 VAL cc_start: 0.8923 (t) cc_final: 0.8609 (p) REVERT: B 156 GLN cc_start: 0.7272 (mm110) cc_final: 0.7004 (mp10) REVERT: B 170 ASP cc_start: 0.8184 (t0) cc_final: 0.7693 (p0) REVERT: B 172 GLU cc_start: 0.8176 (tp30) cc_final: 0.7630 (tp30) REVERT: B 254 ASP cc_start: 0.7205 (t70) cc_final: 0.6898 (t0) REVERT: B 280 LYS cc_start: 0.7828 (tppt) cc_final: 0.7486 (tppp) REVERT: B 298 ASP cc_start: 0.7681 (t0) cc_final: 0.7477 (t0) REVERT: Y 11 GLN cc_start: 0.8798 (pt0) cc_final: 0.8579 (pt0) REVERT: N 6 GLU cc_start: 0.6903 (pt0) cc_final: 0.6165 (mt-10) REVERT: N 110 PHE cc_start: 0.8741 (t80) cc_final: 0.8453 (t80) REVERT: N 220 GLU cc_start: 0.8082 (mp0) cc_final: 0.7840 (mp0) REVERT: N 230 MET cc_start: 0.7684 (ttp) cc_final: 0.7434 (tmm) REVERT: C 210 GLU cc_start: 0.7544 (tt0) cc_final: 0.7154 (tm-30) REVERT: C 321 SER cc_start: 0.7293 (m) cc_final: 0.6858 (p) REVERT: C 327 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7627 (tm-30) REVERT: C 356 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7340 (ttp80) REVERT: C 357 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8066 (tp40) REVERT: C 384 PHE cc_start: 0.8812 (p90) cc_final: 0.8441 (p90) REVERT: C 399 ASN cc_start: 0.8351 (p0) cc_final: 0.7770 (p0) REVERT: C 415 MET cc_start: 0.7346 (ttm) cc_final: 0.7131 (ttm) REVERT: C 449 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8729 (ttmm) REVERT: C 454 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8444 (mm) REVERT: C 457 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.7041 (t70) REVERT: C 497 ASP cc_start: 0.7517 (p0) cc_final: 0.6888 (t0) REVERT: C 567 LYS cc_start: 0.8461 (ttpp) cc_final: 0.8030 (ttpp) REVERT: C 598 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8772 (tp) REVERT: C 708 TRP cc_start: 0.6804 (p-90) cc_final: 0.6512 (m100) REVERT: C 743 LYS cc_start: 0.8393 (tmtt) cc_final: 0.8166 (tmtt) REVERT: C 795 SER cc_start: 0.8685 (m) cc_final: 0.8330 (p) REVERT: C 807 MET cc_start: 0.7529 (mtm) cc_final: 0.7055 (mtm) REVERT: C 812 VAL cc_start: 0.8499 (t) cc_final: 0.8244 (p) REVERT: D 62 MET cc_start: 0.7583 (tmm) cc_final: 0.7373 (tmm) REVERT: D 92 SER cc_start: 0.8684 (t) cc_final: 0.8286 (p) REVERT: D 95 ARG cc_start: 0.7780 (tpp80) cc_final: 0.7431 (mmm-85) REVERT: D 107 GLU cc_start: 0.7111 (mp0) cc_final: 0.6415 (mp0) REVERT: D 112 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7288 (ttpt) REVERT: D 144 GLU cc_start: 0.7172 (pt0) cc_final: 0.6845 (tm-30) REVERT: D 214 ASP cc_start: 0.7644 (t0) cc_final: 0.6947 (t0) REVERT: D 220 TYR cc_start: 0.8584 (t80) cc_final: 0.8374 (t80) REVERT: D 223 ASP cc_start: 0.7970 (p0) cc_final: 0.7599 (p0) REVERT: D 230 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6714 (mm-30) REVERT: D 272 MET cc_start: 0.8041 (ttt) cc_final: 0.7797 (ttt) REVERT: D 311 MET cc_start: 0.7593 (ptp) cc_final: 0.7265 (ptp) REVERT: D 374 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7927 (pp20) REVERT: D 397 ARG cc_start: 0.7928 (mmm160) cc_final: 0.7235 (mmm160) REVERT: D 403 MET cc_start: 0.8399 (mmm) cc_final: 0.8104 (tpt) REVERT: D 416 VAL cc_start: 0.8564 (t) cc_final: 0.7632 (m) REVERT: D 421 GLU cc_start: 0.7320 (tp30) cc_final: 0.7053 (tp30) REVERT: D 427 LYS cc_start: 0.8092 (pttt) cc_final: 0.7773 (ptmm) REVERT: D 450 GLU cc_start: 0.7957 (mp0) cc_final: 0.7688 (mp0) REVERT: D 626 GLU cc_start: 0.7434 (pt0) cc_final: 0.7157 (pp20) REVERT: D 649 GLU cc_start: 0.6986 (mp0) cc_final: 0.6767 (mp0) REVERT: D 702 MET cc_start: 0.8547 (mmp) cc_final: 0.8276 (mmm) REVERT: D 715 ASP cc_start: 0.8074 (p0) cc_final: 0.7776 (p0) outliers start: 63 outliers final: 46 residues processed: 532 average time/residue: 0.1542 time to fit residues: 119.2017 Evaluate side-chains 540 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 487 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 661 TYR Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 710 SER Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 205 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 190 optimal weight: 0.0570 chunk 48 optimal weight: 0.0870 chunk 0 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 186 optimal weight: 0.4980 chunk 182 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 344 ASN D 687 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.118327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.099548 restraints weight = 43040.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.103312 restraints weight = 20656.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.105721 restraints weight = 11744.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.107350 restraints weight = 7462.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108444 restraints weight = 5184.675| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18900 Z= 0.148 Angle : 0.827 14.984 25608 Z= 0.413 Chirality : 0.046 0.448 2874 Planarity : 0.004 0.091 3237 Dihedral : 4.525 39.726 2571 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 2.48 % Allowed : 22.80 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2315 helix: 0.95 (0.17), residues: 968 sheet: 0.47 (0.24), residues: 464 loop : -1.04 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 8 TYR 0.030 0.001 TYR D 268 PHE 0.045 0.001 PHE A 307 TRP 0.013 0.001 TRP B 99 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (18896) covalent geometry : angle 0.82738 / 0.41 (25600) SS BOND : bond 0.00457 / 0.23 ( 4) SS BOND : angle 1.13854 / 0.53 ( 8) hydrogen bonds : bond 0.04203 / 2.84 ( 924) hydrogen bonds : angle 4.32830 / 3.10 ( 2628) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 504 time to evaluate : 0.574 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8625 (m-30) cc_final: 0.8180 (m-30) REVERT: A 10 LYS cc_start: 0.8921 (mttt) cc_final: 0.8661 (mttp) REVERT: A 29 LYS cc_start: 0.8612 (tmtt) cc_final: 0.7995 (tmtt) REVERT: A 32 ARG cc_start: 0.7472 (mpt-90) cc_final: 0.6984 (mpt-90) REVERT: A 76 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7161 (m110) REVERT: A 88 MET cc_start: 0.2122 (OUTLIER) cc_final: 0.1600 (ttt) REVERT: A 105 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7413 (ttp-170) REVERT: A 189 PHE cc_start: 0.6331 (OUTLIER) cc_final: 0.5812 (t80) REVERT: A 194 LEU cc_start: 0.8127 (tp) cc_final: 0.7753 (tp) REVERT: A 213 HIS cc_start: 0.8261 (p-80) cc_final: 0.7985 (p-80) REVERT: A 236 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8733 (pm20) REVERT: A 237 ASP cc_start: 0.8368 (m-30) cc_final: 0.7241 (p0) REVERT: A 240 MET cc_start: 0.7888 (ttt) cc_final: 0.6808 (ttt) REVERT: A 246 SER cc_start: 0.9100 (m) cc_final: 0.8792 (p) REVERT: A 248 LYS cc_start: 0.9176 (mttp) cc_final: 0.8820 (mttm) REVERT: A 266 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7306 (pp) REVERT: A 277 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8083 (ptpp) REVERT: A 283 LEU cc_start: 0.9412 (mt) cc_final: 0.9086 (tp) REVERT: A 307 PHE cc_start: 0.8337 (m-80) cc_final: 0.7865 (m-80) REVERT: A 313 ARG cc_start: 0.8425 (ttp-170) cc_final: 0.8074 (tmm-80) REVERT: A 334 PHE cc_start: 0.8807 (t80) cc_final: 0.8564 (t80) REVERT: A 337 ASP cc_start: 0.8211 (m-30) cc_final: 0.7877 (m-30) REVERT: A 341 ASP cc_start: 0.8325 (m-30) cc_final: 0.7954 (p0) REVERT: A 345 LYS cc_start: 0.8950 (ptpp) cc_final: 0.8618 (ptpp) REVERT: A 346 ASN cc_start: 0.8127 (m-40) cc_final: 0.7845 (m-40) REVERT: B 23 LYS cc_start: 0.9058 (mtmt) cc_final: 0.8662 (mttt) REVERT: B 42 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7588 (ttp80) REVERT: B 45 MET cc_start: 0.7806 (tpp) cc_final: 0.7547 (mmm) REVERT: B 52 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7685 (ptp90) REVERT: B 61 MET cc_start: 0.8233 (tmm) cc_final: 0.7801 (ppp) REVERT: B 96 ARG cc_start: 0.6503 (mmp80) cc_final: 0.6178 (mmp80) REVERT: B 122 SER cc_start: 0.8610 (m) cc_final: 0.8317 (p) REVERT: B 135 VAL cc_start: 0.8922 (t) cc_final: 0.8600 (p) REVERT: B 156 GLN cc_start: 0.7251 (mm110) cc_final: 0.6986 (mp10) REVERT: B 170 ASP cc_start: 0.8128 (t0) cc_final: 0.7653 (p0) REVERT: B 172 GLU cc_start: 0.8133 (tp30) cc_final: 0.7591 (tp30) REVERT: B 254 ASP cc_start: 0.7138 (t70) cc_final: 0.6860 (t0) REVERT: B 280 LYS cc_start: 0.7792 (tppt) cc_final: 0.7481 (tppp) REVERT: B 298 ASP cc_start: 0.7601 (t0) cc_final: 0.7393 (t0) REVERT: Y 32 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8271 (mmtt) REVERT: N 6 GLU cc_start: 0.6898 (pt0) cc_final: 0.6151 (mt-10) REVERT: N 38 ARG cc_start: 0.7854 (ptm-80) cc_final: 0.7212 (ptm-80) REVERT: N 94 TYR cc_start: 0.7958 (m-10) cc_final: 0.7718 (m-80) REVERT: N 110 PHE cc_start: 0.8725 (t80) cc_final: 0.8439 (t80) REVERT: N 230 MET cc_start: 0.7609 (ttp) cc_final: 0.7349 (tmm) REVERT: C 210 GLU cc_start: 0.7533 (tt0) cc_final: 0.7203 (tm-30) REVERT: C 321 SER cc_start: 0.7280 (m) cc_final: 0.6849 (p) REVERT: C 356 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7329 (ttp80) REVERT: C 357 GLN cc_start: 0.8314 (tm-30) cc_final: 0.8024 (tp40) REVERT: C 375 PHE cc_start: 0.8561 (m-80) cc_final: 0.8096 (m-80) REVERT: C 384 PHE cc_start: 0.8772 (p90) cc_final: 0.8415 (p90) REVERT: C 399 ASN cc_start: 0.8309 (p0) cc_final: 0.7778 (p0) REVERT: C 415 MET cc_start: 0.7369 (ttm) cc_final: 0.7134 (ttm) REVERT: C 449 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8709 (ttmm) REVERT: C 454 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8421 (mm) REVERT: C 457 HIS cc_start: 0.7473 (OUTLIER) cc_final: 0.7043 (t70) REVERT: C 497 ASP cc_start: 0.7476 (p0) cc_final: 0.6838 (t0) REVERT: C 567 LYS cc_start: 0.8392 (ttpp) cc_final: 0.7958 (ttpp) REVERT: C 598 LEU cc_start: 0.9040 (mm) cc_final: 0.8788 (tp) REVERT: C 743 LYS cc_start: 0.8398 (tmtt) cc_final: 0.8171 (tmtt) REVERT: C 807 MET cc_start: 0.7553 (mtm) cc_final: 0.7066 (mtm) REVERT: C 812 VAL cc_start: 0.8475 (t) cc_final: 0.8230 (p) REVERT: D 92 SER cc_start: 0.8692 (t) cc_final: 0.8308 (p) REVERT: D 95 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7487 (mmm-85) REVERT: D 144 GLU cc_start: 0.7167 (pt0) cc_final: 0.6937 (tm-30) REVERT: D 214 ASP cc_start: 0.7528 (t0) cc_final: 0.6808 (t0) REVERT: D 222 GLU cc_start: 0.7704 (mp0) cc_final: 0.7387 (mp0) REVERT: D 223 ASP cc_start: 0.7883 (p0) cc_final: 0.7499 (p0) REVERT: D 230 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6748 (mm-30) REVERT: D 272 MET cc_start: 0.8004 (ttt) cc_final: 0.7753 (ttt) REVERT: D 290 TRP cc_start: 0.8609 (p90) cc_final: 0.8296 (p90) REVERT: D 311 MET cc_start: 0.7520 (ptp) cc_final: 0.7184 (ptp) REVERT: D 374 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7786 (pp20) REVERT: D 397 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7277 (mmm160) REVERT: D 416 VAL cc_start: 0.8562 (t) cc_final: 0.8246 (m) REVERT: D 427 LYS cc_start: 0.8086 (pttt) cc_final: 0.7793 (ptmm) REVERT: D 450 GLU cc_start: 0.7908 (mp0) cc_final: 0.7634 (mp0) REVERT: D 626 GLU cc_start: 0.7373 (pt0) cc_final: 0.7092 (pp20) REVERT: D 702 MET cc_start: 0.8513 (mmp) cc_final: 0.8257 (mmm) REVERT: D 715 ASP cc_start: 0.8043 (p0) cc_final: 0.7734 (p0) outliers start: 50 outliers final: 39 residues processed: 529 average time/residue: 0.1561 time to fit residues: 119.6478 Evaluate side-chains 537 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 491 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 661 TYR Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 710 SER Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 63 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 167 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 811 ASN D 194 GLN ** D 344 ASN ** 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 = 0.3939 r_free = 0.3939 target = 0.117862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.099125 restraints weight = 43363.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.102873 restraints weight = 20870.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.105237 restraints weight = 11863.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.106818 restraints weight = 7547.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.107950 restraints weight = 5237.599| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18900 Z= 0.155 Angle : 0.836 14.814 25608 Z= 0.420 Chirality : 0.046 0.442 2874 Planarity : 0.005 0.090 3237 Dihedral : 4.536 39.106 2571 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 2.29 % Allowed : 23.89 % Favored : 73.82 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2315 helix: 0.99 (0.17), residues: 961 sheet: 0.44 (0.24), residues: 472 loop : -0.92 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 8 TYR 0.026 0.001 TYR D 338 PHE 0.041 0.001 PHE A 307 TRP 0.013 0.001 TRP B 99 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (18896) covalent geometry : angle 0.83627 / 0.42 (25600) SS BOND : bond 0.00471 / 0.24 ( 4) SS BOND : angle 1.15257 / 0.53 ( 8) hydrogen bonds : bond 0.04247 / 2.87 ( 924) hydrogen bonds : angle 4.38868 / 3.14 ( 2628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4558.74 seconds wall clock time: 79 minutes 1.19 seconds (4741.19 seconds total)