Starting phenix.real_space_refine on Sat Feb 7 00:56:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7var_31860/02_2026/7var_31860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7var_31860/02_2026/7var_31860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7var_31860/02_2026/7var_31860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7var_31860/02_2026/7var_31860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7var_31860/02_2026/7var_31860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7var_31860/02_2026/7var_31860.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 P 5 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18720 2.51 5 N 5125 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29520 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4476 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4467 Classifications: {'peptide': 577} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain breaks: 1 Chain: "C" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4476 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 314 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 314 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 981 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.99, per 1000 atoms: 0.24 Number of scatterers: 29520 At special positions: 0 Unit cell: (140.8, 174.24, 150.48, 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) S 103 16.00 P 5 15.00 Mg 2 11.99 O 5565 8.00 N 5125 7.00 C 18720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.4 seconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6916 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 24 sheets defined 47.7% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.154A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.408A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 4.109A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.970A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.605A pdb=" N LEU A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 541 removed outlier: 3.524A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.865A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 575 removed outlier: 3.678A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.738A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.666A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 removed outlier: 3.555A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.604A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 532 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.784A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 Processing helix chain 'B' and resid 558 through 576 removed outlier: 3.565A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.833A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.214A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.146A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.523A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.164A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.567A pdb=" N GLN C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.863A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.749A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 4.152A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.502A pdb=" N ARG D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.517A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.111A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.662A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.595A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.564A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 395 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 445 through 446 No H-bonds generated for 'chain 'D' and resid 445 through 446' Processing helix chain 'D' and resid 447 through 451 removed outlier: 3.911A pdb=" N LEU D 451 " --> pdb=" O GLN D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 469 through 473 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.978A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 removed outlier: 3.616A pdb=" N MET E 141 " --> pdb=" O THR E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 175 through 179 Processing helix chain 'E' and resid 197 through 211 removed outlier: 4.059A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.859A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.880A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.592A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 374 through 400 removed outlier: 4.193A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.575A pdb=" N LEU E 451 " --> pdb=" O GLN E 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 removed outlier: 3.552A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.830A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.734A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 removed outlier: 3.512A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 365 Processing helix chain 'F' and resid 374 through 399 removed outlier: 3.527A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 removed outlier: 3.886A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TRP F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 471' Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.913A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.594A pdb=" N VAL G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 115 removed outlier: 3.794A pdb=" N LEU G 113 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 167 removed outlier: 3.582A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 208 removed outlier: 3.605A pdb=" N GLY G 171 " --> pdb=" O VAL G 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 16 Processing helix chain 'H' and resid 25 through 40 Processing helix chain 'H' and resid 54 through 59 Processing helix chain 'H' and resid 76 through 81 Processing helix chain 'H' and resid 85 through 99 removed outlier: 3.729A pdb=" N TYR H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 105 removed outlier: 4.507A pdb=" N ARG I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 3.548A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 93 removed outlier: 3.712A pdb=" N LEU J 66 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.573A pdb=" N LEU J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 130 Processing helix chain 'J' and resid 131 through 139 Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.523A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 83 No H-bonds generated for 'chain 'K' and resid 81 through 83' Processing helix chain 'K' and resid 84 through 105 removed outlier: 4.035A pdb=" N TYR K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 removed outlier: 3.646A pdb=" N GLU K 117 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 93 Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 127 through 130 Processing helix chain 'L' and resid 131 through 139 removed outlier: 3.513A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 188 removed outlier: 4.578A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.509A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.753A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 6.589A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.798A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 6.544A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 5.818A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 5.677A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 144 current: chain 'L' and resid 161 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 290 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 148 removed outlier: 3.928A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 164 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.624A pdb=" N GLY B 164 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 7.011A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.520A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 148 removed outlier: 6.415A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.761A pdb=" N GLY C 155 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.621A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 93 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 91 through 93 current: chain 'D' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 217 through 223 current: chain 'D' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 307 through 315 current: chain 'D' and resid 358 through 359 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.662A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.736A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.688A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 94 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 94 current: chain 'F' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 217 through 223 current: chain 'F' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 307 through 315 current: chain 'F' and resid 358 through 359 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.705A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 89 through 96 Processing sheet with id=AC6, first strand: chain 'H' and resid 19 through 22 removed outlier: 8.114A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1269 hydrogen bonds defined for protein. 3618 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: 5.47 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9966 1.34 - 1.46: 5196 1.46 - 1.58: 14709 1.58 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30074 Sorted by residual: bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C5 ADP A 601 " pdb=" C6 ADP A 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.590 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" N ARG F 372 " pdb=" CA ARG F 372 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.87e+00 bond pdb=" N GLU D 296 " pdb=" CA GLU D 296 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.30e-02 5.92e+03 8.14e+00 ... (remaining 30069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 40645 3.24 - 6.49: 99 6.49 - 9.73: 8 9.73 - 12.98: 1 12.98 - 16.22: 1 Bond angle restraints: 40754 Sorted by residual: angle pdb=" PA ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 120.50 136.72 -16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O2B ADP A 601 " ideal model delta sigma weight residual 119.90 106.99 12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" N THR G 119 " pdb=" CA THR G 119 " pdb=" C THR G 119 " ideal model delta sigma weight residual 109.81 117.95 -8.14 2.21e+00 2.05e-01 1.36e+01 angle pdb=" CA ALA D 298 " pdb=" C ALA D 298 " pdb=" O ALA D 298 " ideal model delta sigma weight residual 121.56 117.98 3.58 1.09e+00 8.42e-01 1.08e+01 angle pdb=" C ALA E 441 " pdb=" N LEU E 442 " pdb=" CA LEU E 442 " ideal model delta sigma weight residual 122.06 116.03 6.03 1.86e+00 2.89e-01 1.05e+01 ... (remaining 40749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.89: 17752 27.89 - 55.78: 511 55.78 - 83.67: 74 83.67 - 111.56: 10 111.56 - 139.45: 2 Dihedral angle restraints: 18349 sinusoidal: 7531 harmonic: 10818 Sorted by residual: dihedral pdb=" O2A ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PA ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 79.45 -139.45 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 78.40 -138.41 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" C THR F 371 " pdb=" N THR F 371 " pdb=" CA THR F 371 " pdb=" CB THR F 371 " ideal model delta harmonic sigma weight residual -122.00 -137.73 15.73 0 2.50e+00 1.60e-01 3.96e+01 ... (remaining 18346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 4331 0.095 - 0.191: 235 0.191 - 0.286: 0 0.286 - 0.381: 0 0.381 - 0.477: 1 Chirality restraints: 4567 Sorted by residual: chirality pdb=" CA THR F 371 " pdb=" N THR F 371 " pdb=" C THR F 371 " pdb=" CB THR F 371 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 4564 not shown) Planarity restraints: 5336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 124 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO L 125 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO L 125 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 125 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 101 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO G 102 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 102 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 102 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO E 324 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " -0.023 5.00e-02 4.00e+02 ... (remaining 5333 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 168 2.61 - 3.18: 25085 3.18 - 3.76: 44702 3.76 - 4.33: 63216 4.33 - 4.90: 106582 Nonbonded interactions: 239753 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 2.038 2.170 nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 2.065 2.170 nonbonded pdb=" OG SER H 25 " pdb=" OE1 GLU H 28 " model vdw 2.145 3.040 nonbonded pdb=" OD1 ASP F 34 " pdb=" OG SER F 74 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR D 263 " pdb=" OD2 ASP D 290 " model vdw 2.228 3.040 ... (remaining 239748 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 32 or resid 34 through 578)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 32 or resid 34 through 578)) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.300 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 30074 Z= 0.143 Angle : 0.556 16.222 40754 Z= 0.308 Chirality : 0.043 0.477 4567 Planarity : 0.004 0.059 5336 Dihedral : 13.345 139.447 11433 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.06 % Allowed : 0.26 % Favored : 99.68 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.80 % 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: 1.46 (0.14), residues: 3761 helix: 1.89 (0.14), residues: 1554 sheet: 0.35 (0.22), residues: 579 loop : 0.42 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 364 TYR 0.010 0.001 TYR G 133 PHE 0.009 0.001 PHE B 143 TRP 0.006 0.001 TRP C 119 HIS 0.003 0.001 HIS F 252 Details of bonding type rmsd covalent geometry : bond 0.00280 (30074) covalent geometry : angle 0.55562 (40754) hydrogen bonds : bond 0.15593 ( 1269) hydrogen bonds : angle 5.84262 ( 3618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 507 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8104 (ptpp) cc_final: 0.7625 (mttp) REVERT: A 143 PHE cc_start: 0.8529 (m-80) cc_final: 0.8188 (m-10) REVERT: A 154 ARG cc_start: 0.7613 (ptm160) cc_final: 0.7105 (ptt90) REVERT: A 445 GLU cc_start: 0.7852 (tp30) cc_final: 0.7442 (tp30) REVERT: A 502 GLU cc_start: 0.7829 (pm20) cc_final: 0.7395 (mp0) REVERT: A 524 LYS cc_start: 0.7697 (mmtp) cc_final: 0.7412 (ptmt) REVERT: A 546 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6668 (mm-30) REVERT: A 547 ARG cc_start: 0.7529 (ttm-80) cc_final: 0.7127 (ttm110) REVERT: B 38 GLU cc_start: 0.7968 (tt0) cc_final: 0.7610 (tt0) REVERT: B 130 ARG cc_start: 0.7341 (mmt-90) cc_final: 0.7077 (mpt180) REVERT: B 467 ILE cc_start: 0.6882 (mm) cc_final: 0.6523 (mt) REVERT: B 502 GLU cc_start: 0.8006 (tt0) cc_final: 0.7764 (mp0) REVERT: C 121 PRO cc_start: 0.8976 (Cg_endo) cc_final: 0.8775 (Cg_exo) REVERT: C 140 GLU cc_start: 0.7594 (tp30) cc_final: 0.7215 (tt0) REVERT: C 488 ARG cc_start: 0.7943 (tmm-80) cc_final: 0.7577 (ttp-170) REVERT: C 546 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7397 (pt0) REVERT: C 550 ARG cc_start: 0.7615 (ttp-110) cc_final: 0.6888 (ttm-80) REVERT: D 74 SER cc_start: 0.8315 (t) cc_final: 0.8100 (m) REVERT: D 275 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7718 (mt-10) REVERT: D 453 ARG cc_start: 0.7418 (mtp85) cc_final: 0.7153 (mtp85) REVERT: E 196 ILE cc_start: 0.8083 (mm) cc_final: 0.7393 (pt) REVERT: E 206 GLN cc_start: 0.7360 (mt0) cc_final: 0.7136 (mp10) REVERT: E 274 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7207 (mtm-85) REVERT: E 410 ARG cc_start: 0.6981 (ttm110) cc_final: 0.6770 (ttt90) REVERT: F 98 LYS cc_start: 0.7501 (mmtm) cc_final: 0.7214 (mmpt) REVERT: F 128 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7376 (mm-30) REVERT: F 178 SER cc_start: 0.8043 (t) cc_final: 0.7735 (p) REVERT: F 210 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7704 (ttm170) REVERT: G 30 LYS cc_start: 0.7502 (mtpp) cc_final: 0.7260 (mttt) REVERT: G 38 GLU cc_start: 0.6987 (tt0) cc_final: 0.6361 (tp30) REVERT: G 96 VAL cc_start: 0.7218 (t) cc_final: 0.6973 (m) REVERT: G 149 LYS cc_start: 0.7259 (mmtt) cc_final: 0.6709 (mtmt) REVERT: H 19 GLU cc_start: 0.4165 (tt0) cc_final: 0.3625 (tp30) REVERT: H 28 GLU cc_start: 0.4253 (pm20) cc_final: 0.3946 (tt0) REVERT: J 122 VAL cc_start: 0.6143 (t) cc_final: 0.5764 (p) REVERT: J 134 LEU cc_start: 0.4500 (pt) cc_final: 0.3618 (mp) REVERT: K 91 ARG cc_start: 0.4595 (ttm170) cc_final: 0.4266 (mtp85) REVERT: K 104 MET cc_start: 0.5725 (ttm) cc_final: 0.5203 (ttp) REVERT: L 105 ARG cc_start: 0.6833 (mtm-85) cc_final: 0.6497 (mtm-85) REVERT: L 119 LYS cc_start: 0.7084 (pttt) cc_final: 0.6746 (pttp) REVERT: L 172 ASP cc_start: 0.7519 (m-30) cc_final: 0.7155 (t0) REVERT: L 181 LYS cc_start: 0.6696 (mmmt) cc_final: 0.6395 (mttm) REVERT: L 187 TRP cc_start: 0.6663 (m-90) cc_final: 0.6377 (m-90) outliers start: 2 outliers final: 1 residues processed: 509 average time/residue: 0.9686 time to fit residues: 553.0039 Evaluate side-chains 293 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 363 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN B 202 ASN B 260 ASN B 423 ASN C 238 GLN D 364 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 181 GLN L 165 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.089249 restraints weight = 44729.899| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.67 r_work: 0.2980 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30074 Z= 0.130 Angle : 0.525 7.809 40754 Z= 0.269 Chirality : 0.044 0.164 4567 Planarity : 0.005 0.050 5336 Dihedral : 6.089 139.036 4232 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.49 % Allowed : 8.40 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.49 (0.14), residues: 3761 helix: 1.91 (0.14), residues: 1564 sheet: 0.47 (0.22), residues: 555 loop : 0.39 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 210 TYR 0.013 0.001 TYR G 133 PHE 0.012 0.001 PHE C 230 TRP 0.015 0.001 TRP A 119 HIS 0.012 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00298 (30074) covalent geometry : angle 0.52503 (40754) hydrogen bonds : bond 0.04818 ( 1269) hydrogen bonds : angle 4.62703 ( 3618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 314 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8232 (mmm) cc_final: 0.7656 (mmm) REVERT: A 124 LYS cc_start: 0.8268 (ptpp) cc_final: 0.7734 (mttp) REVERT: A 154 ARG cc_start: 0.7842 (ptm160) cc_final: 0.7370 (ptt90) REVERT: A 323 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8040 (mtt) REVERT: A 502 GLU cc_start: 0.8148 (pm20) cc_final: 0.7731 (mp0) REVERT: A 546 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7066 (mm-30) REVERT: A 547 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7306 (ttm110) REVERT: B 38 GLU cc_start: 0.8611 (tt0) cc_final: 0.8408 (tt0) REVERT: B 130 ARG cc_start: 0.7849 (mmt-90) cc_final: 0.7610 (mpt180) REVERT: B 170 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: B 408 ARG cc_start: 0.8654 (ttm-80) cc_final: 0.8439 (ttt-90) REVERT: B 467 ILE cc_start: 0.7199 (mm) cc_final: 0.6934 (mt) REVERT: B 502 GLU cc_start: 0.8547 (tt0) cc_final: 0.8077 (mp0) REVERT: B 513 TYR cc_start: 0.8095 (t80) cc_final: 0.7600 (t80) REVERT: B 571 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6474 (mp10) REVERT: C 323 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.7993 (mmt) REVERT: C 441 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: C 476 LEU cc_start: 0.7478 (mp) cc_final: 0.7271 (mt) REVERT: C 488 ARG cc_start: 0.8762 (tmm-80) cc_final: 0.8396 (ttp-170) REVERT: C 550 ARG cc_start: 0.8346 (ttp-110) cc_final: 0.7655 (ttm-80) REVERT: D 25 LYS cc_start: 0.8413 (ptpt) cc_final: 0.8099 (mtpt) REVERT: D 416 ASP cc_start: 0.8504 (m-30) cc_final: 0.8172 (m-30) REVERT: E 162 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: E 410 ARG cc_start: 0.7292 (ttm110) cc_final: 0.7002 (ttt90) REVERT: F 128 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8241 (mm-30) REVERT: F 391 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8176 (m-30) REVERT: G 38 GLU cc_start: 0.7805 (tt0) cc_final: 0.7124 (tp30) REVERT: G 137 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7126 (mt) REVERT: G 149 LYS cc_start: 0.7798 (mmtt) cc_final: 0.7389 (mppt) REVERT: H 28 GLU cc_start: 0.5082 (pm20) cc_final: 0.4564 (tt0) REVERT: J 134 LEU cc_start: 0.4363 (pt) cc_final: 0.3784 (mp) REVERT: J 148 LEU cc_start: 0.3029 (tp) cc_final: 0.2488 (pp) REVERT: J 172 ASP cc_start: 0.5647 (m-30) cc_final: 0.5414 (m-30) REVERT: K 91 ARG cc_start: 0.4736 (ttm170) cc_final: 0.4401 (mtp85) REVERT: L 119 LYS cc_start: 0.7342 (pttt) cc_final: 0.7065 (pttp) REVERT: L 165 ASN cc_start: 0.7550 (t0) cc_final: 0.7170 (t160) REVERT: L 181 LYS cc_start: 0.7107 (mmmt) cc_final: 0.6725 (mttp) outliers start: 46 outliers final: 9 residues processed: 345 average time/residue: 1.0028 time to fit residues: 389.9464 Evaluate side-chains 292 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 275 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 67 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 220 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A 316 GLN A 541 GLN A 571 GLN B 477 GLN E 58 GLN F 310 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.084883 restraints weight = 44983.694| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.75 r_work: 0.2904 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 30074 Z= 0.306 Angle : 0.687 11.162 40754 Z= 0.354 Chirality : 0.051 0.198 4567 Planarity : 0.006 0.054 5336 Dihedral : 6.769 157.238 4230 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.82 % Allowed : 10.84 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.77 (0.14), residues: 3761 helix: 1.35 (0.13), residues: 1548 sheet: 0.04 (0.21), residues: 575 loop : -0.01 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 131 TYR 0.019 0.002 TYR B 304 PHE 0.016 0.002 PHE D 191 TRP 0.018 0.002 TRP G 97 HIS 0.010 0.002 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00761 (30074) covalent geometry : angle 0.68680 (40754) hydrogen bonds : bond 0.06628 ( 1269) hydrogen bonds : angle 4.83868 ( 3618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 277 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8401 (mmm) cc_final: 0.8195 (mmt) REVERT: A 124 LYS cc_start: 0.8391 (ptpp) cc_final: 0.7743 (mttp) REVERT: A 154 ARG cc_start: 0.7884 (ptm160) cc_final: 0.7361 (ptt90) REVERT: A 323 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8091 (mtt) REVERT: A 502 GLU cc_start: 0.8071 (pm20) cc_final: 0.7722 (mp0) REVERT: A 524 LYS cc_start: 0.8668 (ptmt) cc_final: 0.8070 (mmtt) REVERT: A 546 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7335 (tm-30) REVERT: A 547 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7483 (ttt90) REVERT: A 550 ARG cc_start: 0.8175 (mmt90) cc_final: 0.7130 (mtp-110) REVERT: B 93 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7570 (mpp80) REVERT: B 170 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: B 314 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.7916 (ptt90) REVERT: B 408 ARG cc_start: 0.8676 (ttm-80) cc_final: 0.8415 (ttt-90) REVERT: B 410 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: B 450 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8493 (tp) REVERT: B 464 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8291 (tp) REVERT: B 467 ILE cc_start: 0.7146 (mm) cc_final: 0.6802 (mt) REVERT: B 502 GLU cc_start: 0.8582 (tt0) cc_final: 0.8127 (mp0) REVERT: C 124 LYS cc_start: 0.8286 (mppt) cc_final: 0.7616 (mmmt) REVERT: C 323 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.7955 (mmt) REVERT: C 441 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: C 532 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.5901 (mtp85) REVERT: C 550 ARG cc_start: 0.8346 (ttp-110) cc_final: 0.7691 (ttm-80) REVERT: D 25 LYS cc_start: 0.8422 (ptpt) cc_final: 0.7949 (mtpt) REVERT: D 206 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: D 413 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8455 (mp10) REVERT: E 162 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: E 334 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8237 (mm-30) REVERT: E 410 ARG cc_start: 0.7477 (ttm110) cc_final: 0.7240 (ttt90) REVERT: E 452 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7530 (mtpt) REVERT: F 275 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8650 (mt-10) REVERT: F 373 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8158 (pt0) REVERT: F 391 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8125 (m-30) REVERT: G 38 GLU cc_start: 0.7941 (tt0) cc_final: 0.7235 (tp30) REVERT: G 137 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7172 (mt) REVERT: G 139 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6796 (ttm-80) REVERT: G 148 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7362 (mttp) REVERT: G 149 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7476 (mppt) REVERT: H 91 ARG cc_start: 0.6593 (mmm160) cc_final: 0.5844 (mmp80) REVERT: J 148 LEU cc_start: 0.2861 (tp) cc_final: 0.2527 (pp) REVERT: J 164 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5402 (tp30) REVERT: J 172 ASP cc_start: 0.5679 (m-30) cc_final: 0.5404 (m-30) REVERT: K 91 ARG cc_start: 0.4509 (ttm170) cc_final: 0.4192 (mtp85) REVERT: L 119 LYS cc_start: 0.7470 (pttt) cc_final: 0.7167 (pttp) outliers start: 87 outliers final: 26 residues processed: 344 average time/residue: 0.9278 time to fit residues: 361.0331 Evaluate side-chains 307 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 330 optimal weight: 7.9990 chunk 326 optimal weight: 6.9990 chunk 284 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 364 optimal weight: 30.0000 chunk 165 optimal weight: 0.9990 chunk 217 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 368 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.086705 restraints weight = 44461.045| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.77 r_work: 0.2930 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30074 Z= 0.172 Angle : 0.554 10.060 40754 Z= 0.285 Chirality : 0.045 0.168 4567 Planarity : 0.005 0.049 5336 Dihedral : 6.489 169.693 4230 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.47 % Allowed : 12.46 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.91 (0.14), residues: 3761 helix: 1.58 (0.14), residues: 1544 sheet: 0.02 (0.21), residues: 582 loop : -0.03 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 130 TYR 0.013 0.001 TYR G 133 PHE 0.016 0.002 PHE A 230 TRP 0.017 0.001 TRP A 119 HIS 0.006 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00419 (30074) covalent geometry : angle 0.55419 (40754) hydrogen bonds : bond 0.05205 ( 1269) hydrogen bonds : angle 4.56759 ( 3618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 280 time to evaluate : 0.882 Fit side-chains REVERT: A 122 MET cc_start: 0.8319 (mmm) cc_final: 0.8078 (mmt) REVERT: A 124 LYS cc_start: 0.8348 (ptpp) cc_final: 0.7722 (mttp) REVERT: A 143 PHE cc_start: 0.8859 (m-80) cc_final: 0.8587 (m-10) REVERT: A 154 ARG cc_start: 0.7882 (ptm160) cc_final: 0.7330 (ptt90) REVERT: A 323 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8035 (mtt) REVERT: A 502 GLU cc_start: 0.8059 (pm20) cc_final: 0.7715 (mp0) REVERT: A 524 LYS cc_start: 0.8570 (ptmt) cc_final: 0.7969 (mttt) REVERT: A 547 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7445 (ttt90) REVERT: A 550 ARG cc_start: 0.8260 (mmt90) cc_final: 0.7151 (mtp-110) REVERT: B 93 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7414 (mpp80) REVERT: B 170 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7377 (tp30) REVERT: B 314 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.7904 (ptt90) REVERT: B 408 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8428 (ttt-90) REVERT: B 410 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8252 (m-30) REVERT: B 467 ILE cc_start: 0.7095 (mm) cc_final: 0.6759 (mt) REVERT: B 502 GLU cc_start: 0.8626 (tt0) cc_final: 0.8144 (mp0) REVERT: B 557 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: B 567 MET cc_start: 0.7861 (tpt) cc_final: 0.7492 (tpt) REVERT: C 1 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6615 (mmt) REVERT: C 124 LYS cc_start: 0.8277 (mppt) cc_final: 0.7634 (mmmt) REVERT: C 323 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.7976 (mmt) REVERT: C 441 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: C 532 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.5708 (mtp85) REVERT: C 550 ARG cc_start: 0.8352 (ttp-110) cc_final: 0.7660 (ttm-80) REVERT: D 413 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8408 (mp10) REVERT: E 410 ARG cc_start: 0.7409 (ttm110) cc_final: 0.7160 (ttt90) REVERT: E 470 ILE cc_start: 0.5373 (OUTLIER) cc_final: 0.5111 (mp) REVERT: F 391 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8147 (m-30) REVERT: G 38 GLU cc_start: 0.7814 (tt0) cc_final: 0.7123 (tp30) REVERT: G 104 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5932 (tt) REVERT: G 137 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7260 (mt) REVERT: G 148 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7262 (mttp) REVERT: G 149 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7498 (mppt) REVERT: H 77 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.5939 (tp) REVERT: H 91 ARG cc_start: 0.6582 (mmm160) cc_final: 0.5841 (mmp80) REVERT: J 148 LEU cc_start: 0.2808 (tp) cc_final: 0.2579 (pp) REVERT: J 164 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5390 (tp30) REVERT: J 172 ASP cc_start: 0.5769 (m-30) cc_final: 0.5427 (OUTLIER) REVERT: K 91 ARG cc_start: 0.4572 (ttm170) cc_final: 0.4239 (mtp85) REVERT: L 119 LYS cc_start: 0.7429 (pttt) cc_final: 0.7136 (pttp) REVERT: L 165 ASN cc_start: 0.7647 (t0) cc_final: 0.7407 (t0) outliers start: 76 outliers final: 28 residues processed: 337 average time/residue: 0.7823 time to fit residues: 299.7558 Evaluate side-chains 298 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 164 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 100 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 325 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 chunk 286 optimal weight: 8.9990 chunk 204 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 chunk 327 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.088143 restraints weight = 44700.214| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.72 r_work: 0.2954 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30074 Z= 0.123 Angle : 0.512 10.312 40754 Z= 0.262 Chirality : 0.043 0.184 4567 Planarity : 0.005 0.054 5336 Dihedral : 6.278 177.308 4230 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.34 % Allowed : 13.34 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.12 (0.14), residues: 3761 helix: 1.85 (0.14), residues: 1539 sheet: 0.09 (0.21), residues: 580 loop : 0.01 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 130 TYR 0.012 0.001 TYR G 133 PHE 0.015 0.001 PHE A 230 TRP 0.015 0.001 TRP A 119 HIS 0.004 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00286 (30074) covalent geometry : angle 0.51162 (40754) hydrogen bonds : bond 0.04539 ( 1269) hydrogen bonds : angle 4.39576 ( 3618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 263 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8337 (mmm) cc_final: 0.8088 (mmt) REVERT: A 124 LYS cc_start: 0.8338 (ptpp) cc_final: 0.7746 (mttp) REVERT: A 143 PHE cc_start: 0.8821 (m-80) cc_final: 0.8567 (m-10) REVERT: A 154 ARG cc_start: 0.7896 (ptm160) cc_final: 0.7311 (ptt90) REVERT: A 323 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.7966 (mtt) REVERT: A 374 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 416 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8027 (ttm-80) REVERT: A 502 GLU cc_start: 0.8074 (pm20) cc_final: 0.7735 (mp0) REVERT: A 524 LYS cc_start: 0.8590 (ptmt) cc_final: 0.7986 (mttt) REVERT: A 547 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7429 (ttt90) REVERT: A 550 ARG cc_start: 0.8249 (mmt90) cc_final: 0.7142 (mtp-110) REVERT: B 170 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7425 (tp30) REVERT: B 314 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.7813 (ptt90) REVERT: B 408 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8416 (ttt-90) REVERT: B 450 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8409 (tp) REVERT: B 467 ILE cc_start: 0.7073 (mm) cc_final: 0.6811 (mt) REVERT: B 502 GLU cc_start: 0.8602 (tt0) cc_final: 0.8080 (mp0) REVERT: B 513 TYR cc_start: 0.8163 (t80) cc_final: 0.7723 (t80) REVERT: B 557 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: B 567 MET cc_start: 0.7826 (tpt) cc_final: 0.7468 (tpt) REVERT: B 571 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.7068 (mp10) REVERT: C 1 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.6623 (mmt) REVERT: C 124 LYS cc_start: 0.8222 (mppt) cc_final: 0.7592 (mmmt) REVERT: C 323 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8000 (mmt) REVERT: C 441 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: C 532 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5556 (mtp85) REVERT: C 550 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.7626 (ttm-80) REVERT: D 413 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8369 (mp10) REVERT: E 410 ARG cc_start: 0.7481 (ttm110) cc_final: 0.7150 (ttt90) REVERT: E 442 LEU cc_start: 0.8502 (pt) cc_final: 0.8205 (mp) REVERT: F 370 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7610 (mptt) REVERT: F 373 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8121 (pt0) REVERT: G 38 GLU cc_start: 0.7758 (tt0) cc_final: 0.7111 (tp30) REVERT: G 104 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5804 (tt) REVERT: G 137 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7288 (mt) REVERT: G 148 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7269 (mttp) REVERT: G 149 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7544 (mppt) REVERT: H 77 LEU cc_start: 0.6339 (tp) cc_final: 0.6130 (tp) REVERT: H 91 ARG cc_start: 0.6530 (mmm160) cc_final: 0.5865 (mmp80) REVERT: J 148 LEU cc_start: 0.2863 (tp) cc_final: 0.2511 (pp) REVERT: J 164 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5336 (tp30) REVERT: K 91 ARG cc_start: 0.4641 (ttm170) cc_final: 0.4346 (mtp85) REVERT: L 136 ARG cc_start: 0.6190 (mmm160) cc_final: 0.5837 (mmp-170) outliers start: 72 outliers final: 26 residues processed: 314 average time/residue: 0.8556 time to fit residues: 305.0272 Evaluate side-chains 294 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 338 optimal weight: 30.0000 chunk 182 optimal weight: 0.0970 chunk 238 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 371 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN F 23 ASN ** F 437 GLN ** 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 = 0.3524 r_free = 0.3524 target = 0.118694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.085855 restraints weight = 44552.792| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.68 r_work: 0.2922 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 30074 Z= 0.234 Angle : 0.609 9.742 40754 Z= 0.313 Chirality : 0.047 0.173 4567 Planarity : 0.005 0.055 5336 Dihedral : 6.558 169.699 4230 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.82 % Allowed : 13.72 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.81 (0.14), residues: 3761 helix: 1.55 (0.13), residues: 1536 sheet: -0.02 (0.21), residues: 571 loop : -0.13 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 453 TYR 0.015 0.002 TYR C 428 PHE 0.016 0.002 PHE F 130 TRP 0.014 0.002 TRP A 119 HIS 0.006 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00579 (30074) covalent geometry : angle 0.60930 (40754) hydrogen bonds : bond 0.05762 ( 1269) hydrogen bonds : angle 4.60633 ( 3618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 266 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8359 (mmm) cc_final: 0.8122 (mmt) REVERT: A 124 LYS cc_start: 0.8368 (ptpp) cc_final: 0.7820 (mttp) REVERT: A 154 ARG cc_start: 0.7864 (ptm160) cc_final: 0.7294 (ptt90) REVERT: A 323 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8025 (mtt) REVERT: A 374 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: A 416 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8068 (ttm-80) REVERT: A 502 GLU cc_start: 0.8050 (pm20) cc_final: 0.7722 (mp0) REVERT: A 524 LYS cc_start: 0.8622 (ptmt) cc_final: 0.8002 (mttt) REVERT: A 546 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 547 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7424 (ttt90) REVERT: A 550 ARG cc_start: 0.8242 (mmt90) cc_final: 0.7182 (mtp-110) REVERT: B 1 MET cc_start: 0.7059 (ttm) cc_final: 0.6838 (ttm) REVERT: B 93 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7418 (mpp80) REVERT: B 170 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7382 (tp30) REVERT: B 276 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7673 (ttmm) REVERT: B 314 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.7895 (ptt90) REVERT: B 408 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8407 (ttt-90) REVERT: B 450 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8413 (tp) REVERT: B 467 ILE cc_start: 0.7126 (mm) cc_final: 0.6771 (mt) REVERT: B 502 GLU cc_start: 0.8606 (tt0) cc_final: 0.8142 (mp0) REVERT: C 124 LYS cc_start: 0.8326 (mppt) cc_final: 0.7664 (mmmt) REVERT: C 323 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.7933 (mmt) REVERT: C 441 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: C 480 GLU cc_start: 0.6933 (pt0) cc_final: 0.6590 (pm20) REVERT: C 532 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.5780 (mtp85) REVERT: C 550 ARG cc_start: 0.8406 (ttp-110) cc_final: 0.7740 (ttm-80) REVERT: D 206 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: D 413 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8432 (mp10) REVERT: E 410 ARG cc_start: 0.7460 (ttm110) cc_final: 0.7198 (ttt90) REVERT: E 470 ILE cc_start: 0.5293 (OUTLIER) cc_final: 0.5036 (mp) REVERT: F 373 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8186 (pt0) REVERT: G 104 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5685 (tt) REVERT: G 137 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7189 (mt) REVERT: G 148 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7364 (mttp) REVERT: G 149 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7527 (mppt) REVERT: H 77 LEU cc_start: 0.6341 (tp) cc_final: 0.6140 (tp) REVERT: H 91 ARG cc_start: 0.6528 (mmm160) cc_final: 0.5854 (mmp80) REVERT: J 148 LEU cc_start: 0.2694 (OUTLIER) cc_final: 0.2432 (pp) REVERT: J 164 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5349 (tp30) REVERT: J 172 ASP cc_start: 0.5734 (m-30) cc_final: 0.5351 (m-30) REVERT: K 91 ARG cc_start: 0.4531 (ttm170) cc_final: 0.4202 (mtp85) REVERT: L 184 GLN cc_start: 0.6060 (tt0) cc_final: 0.5767 (tm130) outliers start: 87 outliers final: 40 residues processed: 335 average time/residue: 0.7914 time to fit residues: 302.6102 Evaluate side-chains 311 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 251 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 410 ARG Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 75 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 361 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 279 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.088677 restraints weight = 44499.263| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.62 r_work: 0.2966 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30074 Z= 0.118 Angle : 0.507 10.043 40754 Z= 0.259 Chirality : 0.043 0.150 4567 Planarity : 0.004 0.050 5336 Dihedral : 5.991 154.204 4230 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.27 % Allowed : 14.57 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.11 (0.14), residues: 3761 helix: 1.87 (0.14), residues: 1545 sheet: 0.08 (0.22), residues: 580 loop : -0.04 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 453 TYR 0.017 0.001 TYR B 513 PHE 0.016 0.001 PHE A 230 TRP 0.016 0.001 TRP A 119 HIS 0.004 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00271 (30074) covalent geometry : angle 0.50678 (40754) hydrogen bonds : bond 0.04362 ( 1269) hydrogen bonds : angle 4.35603 ( 3618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 263 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8380 (ptpp) cc_final: 0.7867 (mttp) REVERT: A 154 ARG cc_start: 0.7856 (ptm160) cc_final: 0.7272 (ptt90) REVERT: A 323 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.7920 (mtt) REVERT: A 374 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: A 416 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8022 (ttm-80) REVERT: A 502 GLU cc_start: 0.8059 (pm20) cc_final: 0.7754 (mp0) REVERT: A 547 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7358 (ttt90) REVERT: A 550 ARG cc_start: 0.8250 (mmt90) cc_final: 0.7213 (mtp-110) REVERT: B 1 MET cc_start: 0.7013 (ttm) cc_final: 0.6778 (ttm) REVERT: B 170 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: B 276 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7628 (ttmm) REVERT: B 314 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7794 (ptt90) REVERT: B 408 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8402 (ttt-90) REVERT: B 467 ILE cc_start: 0.7005 (mm) cc_final: 0.6721 (mt) REVERT: B 502 GLU cc_start: 0.8559 (tt0) cc_final: 0.8082 (mp0) REVERT: B 567 MET cc_start: 0.8014 (tpt) cc_final: 0.7658 (tpt) REVERT: C 1 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.6630 (mmt) REVERT: C 124 LYS cc_start: 0.8288 (mppt) cc_final: 0.7640 (mmmt) REVERT: C 323 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.7975 (mmt) REVERT: C 441 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: C 470 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.5783 (tp) REVERT: C 532 ARG cc_start: 0.5796 (OUTLIER) cc_final: 0.5447 (mtp85) REVERT: C 550 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.7666 (ttm-80) REVERT: D 413 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8345 (mp10) REVERT: D 416 ASP cc_start: 0.8475 (m-30) cc_final: 0.8155 (m-30) REVERT: E 410 ARG cc_start: 0.7403 (ttm110) cc_final: 0.7066 (ttt90) REVERT: F 373 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8075 (pt0) REVERT: G 104 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5733 (tt) REVERT: G 137 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7284 (mt) REVERT: G 148 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7268 (mttp) REVERT: G 149 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7505 (mppt) REVERT: H 91 ARG cc_start: 0.6490 (mmm160) cc_final: 0.5825 (mmp80) REVERT: J 80 LEU cc_start: 0.5591 (OUTLIER) cc_final: 0.5360 (mm) REVERT: J 148 LEU cc_start: 0.2823 (tp) cc_final: 0.2473 (pp) REVERT: J 164 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5344 (tp30) REVERT: J 172 ASP cc_start: 0.5774 (m-30) cc_final: 0.5329 (OUTLIER) REVERT: K 91 ARG cc_start: 0.4636 (ttm170) cc_final: 0.4307 (mtp85) REVERT: L 85 ARG cc_start: 0.5823 (ttp80) cc_final: 0.5578 (ttp80) REVERT: L 184 GLN cc_start: 0.6076 (tt0) cc_final: 0.5798 (tm130) outliers start: 70 outliers final: 29 residues processed: 318 average time/residue: 0.7876 time to fit residues: 285.6265 Evaluate side-chains 299 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 282 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 287 optimal weight: 1.9990 chunk 335 optimal weight: 30.0000 chunk 283 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 300 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.087678 restraints weight = 44699.172| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.64 r_work: 0.2945 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30074 Z= 0.153 Angle : 0.535 8.468 40754 Z= 0.274 Chirality : 0.044 0.164 4567 Planarity : 0.005 0.050 5336 Dihedral : 5.931 141.869 4230 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.47 % Allowed : 14.80 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.08 (0.14), residues: 3761 helix: 1.81 (0.14), residues: 1554 sheet: 0.10 (0.22), residues: 580 loop : -0.03 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 453 TYR 0.012 0.001 TYR F 203 PHE 0.015 0.001 PHE C 559 TRP 0.014 0.001 TRP A 119 HIS 0.005 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00371 (30074) covalent geometry : angle 0.53544 (40754) hydrogen bonds : bond 0.04712 ( 1269) hydrogen bonds : angle 4.39306 ( 3618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 262 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8368 (ptpp) cc_final: 0.7868 (mttp) REVERT: A 154 ARG cc_start: 0.7856 (ptm160) cc_final: 0.7253 (ptt90) REVERT: A 323 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.7969 (mtt) REVERT: A 374 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: A 416 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8081 (ttm-80) REVERT: A 502 GLU cc_start: 0.8053 (pm20) cc_final: 0.7748 (mp0) REVERT: A 547 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7394 (ttt90) REVERT: A 550 ARG cc_start: 0.8205 (mmt90) cc_final: 0.7229 (mtp-110) REVERT: B 1 MET cc_start: 0.6985 (ttm) cc_final: 0.6729 (ttm) REVERT: B 170 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: B 276 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7648 (ttmm) REVERT: B 314 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7838 (ptt90) REVERT: B 408 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8414 (ttt-90) REVERT: B 467 ILE cc_start: 0.6989 (mm) cc_final: 0.6689 (mt) REVERT: B 502 GLU cc_start: 0.8598 (tt0) cc_final: 0.8080 (mp0) REVERT: B 567 MET cc_start: 0.7947 (tpt) cc_final: 0.7572 (tpt) REVERT: C 1 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.6598 (mmt) REVERT: C 46 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8893 (p) REVERT: C 124 LYS cc_start: 0.8306 (mppt) cc_final: 0.7658 (mmmt) REVERT: C 323 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.7992 (mmt) REVERT: C 441 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: C 480 GLU cc_start: 0.6911 (pt0) cc_final: 0.6643 (pm20) REVERT: C 532 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.5524 (mtp85) REVERT: C 550 ARG cc_start: 0.8369 (ttp-110) cc_final: 0.7665 (ttm-80) REVERT: D 413 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8363 (mp10) REVERT: E 410 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7122 (ttt90) REVERT: E 442 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8139 (mt) REVERT: F 373 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8097 (pt0) REVERT: G 137 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7290 (mt) REVERT: G 148 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7369 (mttp) REVERT: G 149 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7540 (mppt) REVERT: H 91 ARG cc_start: 0.6517 (mmm160) cc_final: 0.5861 (mmp80) REVERT: J 80 LEU cc_start: 0.5563 (OUTLIER) cc_final: 0.5304 (mm) REVERT: J 148 LEU cc_start: 0.2770 (OUTLIER) cc_final: 0.2457 (pp) REVERT: J 164 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5383 (tp30) REVERT: J 172 ASP cc_start: 0.5801 (m-30) cc_final: 0.5342 (OUTLIER) REVERT: K 91 ARG cc_start: 0.4636 (ttm170) cc_final: 0.4314 (mtp85) REVERT: L 184 GLN cc_start: 0.6079 (tt0) cc_final: 0.5801 (tm130) outliers start: 76 outliers final: 43 residues processed: 324 average time/residue: 0.8002 time to fit residues: 296.7420 Evaluate side-chains 311 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 250 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 256 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 249 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 372 optimal weight: 20.0000 chunk 152 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 296 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.088979 restraints weight = 44495.362| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.69 r_work: 0.2971 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30074 Z= 0.114 Angle : 0.507 8.376 40754 Z= 0.258 Chirality : 0.043 0.166 4567 Planarity : 0.004 0.049 5336 Dihedral : 5.543 119.655 4230 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.11 % Allowed : 15.25 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.22 (0.14), residues: 3761 helix: 1.96 (0.14), residues: 1553 sheet: 0.15 (0.22), residues: 580 loop : 0.01 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 453 TYR 0.014 0.001 TYR H 89 PHE 0.015 0.001 PHE A 230 TRP 0.015 0.001 TRP A 119 HIS 0.004 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00265 (30074) covalent geometry : angle 0.50689 (40754) hydrogen bonds : bond 0.04106 ( 1269) hydrogen bonds : angle 4.27456 ( 3618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8354 (ptpp) cc_final: 0.7880 (mttp) REVERT: A 154 ARG cc_start: 0.7858 (ptm160) cc_final: 0.7264 (ptt90) REVERT: A 323 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.7892 (mtt) REVERT: A 416 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8051 (ttm-80) REVERT: A 502 GLU cc_start: 0.8040 (pm20) cc_final: 0.7745 (mp0) REVERT: A 524 LYS cc_start: 0.8560 (ptmt) cc_final: 0.7958 (mttt) REVERT: A 547 ARG cc_start: 0.7820 (ttm-80) cc_final: 0.7363 (ttt90) REVERT: A 550 ARG cc_start: 0.8209 (mmt90) cc_final: 0.7226 (mtp-110) REVERT: B 1 MET cc_start: 0.6968 (ttm) cc_final: 0.6678 (ttm) REVERT: B 170 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7464 (tp30) REVERT: B 314 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.7783 (ptt90) REVERT: B 408 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8400 (ttt-90) REVERT: B 467 ILE cc_start: 0.6954 (mm) cc_final: 0.6684 (mt) REVERT: B 502 GLU cc_start: 0.8607 (tt0) cc_final: 0.8128 (mp0) REVERT: B 513 TYR cc_start: 0.8132 (t80) cc_final: 0.7652 (t80) REVERT: B 547 ARG cc_start: 0.7422 (tpp-160) cc_final: 0.7191 (mpp-170) REVERT: B 567 MET cc_start: 0.8023 (tpt) cc_final: 0.7636 (tpt) REVERT: C 1 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.6597 (mmt) REVERT: C 46 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8894 (p) REVERT: C 124 LYS cc_start: 0.8313 (mppt) cc_final: 0.7669 (mmmt) REVERT: C 323 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8015 (mmt) REVERT: C 441 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: C 480 GLU cc_start: 0.6839 (pt0) cc_final: 0.6578 (pm20) REVERT: C 532 ARG cc_start: 0.5649 (OUTLIER) cc_final: 0.5376 (mtp85) REVERT: C 550 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.7662 (ttm-80) REVERT: D 413 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8343 (mp10) REVERT: D 416 ASP cc_start: 0.8448 (m-30) cc_final: 0.8176 (m-30) REVERT: E 410 ARG cc_start: 0.7420 (ttm110) cc_final: 0.7081 (ttt90) REVERT: F 373 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8071 (pt0) REVERT: F 413 GLN cc_start: 0.8477 (mt0) cc_final: 0.8197 (mt0) REVERT: G 144 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7593 (mm-30) REVERT: G 148 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7351 (mttp) REVERT: G 149 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7495 (mppt) REVERT: H 91 ARG cc_start: 0.6470 (mmm160) cc_final: 0.5825 (mmp80) REVERT: J 80 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.5273 (mm) REVERT: J 148 LEU cc_start: 0.2811 (tp) cc_final: 0.2488 (pp) REVERT: J 164 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5328 (tp30) REVERT: J 172 ASP cc_start: 0.5623 (m-30) cc_final: 0.5182 (m-30) REVERT: K 91 ARG cc_start: 0.4629 (ttm170) cc_final: 0.4310 (mtp85) REVERT: K 104 MET cc_start: 0.5773 (ttm) cc_final: 0.5424 (ttp) REVERT: L 134 LEU cc_start: 0.5198 (OUTLIER) cc_final: 0.4791 (tm) REVERT: L 184 GLN cc_start: 0.6067 (tt0) cc_final: 0.5800 (tm130) outliers start: 65 outliers final: 31 residues processed: 316 average time/residue: 0.8395 time to fit residues: 302.8204 Evaluate side-chains 297 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 337 optimal weight: 0.8980 chunk 232 optimal weight: 0.4980 chunk 358 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 336 optimal weight: 0.3980 chunk 253 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 541 GLN A 571 GLN ** F 437 GLN ** 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 = 0.3571 r_free = 0.3571 target = 0.122192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.089389 restraints weight = 44390.727| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.73 r_work: 0.2977 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30074 Z= 0.104 Angle : 0.498 8.174 40754 Z= 0.253 Chirality : 0.042 0.166 4567 Planarity : 0.004 0.063 5336 Dihedral : 5.391 110.155 4230 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.75 % Allowed : 15.90 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.30 (0.14), residues: 3761 helix: 2.01 (0.14), residues: 1554 sheet: 0.19 (0.22), residues: 580 loop : 0.07 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 453 TYR 0.010 0.001 TYR H 89 PHE 0.014 0.001 PHE A 230 TRP 0.014 0.001 TRP A 119 HIS 0.004 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00236 (30074) covalent geometry : angle 0.49788 (40754) hydrogen bonds : bond 0.03939 ( 1269) hydrogen bonds : angle 4.23087 ( 3618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 259 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8367 (ptpp) cc_final: 0.7898 (mttp) REVERT: A 154 ARG cc_start: 0.7882 (ptm160) cc_final: 0.7274 (ptt90) REVERT: A 323 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.7883 (mtt) REVERT: A 416 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8039 (ttm-80) REVERT: A 502 GLU cc_start: 0.8045 (pm20) cc_final: 0.7746 (mp0) REVERT: A 524 LYS cc_start: 0.8578 (ptmt) cc_final: 0.7959 (mttt) REVERT: A 547 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7345 (ttt90) REVERT: A 550 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7205 (mtp-110) REVERT: B 130 ARG cc_start: 0.7880 (mmp-170) cc_final: 0.7560 (mmp-170) REVERT: B 154 ARG cc_start: 0.8356 (mtp180) cc_final: 0.7924 (ttp-170) REVERT: B 170 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: B 314 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7833 (ptt90) REVERT: B 408 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.8389 (ttt-90) REVERT: B 467 ILE cc_start: 0.6939 (mm) cc_final: 0.6663 (mt) REVERT: B 502 GLU cc_start: 0.8582 (tt0) cc_final: 0.8110 (mp0) REVERT: B 547 ARG cc_start: 0.7385 (tpp-160) cc_final: 0.6823 (tpp80) REVERT: B 567 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7632 (tpt) REVERT: C 1 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.6608 (mmt) REVERT: C 46 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8895 (p) REVERT: C 124 LYS cc_start: 0.8330 (mppt) cc_final: 0.7683 (mmmt) REVERT: C 323 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8011 (mmt) REVERT: C 441 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: C 480 GLU cc_start: 0.6839 (pt0) cc_final: 0.6569 (pm20) REVERT: C 532 ARG cc_start: 0.5673 (OUTLIER) cc_final: 0.5410 (mtp85) REVERT: C 550 ARG cc_start: 0.8326 (ttp-110) cc_final: 0.7629 (ttm-80) REVERT: D 413 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: E 410 ARG cc_start: 0.7411 (ttm110) cc_final: 0.7066 (ttt90) REVERT: F 128 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8214 (mm-30) REVERT: F 370 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7526 (mptt) REVERT: F 373 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: F 413 GLN cc_start: 0.8490 (mt0) cc_final: 0.8207 (mt0) REVERT: G 148 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7392 (mttp) REVERT: G 149 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7530 (mppt) REVERT: H 91 ARG cc_start: 0.6461 (mmm160) cc_final: 0.5812 (mmp80) REVERT: J 80 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.5270 (mm) REVERT: J 148 LEU cc_start: 0.2814 (tp) cc_final: 0.2497 (pp) REVERT: J 164 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5325 (tp30) REVERT: J 172 ASP cc_start: 0.5668 (m-30) cc_final: 0.5224 (m-30) REVERT: K 91 ARG cc_start: 0.4573 (ttm170) cc_final: 0.4275 (mtp85) REVERT: L 134 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.4758 (tm) REVERT: L 184 GLN cc_start: 0.6087 (tt0) cc_final: 0.5821 (tm130) outliers start: 54 outliers final: 29 residues processed: 303 average time/residue: 0.7870 time to fit residues: 273.4096 Evaluate side-chains 296 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 317 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 217 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 286 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 541 GLN A 571 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 180 GLN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.086222 restraints weight = 44858.468| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.66 r_work: 0.2926 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 30074 Z= 0.232 Angle : 0.611 9.514 40754 Z= 0.313 Chirality : 0.047 0.169 4567 Planarity : 0.005 0.072 5336 Dihedral : 5.840 100.325 4230 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.34 % Allowed : 15.44 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.89 (0.14), residues: 3761 helix: 1.63 (0.13), residues: 1547 sheet: -0.02 (0.22), residues: 586 loop : -0.10 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 453 TYR 0.017 0.002 TYR C 428 PHE 0.017 0.002 PHE C 415 TRP 0.011 0.002 TRP A 119 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00573 (30074) covalent geometry : angle 0.61132 (40754) hydrogen bonds : bond 0.05512 ( 1269) hydrogen bonds : angle 4.51085 ( 3618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11105.50 seconds wall clock time: 189 minutes 15.18 seconds (11355.18 seconds total)