Starting phenix.real_space_refine on Fri Feb 6 19:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u6n_63914/02_2026/9u6n_63914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u6n_63914/02_2026/9u6n_63914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u6n_63914/02_2026/9u6n_63914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u6n_63914/02_2026/9u6n_63914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u6n_63914/02_2026/9u6n_63914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u6n_63914/02_2026/9u6n_63914.map" } resolution = 2.85 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= -0.001 sd= 0.052 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 7 5.49 5 Mg 3 5.21 5 S 101 5.16 5 C 17124 2.51 5 N 4648 2.21 5 O 5098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 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: 26981 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4478 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4478 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4478 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3683 Classifications: {'peptide': 470} Modifications used: {'COO': 1} 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: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1620 Classifications: {'peptide': 206} Modifications used: {'COO': 1} 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: "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: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" 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} Time building chain proxies: 6.50, per 1000 atoms: 0.24 Number of scatterers: 26981 At special positions: 0 Unit cell: (138.06, 145.14, 161.66, 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 101 16.00 P 7 15.00 Mg 3 11.99 O 5098 8.00 N 4648 7.00 C 17124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 842.7 milliseconds 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6278 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 25 sheets defined 43.9% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.787A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.723A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (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 315 removed outlier: 4.300A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.676A pdb=" N ALA A 331 " --> pdb=" O THR A 327 " (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 removed outlier: 3.832A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.540A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.268A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.594A 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 removed outlier: 3.760A pdb=" N VAL A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 532 removed outlier: 3.595A pdb=" N LYS A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.750A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 540 " --> pdb=" O ILE A 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 535 through 540' Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.662A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.740A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.816A pdb=" N LYS B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.568A pdb=" N GLN B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.562A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) 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 301 Processing helix chain 'B' and resid 301 through 315 removed outlier: 3.509A pdb=" N VAL B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.877A 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 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.927A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 removed outlier: 3.512A pdb=" N ASP B 436 " --> pdb=" O THR B 432 " (cutoff:3.500A) Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 463 removed outlier: 3.991A pdb=" N ASP B 452 " --> pdb=" O PRO B 448 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.657A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 464 through 469' Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 494 removed outlier: 4.161A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 531 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.685A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 removed outlier: 3.897A pdb=" N VAL B 554 " --> pdb=" O ALA B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 558 through 575 removed outlier: 3.795A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.972A pdb=" N GLU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 259 through 269 removed outlier: 3.558A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.283A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 353 through 364 removed outlier: 4.216A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.582A pdb=" N GLY C 389 " --> pdb=" O PRO C 386 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.865A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.504A pdb=" N ALA C 414 " --> pdb=" O ASP C 410 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 removed outlier: 3.568A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 465 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 477 through 494 removed outlier: 4.242A pdb=" N VAL C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 544 through 550 removed outlier: 3.843A pdb=" N ILE C 548 " --> pdb=" O VAL C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 577 removed outlier: 4.138A pdb=" N GLU C 564 " --> pdb=" O PRO C 560 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.628A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.696A pdb=" N ARG D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 removed outlier: 3.618A pdb=" N MET D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.514A pdb=" N LEU D 177 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 210 removed outlier: 3.506A pdb=" N GLU D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 removed outlier: 3.505A pdb=" N SER D 215 " --> pdb=" O GLY D 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 215' Processing helix chain 'D' and resid 227 through 250 removed outlier: 3.697A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.835A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.591A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.692A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 331 removed outlier: 3.546A pdb=" N TYR D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 365 removed outlier: 3.518A pdb=" N ASN D 364 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.788A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.142A 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 455 through 463 Processing helix chain 'D' and resid 467 through 472 removed outlier: 3.564A pdb=" N GLY D 472 " --> pdb=" O GLU D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.733A pdb=" N MET E 88 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 89' Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.608A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.604A pdb=" N LEU E 177 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 229 through 250 removed outlier: 3.994A pdb=" N LEU E 233 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.877A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.513A 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 removed outlier: 3.538A pdb=" N LYS E 346 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 365 removed outlier: 3.867A pdb=" N ASN E 364 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.990A 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 removed outlier: 3.521A pdb=" N ARG E 420 " --> pdb=" O ASP E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'F' and resid 85 through 89 removed outlier: 4.137A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' 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 removed outlier: 3.637A pdb=" N TYR F 203 " --> pdb=" O ARG F 199 " (cutoff:3.500A) 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 227 through 232 removed outlier: 3.648A pdb=" N GLU F 230 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.825A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 3.816A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.632A 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 Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.614A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU F 395 " --> pdb=" O ASP F 391 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 removed outlier: 3.502A pdb=" N ARG F 420 " --> pdb=" O ASP F 416 " (cutoff:3.500A) 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 removed outlier: 3.713A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 470 Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.704A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU G 59 " --> pdb=" O GLN G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 82 removed outlier: 3.587A pdb=" N VAL G 76 " --> pdb=" O GLY G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 167 removed outlier: 4.246A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE G 138 " --> pdb=" O ALA G 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU G 153 " --> pdb=" O LYS G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 205 removed outlier: 3.748A pdb=" N GLY G 171 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU G 194 " --> pdb=" O ASP G 190 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY G 199 " --> pdb=" O LYS G 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 16 removed outlier: 3.583A pdb=" N ALA H 10 " --> pdb=" O ASP H 6 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN H 11 " --> pdb=" O PRO H 7 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA H 16 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 38 Processing helix chain 'H' and resid 54 through 59 removed outlier: 3.705A pdb=" N ALA H 58 " --> pdb=" O ASP H 54 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL H 59 " --> pdb=" O PRO H 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 54 through 59' Processing helix chain 'H' and resid 60 through 63 Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.709A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 98 removed outlier: 4.242A pdb=" N TYR H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.650A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.219A 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: 5.641A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.682A 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: 6.024A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (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: 5.921A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.833A 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: 6.501A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.009A 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: 5.703A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.595A 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: 5.781A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) 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 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 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 117 through 119 Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.957A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.712A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA8, 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 291 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 291 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=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 143 through 148 removed outlier: 3.877A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 164 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.939A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (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 144 through 148 removed outlier: 3.956A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 5.964A 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: 6.929A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 173 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.602A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 92 through 93 removed outlier: 3.511A pdb=" N LEU D 257 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.768A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.577A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 93 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 92 through 93 current: chain 'E' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 217 through 223 current: chain 'E' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 307 through 315 current: chain 'E' and resid 358 through 359 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.524A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC4, first strand: chain 'F' and resid 92 through 93 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 93 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=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC6, first strand: chain 'G' and resid 92 through 96 Processing sheet with id=AC7, first strand: chain 'H' and resid 19 through 22 1012 hydrogen bonds defined for protein. 2886 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: 4.45 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4684 1.32 - 1.45: 6840 1.45 - 1.57: 15783 1.57 - 1.70: 11 1.70 - 1.83: 190 Bond restraints: 27508 Sorted by residual: bond pdb=" CA SER C 232 " pdb=" CB SER C 232 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.58e-02 4.01e+03 2.06e+01 bond pdb=" CA SER B 232 " pdb=" CB SER B 232 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.54e-02 4.22e+03 1.17e+01 bond pdb=" CA SER A 232 " pdb=" CB SER A 232 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.74e-02 3.30e+03 1.15e+01 bond pdb=" O3 PO4 B 601 " pdb=" P PO4 B 601 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" O2 PO4 B 601 " pdb=" P PO4 B 601 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.57e+00 ... (remaining 27503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 36880 2.88 - 5.75: 348 5.75 - 8.63: 48 8.63 - 11.50: 9 11.50 - 14.38: 4 Bond angle restraints: 37289 Sorted by residual: angle pdb=" CA LYS D 183 " pdb=" CB LYS D 183 " pdb=" CG LYS D 183 " ideal model delta sigma weight residual 114.10 125.52 -11.42 2.00e+00 2.50e-01 3.26e+01 angle pdb=" CA PHE C 230 " pdb=" CB PHE C 230 " pdb=" CG PHE C 230 " ideal model delta sigma weight residual 113.80 119.51 -5.71 1.00e+00 1.00e+00 3.26e+01 angle pdb=" CA PHE A 230 " pdb=" CB PHE A 230 " pdb=" CG PHE A 230 " ideal model delta sigma weight residual 113.80 118.98 -5.18 1.00e+00 1.00e+00 2.69e+01 angle pdb=" CA GLU F 128 " pdb=" CB GLU F 128 " pdb=" CG GLU F 128 " ideal model delta sigma weight residual 114.10 124.34 -10.24 2.00e+00 2.50e-01 2.62e+01 angle pdb=" C GLU B 347 " pdb=" CA GLU B 347 " pdb=" CB GLU B 347 " ideal model delta sigma weight residual 116.54 110.68 5.86 1.15e+00 7.56e-01 2.59e+01 ... (remaining 37284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 15555 23.20 - 46.41: 969 46.41 - 69.61: 130 69.61 - 92.82: 39 92.82 - 116.02: 2 Dihedral angle restraints: 16695 sinusoidal: 6846 harmonic: 9849 Sorted by residual: dihedral pdb=" O1B ADP B 603 " pdb=" O3A ADP B 603 " pdb=" PB ADP B 603 " pdb=" PA ADP B 603 " ideal model delta sinusoidal sigma weight residual -60.00 -176.03 116.02 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" O1B ADP A 602 " pdb=" O3A ADP A 602 " pdb=" PB ADP A 602 " pdb=" PA ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 -156.44 96.44 1 2.00e+01 2.50e-03 2.67e+01 dihedral pdb=" CA LYS B 575 " pdb=" C LYS B 575 " pdb=" N ALA B 576 " pdb=" CA ALA B 576 " ideal model delta harmonic sigma weight residual 180.00 158.93 21.07 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 16692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3096 0.048 - 0.095: 789 0.095 - 0.143: 259 0.143 - 0.190: 11 0.190 - 0.238: 6 Chirality restraints: 4161 Sorted by residual: 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 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL H 37 " pdb=" CA VAL H 37 " pdb=" CG1 VAL H 37 " pdb=" CG2 VAL H 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE B 226 " pdb=" CA ILE B 226 " pdb=" CG1 ILE B 226 " pdb=" CG2 ILE B 226 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 4158 not shown) Planarity restraints: 4874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 229 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.83e+00 pdb=" C PRO C 229 " 0.051 2.00e-02 2.50e+03 pdb=" O PRO C 229 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE C 230 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 290 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" CG ASP E 290 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP E 290 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP E 290 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 318 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" CG ASP F 318 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP F 318 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 318 " -0.015 2.00e-02 2.50e+03 ... (remaining 4871 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 3 2.09 - 2.79: 6207 2.79 - 3.49: 34747 3.49 - 4.20: 59926 4.20 - 4.90: 110218 Nonbonded interactions: 211101 Sorted by model distance: nonbonded pdb=" OG1 THR B 235 " pdb="MG MG B 602 " model vdw 1.382 2.170 nonbonded pdb=" O1B ADP C 601 " pdb="MG MG C 602 " model vdw 2.057 2.170 nonbonded pdb=" OG1 THR A 235 " pdb="MG MG A 601 " model vdw 2.059 2.170 nonbonded pdb="MG MG A 601 " pdb=" O2B ADP A 602 " model vdw 2.118 2.170 nonbonded pdb=" O LEU H 93 " pdb=" OG1 THR H 97 " model vdw 2.175 3.040 ... (remaining 211096 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 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 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) } 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: 2.590 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.620 Find NCS groups from input model: 0.530 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: 0.000 Load rotamer database and sin/cos tables:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.004 0.072 27508 Z= 0.190 Angle : 0.753 14.379 37289 Z= 0.416 Chirality : 0.047 0.238 4161 Planarity : 0.006 0.088 4874 Dihedral : 15.115 116.025 10417 Min Nonbonded Distance : 1.382 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.74 % Allowed : 14.16 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.23 (0.14), residues: 3437 helix: 0.42 (0.15), residues: 1268 sheet: 0.56 (0.24), residues: 556 loop : -0.06 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 57 TYR 0.026 0.001 TYR H 21 PHE 0.029 0.001 PHE C 230 TRP 0.009 0.001 TRP F 471 HIS 0.003 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00390 (27508) covalent geometry : angle 0.75344 (37289) hydrogen bonds : bond 0.18553 ( 1012) hydrogen bonds : angle 6.32422 ( 2886) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 451 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8589 (mt0) cc_final: 0.8179 (mp10) REVERT: A 45 ASP cc_start: 0.7742 (t0) cc_final: 0.7191 (t0) REVERT: A 213 ASP cc_start: 0.8269 (m-30) cc_final: 0.7979 (m-30) REVERT: A 290 ASN cc_start: 0.7991 (t0) cc_final: 0.7762 (t0) REVERT: A 393 GLU cc_start: 0.7039 (tt0) cc_final: 0.6781 (tt0) REVERT: A 488 ARG cc_start: 0.7678 (ttp80) cc_final: 0.6607 (tmm160) REVERT: A 489 ILE cc_start: 0.7788 (mm) cc_final: 0.7506 (mt) REVERT: A 492 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8036 (mp0) REVERT: B 304 TYR cc_start: 0.8457 (m-80) cc_final: 0.7942 (m-80) REVERT: B 325 ASP cc_start: 0.8447 (t0) cc_final: 0.8101 (t70) REVERT: B 332 GLU cc_start: 0.7576 (tp30) cc_final: 0.7193 (tm-30) REVERT: B 343 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7933 (mm-30) REVERT: B 363 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7662 (tp30) REVERT: B 476 LEU cc_start: 0.8711 (mp) cc_final: 0.8493 (mp) REVERT: B 480 GLU cc_start: 0.8264 (mp0) cc_final: 0.7984 (mp0) REVERT: B 485 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7972 (mm-30) REVERT: C 24 MET cc_start: 0.8803 (mmm) cc_final: 0.8527 (tpt) REVERT: C 122 MET cc_start: 0.9043 (mtp) cc_final: 0.8800 (mtm) REVERT: C 133 MET cc_start: 0.7823 (mtm) cc_final: 0.7436 (mtp) REVERT: C 410 ASP cc_start: 0.7794 (t0) cc_final: 0.7306 (t0) REVERT: C 467 ILE cc_start: 0.7424 (mt) cc_final: 0.7059 (mt) REVERT: C 481 ARG cc_start: 0.7913 (mtp180) cc_final: 0.7521 (mtp-110) REVERT: C 534 VAL cc_start: 0.6535 (t) cc_final: 0.6168 (p) REVERT: C 567 MET cc_start: 0.8493 (mmm) cc_final: 0.7850 (mmm) REVERT: D 52 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7676 (mt-10) REVERT: D 275 GLU cc_start: 0.7984 (mp0) cc_final: 0.7610 (mp0) REVERT: D 391 ASP cc_start: 0.7515 (t70) cc_final: 0.7302 (p0) REVERT: E 25 LYS cc_start: 0.8981 (ttpp) cc_final: 0.8490 (tppp) REVERT: E 226 ASP cc_start: 0.7523 (m-30) cc_final: 0.6934 (m-30) REVERT: E 243 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7755 (mt-10) REVERT: E 302 GLU cc_start: 0.7786 (tp30) cc_final: 0.7369 (tt0) REVERT: E 398 ILE cc_start: 0.8876 (mt) cc_final: 0.8665 (mm) REVERT: E 465 GLN cc_start: 0.6816 (mp10) cc_final: 0.6560 (tp-100) REVERT: E 467 LEU cc_start: 0.7211 (tm) cc_final: 0.6918 (mt) REVERT: F 6 LYS cc_start: 0.5801 (mmtt) cc_final: 0.5421 (mmtt) REVERT: F 36 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7957 (tmmt) REVERT: F 81 ARG cc_start: 0.8342 (mtt180) cc_final: 0.7967 (mpp80) REVERT: F 109 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7856 (tp30) REVERT: F 200 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7332 (mp0) REVERT: F 334 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8039 (mt-10) REVERT: F 345 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8182 (ttp-170) REVERT: F 465 GLN cc_start: 0.7822 (mt0) cc_final: 0.7595 (tt0) REVERT: G 47 MET cc_start: 0.7970 (ttm) cc_final: 0.7718 (ptt) REVERT: G 133 TYR cc_start: 0.7718 (t80) cc_final: 0.7148 (t80) REVERT: G 184 GLU cc_start: 0.6802 (tp30) cc_final: 0.6224 (tp30) REVERT: G 185 GLN cc_start: 0.7434 (tp-100) cc_final: 0.7195 (tp40) REVERT: G 187 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7593 (pp20) REVERT: H 21 TYR cc_start: 0.6848 (m-10) cc_final: 0.6621 (m-10) outliers start: 21 outliers final: 9 residues processed: 468 average time/residue: 0.7083 time to fit residues: 378.2938 Evaluate side-chains 291 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 282 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 402 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0040 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.4980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 469 GLN B 316 GLN C 81 ASN D 310 GLN E 458 HIS F 23 ASN G 185 GLN H 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.102811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079699 restraints weight = 48450.533| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.75 r_work: 0.2952 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27508 Z= 0.117 Angle : 0.566 8.943 37289 Z= 0.281 Chirality : 0.044 0.198 4161 Planarity : 0.005 0.044 4874 Dihedral : 5.758 111.800 3867 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.26 % Allowed : 13.98 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.62 (0.15), residues: 3437 helix: 0.85 (0.15), residues: 1304 sheet: 0.53 (0.23), residues: 571 loop : 0.13 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 420 TYR 0.013 0.001 TYR C 500 PHE 0.011 0.001 PHE H 13 TRP 0.008 0.001 TRP B 119 HIS 0.003 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00243 (27508) covalent geometry : angle 0.56646 (37289) hydrogen bonds : bond 0.04607 ( 1012) hydrogen bonds : angle 4.75210 ( 2886) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 315 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8092 (t0) cc_final: 0.7629 (t0) REVERT: A 393 GLU cc_start: 0.7512 (tt0) cc_final: 0.7267 (tt0) REVERT: A 488 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7253 (tmm160) REVERT: B 304 TYR cc_start: 0.8824 (m-80) cc_final: 0.8407 (m-80) REVERT: B 476 LEU cc_start: 0.8926 (mp) cc_final: 0.8703 (mp) REVERT: C 410 ASP cc_start: 0.8030 (t0) cc_final: 0.7809 (t0) REVERT: C 534 VAL cc_start: 0.7116 (t) cc_final: 0.6886 (p) REVERT: C 557 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: C 567 MET cc_start: 0.8873 (mmm) cc_final: 0.8307 (mmm) REVERT: D 275 GLU cc_start: 0.8145 (mp0) cc_final: 0.7825 (mp0) REVERT: E 15 SER cc_start: 0.7512 (OUTLIER) cc_final: 0.6857 (p) REVERT: E 25 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8621 (tppp) REVERT: E 194 MET cc_start: 0.9025 (mtm) cc_final: 0.8820 (mtm) REVERT: E 226 ASP cc_start: 0.8105 (m-30) cc_final: 0.7556 (m-30) REVERT: E 398 ILE cc_start: 0.8861 (mt) cc_final: 0.8618 (mm) REVERT: E 419 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: F 81 ARG cc_start: 0.8810 (mtt180) cc_final: 0.8567 (mmm-85) REVERT: F 334 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8189 (mt-10) REVERT: F 345 ARG cc_start: 0.8578 (ttm-80) cc_final: 0.8376 (ttp-170) REVERT: G 13 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8462 (tm-30) REVERT: G 47 MET cc_start: 0.8243 (ttm) cc_final: 0.7928 (ptt) REVERT: G 55 GLN cc_start: 0.8002 (tm130) cc_final: 0.7451 (tm-30) REVERT: G 133 TYR cc_start: 0.7588 (t80) cc_final: 0.7351 (t80) REVERT: G 184 GLU cc_start: 0.7455 (tp30) cc_final: 0.7249 (tp30) REVERT: G 187 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7947 (tm-30) REVERT: H 13 PHE cc_start: 0.8849 (m-80) cc_final: 0.8615 (m-80) REVERT: H 14 ARG cc_start: 0.7810 (mtt-85) cc_final: 0.7330 (ttm110) outliers start: 64 outliers final: 10 residues processed: 352 average time/residue: 0.7256 time to fit residues: 292.1190 Evaluate side-chains 272 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 259 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 197 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 151 optimal weight: 7.9990 chunk 149 optimal weight: 0.0670 chunk 188 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 339 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN D 310 GLN ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN F 170 GLN G 175 GLN G 180 GLN H 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.098409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.075238 restraints weight = 49032.973| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.71 r_work: 0.2883 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 27508 Z= 0.235 Angle : 0.656 9.979 37289 Z= 0.332 Chirality : 0.048 0.181 4161 Planarity : 0.005 0.043 4874 Dihedral : 5.873 113.265 3857 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.28 % Allowed : 14.65 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.38 (0.14), residues: 3437 helix: 0.93 (0.15), residues: 1290 sheet: 0.21 (0.23), residues: 555 loop : -0.19 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 547 TYR 0.020 0.002 TYR C 562 PHE 0.018 0.002 PHE C 230 TRP 0.012 0.002 TRP B 119 HIS 0.007 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00568 (27508) covalent geometry : angle 0.65614 (37289) hydrogen bonds : bond 0.06019 ( 1012) hydrogen bonds : angle 4.70836 ( 2886) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 269 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7984 (mmt-90) REVERT: A 124 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8677 (ptpp) REVERT: A 488 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7942 (tmm160) REVERT: B 294 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8323 (mtm) REVERT: B 332 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7783 (tm-30) REVERT: B 400 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8735 (mp) REVERT: B 567 MET cc_start: 0.7947 (mmm) cc_final: 0.7315 (tmm) REVERT: C 534 VAL cc_start: 0.7798 (t) cc_final: 0.7581 (p) REVERT: C 557 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: C 567 MET cc_start: 0.8698 (mmm) cc_final: 0.8161 (mmm) REVERT: D 391 ASP cc_start: 0.8418 (p0) cc_final: 0.8144 (p0) REVERT: E 25 LYS cc_start: 0.9073 (ttpp) cc_final: 0.8766 (ttmm) REVERT: E 158 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9056 (mt) REVERT: E 226 ASP cc_start: 0.8161 (m-30) cc_final: 0.7475 (m-30) REVERT: E 399 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8090 (tp) REVERT: E 420 ARG cc_start: 0.8417 (ttm170) cc_final: 0.8216 (ttp80) REVERT: F 6 LYS cc_start: 0.6475 (mmtt) cc_final: 0.5799 (mmtt) REVERT: F 81 ARG cc_start: 0.9020 (mtt180) cc_final: 0.8803 (mmm-85) REVERT: F 280 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8080 (mtt180) REVERT: F 334 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8407 (mt-10) REVERT: F 345 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.8450 (ttp-170) REVERT: G 13 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8414 (tm-30) REVERT: G 47 MET cc_start: 0.8428 (ttm) cc_final: 0.7993 (ptt) REVERT: G 165 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8236 (tm-30) REVERT: G 184 GLU cc_start: 0.7823 (tp30) cc_final: 0.7509 (tp30) REVERT: G 187 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8072 (tm-30) REVERT: H 13 PHE cc_start: 0.8836 (m-80) cc_final: 0.8618 (m-80) REVERT: H 57 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7863 (tmm160) REVERT: H 92 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7918 (tp30) outliers start: 93 outliers final: 27 residues processed: 333 average time/residue: 0.6897 time to fit residues: 262.8697 Evaluate side-chains 265 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 92 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 195 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 289 optimal weight: 0.7980 chunk 307 optimal weight: 5.9990 chunk 273 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 262 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 239 GLN E 363 ASN F 166 GLN G 180 GLN H 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.075761 restraints weight = 48752.480| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.75 r_work: 0.2889 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27508 Z= 0.149 Angle : 0.552 8.033 37289 Z= 0.273 Chirality : 0.044 0.222 4161 Planarity : 0.004 0.042 4874 Dihedral : 5.432 111.226 3855 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.54 % Allowed : 16.07 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.61 (0.15), residues: 3437 helix: 1.28 (0.15), residues: 1284 sheet: 0.38 (0.23), residues: 561 loop : -0.23 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 66 TYR 0.012 0.001 TYR C 562 PHE 0.018 0.001 PHE H 81 TRP 0.012 0.001 TRP B 119 HIS 0.003 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00355 (27508) covalent geometry : angle 0.55192 (37289) hydrogen bonds : bond 0.04671 ( 1012) hydrogen bonds : angle 4.41195 ( 2886) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 256 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.9053 (mmm) cc_final: 0.8792 (tpt) REVERT: A 124 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8660 (ptpp) REVERT: A 288 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8954 (mp) REVERT: A 393 GLU cc_start: 0.7753 (tt0) cc_final: 0.7552 (tt0) REVERT: A 488 ARG cc_start: 0.8275 (ttp80) cc_final: 0.8033 (tmm160) REVERT: A 568 LYS cc_start: 0.8289 (tttm) cc_final: 0.8047 (mttt) REVERT: A 571 GLN cc_start: 0.7458 (mt0) cc_final: 0.7254 (mt0) REVERT: B 207 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.9053 (m) REVERT: B 332 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: B 567 MET cc_start: 0.8072 (mmm) cc_final: 0.7281 (tmm) REVERT: B 570 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 43 ASP cc_start: 0.8603 (t0) cc_final: 0.8395 (t0) REVERT: C 442 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8445 (m110) REVERT: C 461 GLU cc_start: 0.8850 (tp30) cc_final: 0.8632 (tp30) REVERT: C 557 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: C 567 MET cc_start: 0.8592 (mmm) cc_final: 0.8061 (mmm) REVERT: D 275 GLU cc_start: 0.8080 (mp0) cc_final: 0.7873 (mp0) REVERT: D 391 ASP cc_start: 0.8304 (p0) cc_final: 0.8064 (p0) REVERT: E 25 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8754 (ttmm) REVERT: E 150 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9089 (tp) REVERT: E 226 ASP cc_start: 0.7909 (m-30) cc_final: 0.7263 (m-30) REVERT: E 380 ASP cc_start: 0.8428 (m-30) cc_final: 0.8168 (m-30) REVERT: F 6 LYS cc_start: 0.6511 (mmtt) cc_final: 0.6053 (mmtt) REVERT: F 79 VAL cc_start: 0.8003 (t) cc_final: 0.7713 (p) REVERT: F 81 ARG cc_start: 0.9023 (mtt180) cc_final: 0.8803 (mmm-85) REVERT: F 280 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.7979 (mtt180) REVERT: F 290 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8294 (t70) REVERT: G 13 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8566 (tm-30) REVERT: G 47 MET cc_start: 0.8374 (ttm) cc_final: 0.7999 (ptt) REVERT: G 131 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8087 (tpp-160) REVERT: G 165 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8169 (tm-30) REVERT: G 184 GLU cc_start: 0.7851 (tp30) cc_final: 0.7488 (tp30) REVERT: G 187 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7995 (tm-30) REVERT: G 190 ASP cc_start: 0.8164 (m-30) cc_final: 0.7707 (m-30) REVERT: H 13 PHE cc_start: 0.8878 (m-80) cc_final: 0.8646 (m-80) REVERT: H 57 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7936 (ptm-80) REVERT: H 91 ARG cc_start: 0.8022 (mtp180) cc_final: 0.7753 (mpp80) outliers start: 72 outliers final: 32 residues processed: 308 average time/residue: 0.7302 time to fit residues: 256.7995 Evaluate side-chains 269 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 197 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 329 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 chunk 311 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 285 optimal weight: 0.9980 chunk 257 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN E 413 GLN G 180 GLN H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.096882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.073714 restraints weight = 49094.525| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.71 r_work: 0.2855 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27508 Z= 0.245 Angle : 0.610 8.265 37289 Z= 0.306 Chirality : 0.047 0.212 4161 Planarity : 0.005 0.043 4874 Dihedral : 5.626 112.124 3855 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.97 % Allowed : 16.49 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.39 (0.14), residues: 3437 helix: 1.16 (0.15), residues: 1300 sheet: 0.10 (0.22), residues: 571 loop : -0.36 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 66 TYR 0.016 0.001 TYR C 562 PHE 0.017 0.002 PHE E 130 TRP 0.012 0.001 TRP B 119 HIS 0.005 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00601 (27508) covalent geometry : angle 0.60983 (37289) hydrogen bonds : bond 0.05549 ( 1012) hydrogen bonds : angle 4.50733 ( 2886) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 238 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8503 (mtpp) REVERT: A 133 MET cc_start: 0.8797 (mtp) cc_final: 0.8452 (mtm) REVERT: A 288 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8952 (mp) REVERT: A 393 GLU cc_start: 0.7892 (tt0) cc_final: 0.7664 (tt0) REVERT: B 294 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8422 (mtm) REVERT: B 332 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: B 343 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8148 (mm-30) REVERT: B 363 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8261 (mm-30) REVERT: B 567 MET cc_start: 0.7889 (mmm) cc_final: 0.7396 (tmm) REVERT: C 133 MET cc_start: 0.8170 (mtp) cc_final: 0.7795 (mtm) REVERT: C 200 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8269 (p0) REVERT: C 461 GLU cc_start: 0.8889 (tp30) cc_final: 0.8640 (tp30) REVERT: C 557 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: D 391 ASP cc_start: 0.8207 (p0) cc_final: 0.8002 (p0) REVERT: E 25 LYS cc_start: 0.9023 (ttpp) cc_final: 0.8730 (ttmm) REVERT: E 226 ASP cc_start: 0.8022 (m-30) cc_final: 0.7415 (m-30) REVERT: E 380 ASP cc_start: 0.8476 (m-30) cc_final: 0.8217 (m-30) REVERT: F 6 LYS cc_start: 0.6409 (mmtt) cc_final: 0.5955 (mmtt) REVERT: F 81 ARG cc_start: 0.8987 (mtt180) cc_final: 0.8725 (mmm-85) REVERT: F 280 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.8164 (mtt180) REVERT: F 345 ARG cc_start: 0.8793 (ttm-80) cc_final: 0.8506 (ttp-170) REVERT: G 13 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8352 (tm-30) REVERT: G 47 MET cc_start: 0.8439 (ttm) cc_final: 0.8034 (ptt) REVERT: G 131 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8047 (tpp-160) REVERT: G 165 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8210 (tm-30) REVERT: G 181 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8229 (mm-40) REVERT: G 184 GLU cc_start: 0.7961 (tp30) cc_final: 0.7580 (tp30) REVERT: G 187 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7825 (tm-30) REVERT: G 190 ASP cc_start: 0.8040 (m-30) cc_final: 0.7543 (m-30) REVERT: H 13 PHE cc_start: 0.8852 (m-80) cc_final: 0.8640 (m-80) REVERT: H 72 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7046 (tm) outliers start: 84 outliers final: 40 residues processed: 291 average time/residue: 0.7254 time to fit residues: 241.3534 Evaluate side-chains 271 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 157 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 279 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 327 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN G 180 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.076799 restraints weight = 48459.788| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.71 r_work: 0.2907 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27508 Z= 0.106 Angle : 0.527 7.791 37289 Z= 0.260 Chirality : 0.043 0.212 4161 Planarity : 0.004 0.042 4874 Dihedral : 5.258 110.509 3855 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.08 % Allowed : 17.44 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.75 (0.15), residues: 3437 helix: 1.55 (0.15), residues: 1278 sheet: 0.36 (0.22), residues: 571 loop : -0.26 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 66 TYR 0.011 0.001 TYR C 500 PHE 0.013 0.001 PHE E 130 TRP 0.011 0.001 TRP B 119 HIS 0.002 0.000 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00242 (27508) covalent geometry : angle 0.52737 (37289) hydrogen bonds : bond 0.03972 ( 1012) hydrogen bonds : angle 4.24923 ( 2886) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 253 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 133 MET cc_start: 0.8763 (mtp) cc_final: 0.8434 (mtm) REVERT: A 268 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8002 (tm-30) REVERT: A 288 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8970 (mp) REVERT: A 571 GLN cc_start: 0.7867 (mt0) cc_final: 0.7649 (mt0) REVERT: B 85 ASP cc_start: 0.8074 (p0) cc_final: 0.7839 (p0) REVERT: B 294 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8209 (mtm) REVERT: B 332 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: B 441 GLU cc_start: 0.8681 (tp30) cc_final: 0.8375 (tp30) REVERT: B 567 MET cc_start: 0.8112 (mmm) cc_final: 0.7337 (tmm) REVERT: C 43 ASP cc_start: 0.8510 (t0) cc_final: 0.8309 (t0) REVERT: C 133 MET cc_start: 0.8064 (mtp) cc_final: 0.7722 (mtp) REVERT: C 461 GLU cc_start: 0.8830 (tp30) cc_final: 0.8608 (tp30) REVERT: C 557 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: C 567 MET cc_start: 0.8267 (mmm) cc_final: 0.7540 (mmm) REVERT: D 276 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: D 420 ARG cc_start: 0.8908 (tmm-80) cc_final: 0.8412 (tmt90) REVERT: E 25 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8730 (ttmm) REVERT: E 226 ASP cc_start: 0.7914 (m-30) cc_final: 0.7342 (m-30) REVERT: E 380 ASP cc_start: 0.8419 (m-30) cc_final: 0.8114 (m-30) REVERT: E 456 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8989 (tppp) REVERT: F 6 LYS cc_start: 0.6348 (mmtt) cc_final: 0.5724 (mmtt) REVERT: F 79 VAL cc_start: 0.8151 (t) cc_final: 0.7897 (p) REVERT: F 81 ARG cc_start: 0.8963 (mtt180) cc_final: 0.8728 (mmm-85) REVERT: F 280 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.7961 (mtt180) REVERT: F 290 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8360 (t70) REVERT: F 345 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8444 (ttp-170) REVERT: G 13 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8461 (tm-30) REVERT: G 47 MET cc_start: 0.8360 (ttm) cc_final: 0.8040 (ptt) REVERT: G 131 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8097 (tpp-160) REVERT: G 165 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8089 (tm-30) REVERT: G 181 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8099 (mm-40) REVERT: G 184 GLU cc_start: 0.7926 (tp30) cc_final: 0.7494 (tp30) REVERT: G 187 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7772 (tm-30) REVERT: G 190 ASP cc_start: 0.8107 (m-30) cc_final: 0.7646 (m-30) REVERT: H 1 MET cc_start: 0.4605 (ppp) cc_final: 0.4367 (ppp) REVERT: H 13 PHE cc_start: 0.8864 (m-80) cc_final: 0.8615 (m-80) REVERT: H 72 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7020 (tm) outliers start: 59 outliers final: 25 residues processed: 292 average time/residue: 0.7295 time to fit residues: 242.9813 Evaluate side-chains 272 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 456 LYS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 82 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 294 optimal weight: 6.9990 chunk 309 optimal weight: 4.9990 chunk 330 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 148 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 397 GLN G 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.074676 restraints weight = 48407.242| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.73 r_work: 0.2899 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 27508 Z= 0.189 Angle : 0.583 17.410 37289 Z= 0.288 Chirality : 0.045 0.203 4161 Planarity : 0.004 0.045 4874 Dihedral : 5.282 109.376 3851 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.65 % Allowed : 17.51 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.66 (0.15), residues: 3437 helix: 1.52 (0.15), residues: 1280 sheet: 0.25 (0.23), residues: 556 loop : -0.32 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 66 TYR 0.013 0.001 TYR C 562 PHE 0.021 0.001 PHE H 81 TRP 0.012 0.001 TRP B 119 HIS 0.004 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00463 (27508) covalent geometry : angle 0.58299 (37289) hydrogen bonds : bond 0.04733 ( 1012) hydrogen bonds : angle 4.33720 ( 2886) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 233 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8547 (mtpp) REVERT: A 133 MET cc_start: 0.8746 (mtp) cc_final: 0.8416 (mtm) REVERT: A 288 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8970 (mp) REVERT: A 571 GLN cc_start: 0.7759 (mt0) cc_final: 0.7456 (mt0) REVERT: B 294 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8272 (mtm) REVERT: B 332 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: B 567 MET cc_start: 0.7884 (mmm) cc_final: 0.7358 (tmm) REVERT: C 133 MET cc_start: 0.8092 (mtp) cc_final: 0.7708 (mtm) REVERT: C 461 GLU cc_start: 0.8833 (tp30) cc_final: 0.8582 (tp30) REVERT: C 557 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: C 567 MET cc_start: 0.8377 (mmm) cc_final: 0.8175 (mmm) REVERT: D 276 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: D 391 ASP cc_start: 0.8199 (p0) cc_final: 0.7991 (p0) REVERT: E 25 LYS cc_start: 0.9012 (ttpp) cc_final: 0.8711 (ttmm) REVERT: E 226 ASP cc_start: 0.7945 (m-30) cc_final: 0.7327 (m-30) REVERT: E 380 ASP cc_start: 0.8463 (m-30) cc_final: 0.8185 (m-30) REVERT: F 79 VAL cc_start: 0.8199 (t) cc_final: 0.7941 (p) REVERT: F 81 ARG cc_start: 0.8966 (mtt180) cc_final: 0.8702 (mmm-85) REVERT: F 280 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.8076 (mtt180) REVERT: F 290 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8225 (t70) REVERT: G 13 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8493 (tm-30) REVERT: G 47 MET cc_start: 0.8410 (ttm) cc_final: 0.7998 (ptt) REVERT: G 131 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8054 (tpp-160) REVERT: G 165 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8191 (tm-30) REVERT: G 181 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8139 (mm-40) REVERT: G 184 GLU cc_start: 0.7958 (tp30) cc_final: 0.7531 (tp30) REVERT: G 187 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7779 (tm-30) REVERT: G 190 ASP cc_start: 0.8037 (m-30) cc_final: 0.7563 (m-30) REVERT: H 1 MET cc_start: 0.4889 (ppp) cc_final: 0.4604 (ppp) REVERT: H 4 ILE cc_start: 0.7346 (mt) cc_final: 0.7142 (tt) REVERT: H 13 PHE cc_start: 0.8837 (m-80) cc_final: 0.8627 (m-80) REVERT: H 72 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7113 (tm) REVERT: H 74 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7293 (tp) outliers start: 75 outliers final: 35 residues processed: 282 average time/residue: 0.7076 time to fit residues: 227.6675 Evaluate side-chains 268 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 411 TYR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 211 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 76 optimal weight: 0.0570 chunk 310 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN G 180 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.076565 restraints weight = 48683.922| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.72 r_work: 0.2907 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27508 Z= 0.111 Angle : 0.549 19.299 37289 Z= 0.269 Chirality : 0.044 0.214 4161 Planarity : 0.004 0.051 4874 Dihedral : 5.110 109.295 3851 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.12 % Allowed : 18.15 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.84 (0.15), residues: 3437 helix: 1.66 (0.15), residues: 1278 sheet: 0.35 (0.22), residues: 581 loop : -0.21 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 66 TYR 0.014 0.001 TYR C 500 PHE 0.014 0.001 PHE E 130 TRP 0.012 0.001 TRP B 119 HIS 0.002 0.000 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00258 (27508) covalent geometry : angle 0.54944 (37289) hydrogen bonds : bond 0.03930 ( 1012) hydrogen bonds : angle 4.21211 ( 2886) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 240 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 133 MET cc_start: 0.8736 (mtp) cc_final: 0.8421 (mtm) REVERT: A 268 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8034 (tm-30) REVERT: A 288 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8925 (mp) REVERT: B 294 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8110 (mtm) REVERT: B 332 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: B 343 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7857 (mm-30) REVERT: B 518 MET cc_start: 0.7055 (ppp) cc_final: 0.6651 (ptm) REVERT: B 567 MET cc_start: 0.8083 (mmm) cc_final: 0.7336 (tmm) REVERT: C 133 MET cc_start: 0.8125 (mtp) cc_final: 0.7751 (mtm) REVERT: C 461 GLU cc_start: 0.8833 (tp30) cc_final: 0.8588 (tp30) REVERT: C 557 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: C 567 MET cc_start: 0.8388 (mmm) cc_final: 0.8179 (mmm) REVERT: D 276 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: D 391 ASP cc_start: 0.8128 (p0) cc_final: 0.7864 (p0) REVERT: E 25 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8659 (ttmm) REVERT: E 226 ASP cc_start: 0.7881 (m-30) cc_final: 0.7245 (m-30) REVERT: E 274 ARG cc_start: 0.7826 (mtp180) cc_final: 0.7471 (tpt-90) REVERT: E 380 ASP cc_start: 0.8452 (m-30) cc_final: 0.8116 (m-30) REVERT: E 398 ILE cc_start: 0.8861 (mt) cc_final: 0.8635 (mm) REVERT: F 79 VAL cc_start: 0.8210 (t) cc_final: 0.7963 (p) REVERT: F 81 ARG cc_start: 0.8947 (mtt180) cc_final: 0.8713 (mmm-85) REVERT: F 280 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.7956 (mtt180) REVERT: F 290 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8368 (t70) REVERT: G 47 MET cc_start: 0.8371 (ttm) cc_final: 0.8027 (ptt) REVERT: G 131 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8141 (tpp-160) REVERT: G 165 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8132 (tm-30) REVERT: G 184 GLU cc_start: 0.7950 (tp30) cc_final: 0.7533 (tp30) REVERT: G 187 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7816 (tm-30) REVERT: G 190 ASP cc_start: 0.8098 (m-30) cc_final: 0.7635 (m-30) REVERT: H 1 MET cc_start: 0.5372 (ppp) cc_final: 0.4845 (ppp) REVERT: H 13 PHE cc_start: 0.8815 (m-80) cc_final: 0.8543 (m-80) REVERT: H 42 TYR cc_start: 0.7273 (m-10) cc_final: 0.6866 (m-80) REVERT: H 72 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7171 (tm) REVERT: H 74 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7400 (tp) outliers start: 60 outliers final: 32 residues processed: 279 average time/residue: 0.7326 time to fit residues: 233.0425 Evaluate side-chains 269 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 411 TYR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 82 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 163 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 293 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN G 180 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.073034 restraints weight = 49373.369| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.74 r_work: 0.2844 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 27508 Z= 0.303 Angle : 0.665 18.051 37289 Z= 0.331 Chirality : 0.049 0.197 4161 Planarity : 0.005 0.050 4874 Dihedral : 5.489 110.745 3851 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.37 % Allowed : 18.08 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.46 (0.15), residues: 3437 helix: 1.33 (0.15), residues: 1294 sheet: 0.11 (0.22), residues: 584 loop : -0.43 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 66 TYR 0.018 0.002 TYR C 500 PHE 0.020 0.002 PHE C 230 TRP 0.011 0.001 TRP A 119 HIS 0.006 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00746 (27508) covalent geometry : angle 0.66477 (37289) hydrogen bonds : bond 0.05614 ( 1012) hydrogen bonds : angle 4.47662 ( 2886) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8453 (mtpp) REVERT: A 133 MET cc_start: 0.8747 (mtp) cc_final: 0.8415 (mtm) REVERT: A 288 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8930 (mp) REVERT: A 571 GLN cc_start: 0.8150 (mt0) cc_final: 0.7897 (mp10) REVERT: B 294 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8439 (mtm) REVERT: B 332 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7982 (tm-30) REVERT: B 343 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7939 (mm-30) REVERT: B 441 GLU cc_start: 0.8706 (tp30) cc_final: 0.8471 (tp30) REVERT: B 567 MET cc_start: 0.7916 (mmm) cc_final: 0.7356 (tmm) REVERT: C 24 MET cc_start: 0.9214 (mmm) cc_final: 0.8856 (mmm) REVERT: C 133 MET cc_start: 0.8142 (mtp) cc_final: 0.7702 (mtm) REVERT: C 461 GLU cc_start: 0.8858 (tp30) cc_final: 0.8583 (tp30) REVERT: C 557 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: D 276 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: D 391 ASP cc_start: 0.8150 (p0) cc_final: 0.7888 (p0) REVERT: E 25 LYS cc_start: 0.9057 (ttpp) cc_final: 0.8727 (ttmm) REVERT: E 226 ASP cc_start: 0.8007 (m-30) cc_final: 0.7433 (m-30) REVERT: E 274 ARG cc_start: 0.7985 (mtp180) cc_final: 0.7585 (tpt-90) REVERT: E 380 ASP cc_start: 0.8497 (m-30) cc_final: 0.8229 (m-30) REVERT: F 81 ARG cc_start: 0.8940 (mtt180) cc_final: 0.8665 (mmm-85) REVERT: F 280 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.8103 (mtt180) REVERT: F 345 ARG cc_start: 0.8837 (ttm-80) cc_final: 0.8382 (ttp-170) REVERT: F 401 GLU cc_start: 0.8271 (pm20) cc_final: 0.7924 (tm-30) REVERT: G 47 MET cc_start: 0.8426 (ttm) cc_final: 0.7995 (ptt) REVERT: G 131 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7982 (tpp-160) REVERT: G 165 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8242 (tm-30) REVERT: G 184 GLU cc_start: 0.7915 (tp30) cc_final: 0.7499 (tp30) REVERT: G 187 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7738 (tm-30) REVERT: H 13 PHE cc_start: 0.8866 (m-80) cc_final: 0.8602 (m-80) REVERT: H 42 TYR cc_start: 0.7469 (m-10) cc_final: 0.7149 (m-80) REVERT: H 72 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7205 (tm) REVERT: H 74 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7272 (tp) outliers start: 67 outliers final: 37 residues processed: 267 average time/residue: 0.7344 time to fit residues: 223.9104 Evaluate side-chains 261 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 411 TYR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 116 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 320 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN G 180 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.075995 restraints weight = 48462.213| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.71 r_work: 0.2921 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27508 Z= 0.115 Angle : 0.566 19.108 37289 Z= 0.277 Chirality : 0.044 0.200 4161 Planarity : 0.004 0.056 4874 Dihedral : 5.213 110.717 3851 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.73 % Allowed : 18.68 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.74 (0.15), residues: 3437 helix: 1.60 (0.15), residues: 1284 sheet: 0.33 (0.23), residues: 577 loop : -0.30 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 66 TYR 0.013 0.001 TYR C 500 PHE 0.016 0.001 PHE E 130 TRP 0.012 0.001 TRP B 119 HIS 0.002 0.000 HIS E 375 Details of bonding type rmsd covalent geometry : bond 0.00271 (27508) covalent geometry : angle 0.56643 (37289) hydrogen bonds : bond 0.04116 ( 1012) hydrogen bonds : angle 4.22410 ( 2886) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8716 (mtp) cc_final: 0.8399 (mtm) REVERT: A 268 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8060 (tm-30) REVERT: A 288 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8933 (mp) REVERT: A 323 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8048 (mtp) REVERT: A 571 GLN cc_start: 0.8066 (mt0) cc_final: 0.7839 (mp10) REVERT: B 294 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8173 (mtm) REVERT: B 332 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: B 441 GLU cc_start: 0.8737 (tp30) cc_final: 0.8519 (tp30) REVERT: B 518 MET cc_start: 0.7320 (ppp) cc_final: 0.6952 (ptm) REVERT: B 567 MET cc_start: 0.8075 (mmm) cc_final: 0.7327 (tmm) REVERT: C 133 MET cc_start: 0.8150 (mtp) cc_final: 0.7751 (mtm) REVERT: C 461 GLU cc_start: 0.8834 (tp30) cc_final: 0.8585 (tp30) REVERT: C 557 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: C 567 MET cc_start: 0.8319 (mmm) cc_final: 0.7663 (mmm) REVERT: D 276 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: D 391 ASP cc_start: 0.8150 (p0) cc_final: 0.7865 (p0) REVERT: E 25 LYS cc_start: 0.8947 (ttpp) cc_final: 0.8625 (ttmm) REVERT: E 206 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7871 (mm-40) REVERT: E 226 ASP cc_start: 0.7931 (m-30) cc_final: 0.7342 (m-30) REVERT: E 274 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7451 (tpt-90) REVERT: E 380 ASP cc_start: 0.8442 (m-30) cc_final: 0.8124 (m-30) REVERT: F 78 ASP cc_start: 0.7769 (p0) cc_final: 0.7562 (m-30) REVERT: F 79 VAL cc_start: 0.8252 (t) cc_final: 0.8041 (p) REVERT: F 81 ARG cc_start: 0.8929 (mtt180) cc_final: 0.8686 (mmm-85) REVERT: F 280 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.7983 (mtt180) REVERT: F 314 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8962 (pp) REVERT: F 401 GLU cc_start: 0.8244 (pm20) cc_final: 0.8004 (tt0) REVERT: G 47 MET cc_start: 0.8370 (ttm) cc_final: 0.8010 (ptt) REVERT: G 131 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8119 (tpp-160) REVERT: G 165 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8124 (tm-30) REVERT: G 184 GLU cc_start: 0.7895 (tp30) cc_final: 0.7446 (tp30) REVERT: G 187 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7822 (tm-30) REVERT: G 190 ASP cc_start: 0.8011 (m-30) cc_final: 0.7589 (m-30) REVERT: H 1 MET cc_start: 0.4641 (ppp) cc_final: 0.3958 (ppp) REVERT: H 13 PHE cc_start: 0.8843 (m-80) cc_final: 0.8557 (m-80) REVERT: H 42 TYR cc_start: 0.7521 (m-10) cc_final: 0.7196 (m-80) REVERT: H 72 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7270 (tm) REVERT: H 74 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7336 (tp) outliers start: 49 outliers final: 31 residues processed: 262 average time/residue: 0.7474 time to fit residues: 223.8079 Evaluate side-chains 268 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 411 TYR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 82 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 163 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 322 optimal weight: 0.0970 chunk 110 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 315 optimal weight: 4.9990 chunk 211 optimal weight: 0.1980 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN G 180 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.099987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.076878 restraints weight = 48260.286| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.70 r_work: 0.2936 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27508 Z= 0.107 Angle : 0.558 18.959 37289 Z= 0.271 Chirality : 0.044 0.204 4161 Planarity : 0.004 0.062 4874 Dihedral : 5.012 107.266 3851 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.62 % Allowed : 18.89 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.90 (0.15), residues: 3437 helix: 1.75 (0.15), residues: 1272 sheet: 0.39 (0.23), residues: 577 loop : -0.22 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG H 66 TYR 0.012 0.001 TYR C 500 PHE 0.016 0.001 PHE E 130 TRP 0.011 0.001 TRP B 119 HIS 0.007 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00248 (27508) covalent geometry : angle 0.55812 (37289) hydrogen bonds : bond 0.03781 ( 1012) hydrogen bonds : angle 4.14610 ( 2886) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7349.55 seconds wall clock time: 126 minutes 0.11 seconds (7560.11 seconds total)