Starting phenix.real_space_refine on Fri Jul 3 07:47:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sn8_25214/07_2026/7sn8_25214.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sn8_25214/07_2026/7sn8_25214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sn8_25214/07_2026/7sn8_25214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sn8_25214/07_2026/7sn8_25214.map" model { file = "/net/cci-nas-00/data/ceres_data/7sn8_25214/07_2026/7sn8_25214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sn8_25214/07_2026/7sn8_25214.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sn8_25214/07_2026/7sn8_25214.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sn8_25214/07_2026/7sn8_25214.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 S 105 5.16 5 C 8214 2.51 5 N 2163 2.21 5 O 2370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12860 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3147 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 4, 'TRANS': 394} Chain breaks: 5 Chain: "K" Number of atoms: 4665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4665 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain breaks: 2 Chain: "I" Number of atoms: 5010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5010 Classifications: {'peptide': 634} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 591} Chain breaks: 2 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.78, per 1000 atoms: 0.22 Number of scatterers: 12860 At special positions: 0 Unit cell: (142.956, 122.379, 109.383, 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) Zn 2 29.99 S 105 16.00 P 6 15.00 O 2370 8.00 N 2163 7.00 C 8214 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: 1.04 Conformation dependent library (CDL) restraints added in 599.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 800 " pdb="ZN ZN K 800 " - pdb=" ND1 HIS K 70 " pdb="ZN ZN K 800 " - pdb=" NE2 HIS K 68 " pdb="ZN ZN K 800 " - pdb=" NE2 HIS K 157 " pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" NE2 HIS K 73 " pdb="ZN ZN K 801 " - pdb=" NE2 HIS K 414 " 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3064 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 12 sheets defined 45.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'D' and resid 103 through 118 Processing helix chain 'D' and resid 127 through 142 removed outlier: 3.893A pdb=" N GLN D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 removed outlier: 4.028A pdb=" N ARG D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 184 removed outlier: 3.835A pdb=" N LYS D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 206 Processing helix chain 'D' and resid 210 through 228 removed outlier: 3.686A pdb=" N GLN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 244 Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 260 through 263 Processing helix chain 'D' and resid 265 through 282 removed outlier: 3.519A pdb=" N ARG D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 removed outlier: 4.211A pdb=" N ARG D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 300 removed outlier: 3.831A pdb=" N ASP D 300 " --> pdb=" O ALA D 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 297 through 300' Processing helix chain 'D' and resid 302 through 320 removed outlier: 4.093A pdb=" N GLU D 308 " --> pdb=" O CYS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 346 Processing helix chain 'D' and resid 347 through 350 removed outlier: 3.721A pdb=" N ASP D 350 " --> pdb=" O ALA D 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 347 through 350' Processing helix chain 'D' and resid 352 through 364 removed outlier: 4.277A pdb=" N GLY D 364 " --> pdb=" O ALA D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 377 Processing helix chain 'D' and resid 434 through 441 Processing helix chain 'D' and resid 445 through 462 removed outlier: 3.614A pdb=" N ALA D 450 " --> pdb=" O GLU D 446 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 469 through 476 removed outlier: 4.035A pdb=" N LEU D 473 " --> pdb=" O SER D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 479 No H-bonds generated for 'chain 'D' and resid 477 through 479' Processing helix chain 'D' and resid 481 through 496 Processing helix chain 'D' and resid 502 through 511 removed outlier: 3.707A pdb=" N ILE D 508 " --> pdb=" O ASP D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 531 Processing helix chain 'D' and resid 538 through 551 removed outlier: 3.593A pdb=" N VAL D 542 " --> pdb=" O CYS D 538 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP D 548 " --> pdb=" O GLN D 544 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 549 " --> pdb=" O LYS D 545 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 550 " --> pdb=" O LEU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 569 Processing helix chain 'K' and resid 41 through 45 removed outlier: 3.672A pdb=" N PHE K 45 " --> pdb=" O GLU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 76 through 83 Processing helix chain 'K' and resid 94 through 114 Proline residue: K 101 - end of helix removed outlier: 3.747A pdb=" N GLU K 113 " --> pdb=" O LYS K 109 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG K 114 " --> pdb=" O VAL K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 130 Processing helix chain 'K' and resid 213 through 230 removed outlier: 3.587A pdb=" N ARG K 217 " --> pdb=" O SER K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 259 removed outlier: 3.673A pdb=" N LEU K 248 " --> pdb=" O ARG K 244 " (cutoff:3.500A) Processing helix chain 'K' and resid 274 through 282 removed outlier: 3.890A pdb=" N TYR K 278 " --> pdb=" O LYS K 274 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR K 279 " --> pdb=" O ALA K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 286 Processing helix chain 'K' and resid 287 through 294 removed outlier: 3.673A pdb=" N THR K 293 " --> pdb=" O LYS K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 313 Processing helix chain 'K' and resid 325 through 329 removed outlier: 3.947A pdb=" N LEU K 328 " --> pdb=" O PRO K 325 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS K 329 " --> pdb=" O GLY K 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 325 through 329' Processing helix chain 'K' and resid 331 through 341 Processing helix chain 'K' and resid 358 through 365 removed outlier: 3.557A pdb=" N LYS K 362 " --> pdb=" O THR K 358 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 406 Processing helix chain 'K' and resid 416 through 432 Processing helix chain 'K' and resid 458 through 469 Processing helix chain 'K' and resid 496 through 505 Processing helix chain 'K' and resid 524 through 540 Processing helix chain 'K' and resid 582 through 595 removed outlier: 4.843A pdb=" N ILE K 589 " --> pdb=" O ILE K 585 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU K 590 " --> pdb=" O GLY K 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 38 removed outlier: 4.159A pdb=" N THR I 34 " --> pdb=" O THR I 31 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU I 36 " --> pdb=" O GLN I 33 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN I 37 " --> pdb=" O THR I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 109 removed outlier: 4.175A pdb=" N LEU I 109 " --> pdb=" O LEU I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 116 removed outlier: 3.605A pdb=" N ILE I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 148 removed outlier: 4.431A pdb=" N SER I 148 " --> pdb=" O TYR I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 191 Processing helix chain 'I' and resid 251 through 255 removed outlier: 3.660A pdb=" N LEU I 254 " --> pdb=" O GLN I 251 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS I 255 " --> pdb=" O SER I 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 251 through 255' Processing helix chain 'I' and resid 272 through 290 Processing helix chain 'I' and resid 303 through 318 removed outlier: 3.950A pdb=" N GLU I 309 " --> pdb=" O TYR I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 340 removed outlier: 4.079A pdb=" N ASN I 340 " --> pdb=" O LEU I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 346 removed outlier: 5.190A pdb=" N GLU I 344 " --> pdb=" O ILE I 341 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU I 346 " --> pdb=" O ALA I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 352 Processing helix chain 'I' and resid 353 through 355 No H-bonds generated for 'chain 'I' and resid 353 through 355' Processing helix chain 'I' and resid 362 through 369 Processing helix chain 'I' and resid 382 through 387 Processing helix chain 'I' and resid 403 through 412 removed outlier: 4.479A pdb=" N HIS I 407 " --> pdb=" O GLY I 403 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 433 Processing helix chain 'I' and resid 434 through 437 removed outlier: 3.672A pdb=" N GLN I 437 " --> pdb=" O ALA I 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 434 through 437' Processing helix chain 'I' and resid 453 through 465 removed outlier: 3.551A pdb=" N LYS I 459 " --> pdb=" O GLN I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 517 through 523 Processing helix chain 'I' and resid 574 through 578 removed outlier: 3.578A pdb=" N VAL I 578 " --> pdb=" O LEU I 575 " (cutoff:3.500A) Processing helix chain 'I' and resid 589 through 595 Processing helix chain 'I' and resid 636 through 650 removed outlier: 4.025A pdb=" N ARG I 640 " --> pdb=" O LYS I 636 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU I 641 " --> pdb=" O PRO I 637 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS I 642 " --> pdb=" O THR I 638 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU I 643 " --> pdb=" O THR I 639 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS I 650 " --> pdb=" O THR I 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 133 through 136 removed outlier: 5.705A pdb=" N ILE K 90 " --> pdb=" O ILE K 134 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL K 136 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N MET K 92 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL K 64 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N THR K 93 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASN K 28 " --> pdb=" O CYS K 63 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE K 65 " --> pdb=" O ASN K 28 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET K 30 " --> pdb=" O ILE K 65 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N CYS K 19 " --> pdb=" O LEU K 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 142 through 143 removed outlier: 7.076A pdb=" N SER K 172 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ILE K 201 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL K 174 " --> pdb=" O ILE K 201 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLU K 203 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER K 204 " --> pdb=" O VAL K 413 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY K 415 " --> pdb=" O SER K 204 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL K 410 " --> pdb=" O TYR K 436 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 305 through 307 removed outlier: 6.658A pdb=" N ILE K 265 " --> pdb=" O LYS K 306 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR K 266 " --> pdb=" O PHE K 322 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU K 236 " --> pdb=" O ILE K 349 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 369 through 371 Processing sheet with id=AA5, first strand: chain 'I' and resid 511 through 515 removed outlier: 5.453A pdb=" N ILE K 492 " --> pdb=" O PRO K 453 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET K 487 " --> pdb=" O THR I 534 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR I 534 " --> pdb=" O MET K 487 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 508 through 509 removed outlier: 4.212A pdb=" N GLU I 581 " --> pdb=" O HIS K 509 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 546 through 548 removed outlier: 6.376A pdb=" N ARG K 512 " --> pdb=" O ILE I 631 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR I 620 " --> pdb=" O LEU I 615 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 3 through 5 removed outlier: 6.670A pdb=" N ARG I 23 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU I 101 " --> pdb=" O ARG I 23 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N MET I 25 " --> pdb=" O LEU I 101 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE I 100 " --> pdb=" O TYR I 125 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N THR I 127 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL I 124 " --> pdb=" O THR I 194 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET I 196 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA I 126 " --> pdb=" O MET I 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 69 through 71 Processing sheet with id=AB1, first strand: chain 'I' and resid 202 through 204 removed outlier: 3.744A pdb=" N PHE I 208 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS I 232 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ILE I 261 " --> pdb=" O LYS I 232 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS I 234 " --> pdb=" O ILE I 261 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU I 260 " --> pdb=" O VAL I 470 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N MET I 262 " --> pdb=" O PRO I 472 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU I 469 " --> pdb=" O ILE I 495 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE I 497 " --> pdb=" O LEU I 469 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE I 471 " --> pdb=" O PHE I 497 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 372 through 375 removed outlier: 5.952A pdb=" N PHE I 326 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 541 through 542 534 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.41 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: 2117 1.32 - 1.44: 3245 1.44 - 1.56: 7575 1.56 - 1.69: 6 1.69 - 1.81: 167 Bond restraints: 13110 Sorted by residual: bond pdb=" C5 IHP I 701 " pdb=" O15 IHP I 701 " ideal model delta sigma weight residual 1.389 1.465 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 IHP I 701 " pdb=" O11 IHP I 701 " ideal model delta sigma weight residual 1.392 1.463 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C3 IHP I 701 " pdb=" O13 IHP I 701 " ideal model delta sigma weight residual 1.393 1.463 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C6 IHP I 701 " pdb=" O16 IHP I 701 " ideal model delta sigma weight residual 1.394 1.463 -0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C4 IHP I 701 " pdb=" O14 IHP I 701 " ideal model delta sigma weight residual 1.394 1.463 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 13105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 16947 1.95 - 3.90: 607 3.90 - 5.85: 122 5.85 - 7.80: 33 7.80 - 9.75: 9 Bond angle restraints: 17718 Sorted by residual: angle pdb=" CA PHE D 444 " pdb=" C PHE D 444 " pdb=" O PHE D 444 " ideal model delta sigma weight residual 119.48 109.95 9.53 1.18e+00 7.18e-01 6.52e+01 angle pdb=" N PHE D 444 " pdb=" CA PHE D 444 " pdb=" C PHE D 444 " ideal model delta sigma weight residual 112.94 120.75 -7.81 1.41e+00 5.03e-01 3.07e+01 angle pdb=" C VAL I 544 " pdb=" N LYS I 545 " pdb=" CA LYS I 545 " ideal model delta sigma weight residual 121.54 131.29 -9.75 1.91e+00 2.74e-01 2.61e+01 angle pdb=" CA PRO I 428 " pdb=" C PRO I 428 " pdb=" O PRO I 428 " ideal model delta sigma weight residual 121.32 116.03 5.29 1.09e+00 8.42e-01 2.36e+01 angle pdb=" CA PHE D 444 " pdb=" C PHE D 444 " pdb=" N LEU D 445 " ideal model delta sigma weight residual 118.27 124.44 -6.17 1.30e+00 5.92e-01 2.25e+01 ... (remaining 17713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 7166 18.04 - 36.07: 685 36.07 - 54.11: 108 54.11 - 72.14: 25 72.14 - 90.18: 8 Dihedral angle restraints: 7992 sinusoidal: 3264 harmonic: 4728 Sorted by residual: dihedral pdb=" CA LYS I 545 " pdb=" C LYS I 545 " pdb=" N ASP I 546 " pdb=" CA ASP I 546 " ideal model delta harmonic sigma weight residual 180.00 150.89 29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ILE I 495 " pdb=" C ILE I 495 " pdb=" N THR I 496 " pdb=" CA THR I 496 " ideal model delta harmonic sigma weight residual 180.00 -152.06 -27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR I 355 " pdb=" C TYR I 355 " pdb=" N LEU I 356 " pdb=" CA LEU I 356 " ideal model delta harmonic sigma weight residual 180.00 152.37 27.63 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 7989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1934 0.123 - 0.246: 81 0.246 - 0.370: 3 0.370 - 0.493: 1 0.493 - 0.616: 1 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CA PHE D 444 " pdb=" N PHE D 444 " pdb=" C PHE D 444 " pdb=" CB PHE D 444 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.49e+00 chirality pdb=" CB VAL I 213 " pdb=" CA VAL I 213 " pdb=" CG1 VAL I 213 " pdb=" CG2 VAL I 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C1 IHP I 701 " pdb=" C2 IHP I 701 " pdb=" C6 IHP I 701 " pdb=" O11 IHP I 701 " both_signs ideal model delta sigma weight residual False 2.32 2.65 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 2017 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE I 394 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C PHE I 394 " -0.051 2.00e-02 2.50e+03 pdb=" O PHE I 394 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS I 395 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 81 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO I 82 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO I 82 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO I 82 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO I 428 " -0.011 2.00e-02 2.50e+03 2.36e-02 5.57e+00 pdb=" C PRO I 428 " 0.041 2.00e-02 2.50e+03 pdb=" O PRO I 428 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR I 429 " -0.014 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1153 2.74 - 3.28: 12297 3.28 - 3.82: 20671 3.82 - 4.36: 25212 4.36 - 4.90: 43195 Nonbonded interactions: 102528 Sorted by model distance: nonbonded pdb=" O ASP K 521 " pdb=" CA LYS K 570 " model vdw 2.204 3.470 nonbonded pdb=" O THR I 263 " pdb=" OH TYR I 475 " model vdw 2.240 3.040 nonbonded pdb=" O ALA K 268 " pdb=" OG1 THR K 324 " model vdw 2.255 3.040 nonbonded pdb=" O SER I 215 " pdb=" OG SER I 221 " model vdw 2.266 3.040 nonbonded pdb=" O ILE I 114 " pdb=" OG1 THR I 118 " model vdw 2.270 3.040 ... (remaining 102523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.080 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.330 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.006 0.076 13115 Z= 0.269 Angle : 0.911 9.751 17718 Z= 0.506 Chirality : 0.059 0.616 2020 Planarity : 0.006 0.068 2235 Dihedral : 14.518 90.175 4928 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.28 % Allowed : 0.35 % Favored : 99.37 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.20), residues: 1597 helix: -0.38 (0.20), residues: 644 sheet: 0.18 (0.40), residues: 183 loop : -1.93 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 23 TYR 0.019 0.002 TYR I 4 PHE 0.033 0.002 PHE I 181 TRP 0.010 0.002 TRP K 165 HIS 0.012 0.002 HIS K 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.27 (13110) covalent geometry : angle 0.91093 / 0.51 (17718) hydrogen bonds : bond 0.15430 / 10.00 ( 534) hydrogen bonds : angle 6.60418 / 4.66 ( 1518) metal coordination : bond 0.00503 / 0.30 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 0.398 Fit side-chains REVERT: D 105 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7619 (ttm170) REVERT: D 195 MET cc_start: 0.9098 (mmp) cc_final: 0.8628 (mmp) REVERT: D 207 HIS cc_start: 0.7189 (p-80) cc_final: 0.6753 (p-80) REVERT: D 443 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: D 565 ARG cc_start: 0.4649 (ttm-80) cc_final: 0.4068 (tpp-160) REVERT: D 566 LYS cc_start: 0.7263 (mtmt) cc_final: 0.6970 (mtmm) REVERT: K 511 MET cc_start: 0.6463 (ptp) cc_final: 0.5728 (ptp) REVERT: I 9 ASP cc_start: 0.7914 (t70) cc_final: 0.7662 (t70) REVERT: I 279 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6846 (mm-30) outliers start: 4 outliers final: 0 residues processed: 166 average time/residue: 0.6935 time to fit residues: 123.8487 Evaluate side-chains 133 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 443 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 329 HIS K 356 GLN I 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.173748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134502 restraints weight = 15452.092| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.37 r_work: 0.3381 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13115 Z= 0.136 Angle : 0.643 11.700 17718 Z= 0.341 Chirality : 0.046 0.166 2020 Planarity : 0.005 0.052 2235 Dihedral : 6.695 57.148 1743 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.61 % Allowed : 7.92 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.93 (0.21), residues: 1597 helix: 0.38 (0.20), residues: 650 sheet: 0.45 (0.40), residues: 183 loop : -1.82 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 242 TYR 0.014 0.001 TYR D 302 PHE 0.014 0.001 PHE K 69 TRP 0.008 0.001 TRP K 165 HIS 0.007 0.001 HIS K 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (13110) covalent geometry : angle 0.64288 / 0.34 (17718) hydrogen bonds : bond 0.04147 / 2.73 ( 534) hydrogen bonds : angle 5.19321 / 3.66 ( 1518) metal coordination : bond 0.00189 / 0.11 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.464 Fit side-chains REVERT: D 105 ARG cc_start: 0.8285 (ttm-80) cc_final: 0.8063 (ttm170) REVERT: D 195 MET cc_start: 0.9209 (mmp) cc_final: 0.8971 (mmt) REVERT: D 565 ARG cc_start: 0.4989 (ttm-80) cc_final: 0.4531 (tpp-160) REVERT: K 125 MET cc_start: 0.8485 (ptp) cc_final: 0.8154 (ptm) REVERT: K 385 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7348 (mm-30) REVERT: K 416 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: K 547 MET cc_start: 0.3198 (tpp) cc_final: 0.2617 (mtm) REVERT: I 155 ARG cc_start: 0.7798 (ptp-110) cc_final: 0.7498 (pmm-80) REVERT: I 279 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7613 (mm-30) REVERT: I 411 MET cc_start: 0.8348 (ttp) cc_final: 0.7920 (ttp) outliers start: 23 outliers final: 7 residues processed: 156 average time/residue: 0.6762 time to fit residues: 113.9372 Evaluate side-chains 137 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 416 GLU Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 282 MET Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 518 SER Chi-restraints excluded: chain I residue 534 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 121 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.1980 chunk 60 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 157 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 375 HIS K 329 HIS K 496 ASN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.175354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.127144 restraints weight = 15506.464| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.05 r_work: 0.3407 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13115 Z= 0.113 Angle : 0.579 10.719 17718 Z= 0.307 Chirality : 0.044 0.181 2020 Planarity : 0.004 0.044 2235 Dihedral : 5.918 52.067 1740 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 1.54 % Allowed : 11.29 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.21), residues: 1597 helix: 0.85 (0.21), residues: 655 sheet: 0.72 (0.39), residues: 194 loop : -1.72 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 491 TYR 0.011 0.001 TYR D 302 PHE 0.009 0.001 PHE I 444 TRP 0.007 0.001 TRP K 165 HIS 0.005 0.001 HIS I 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (13110) covalent geometry : angle 0.57863 / 0.31 (17718) hydrogen bonds : bond 0.03414 / 2.27 ( 534) hydrogen bonds : angle 4.78941 / 3.36 ( 1518) metal coordination : bond 0.00139 / 0.08 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: D 105 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.8040 (ttm170) REVERT: D 195 MET cc_start: 0.9194 (mmp) cc_final: 0.8964 (mmt) REVERT: D 319 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6955 (mtp180) REVERT: D 565 ARG cc_start: 0.4756 (ttm-80) cc_final: 0.4533 (tpp-160) REVERT: K 107 MET cc_start: 0.8008 (tmm) cc_final: 0.7760 (ttp) REVERT: K 125 MET cc_start: 0.8384 (ptp) cc_final: 0.8157 (ptm) REVERT: K 299 MET cc_start: 0.7949 (mtt) cc_final: 0.7661 (mtt) REVERT: K 385 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7465 (mm-30) REVERT: K 547 MET cc_start: 0.3481 (tpp) cc_final: 0.2531 (mtm) REVERT: I 88 MET cc_start: 0.8501 (mtt) cc_final: 0.8296 (mtt) REVERT: I 155 ARG cc_start: 0.7911 (ptp-110) cc_final: 0.7614 (pmm-80) REVERT: I 279 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7520 (mm-30) REVERT: I 411 MET cc_start: 0.8370 (ttp) cc_final: 0.7934 (ttp) outliers start: 22 outliers final: 7 residues processed: 159 average time/residue: 0.7158 time to fit residues: 122.7789 Evaluate side-chains 139 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 419 SER Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 533 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 114 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 496 ASN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.172949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.124444 restraints weight = 15483.095| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.04 r_work: 0.3372 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13115 Z= 0.145 Angle : 0.611 11.124 17718 Z= 0.322 Chirality : 0.046 0.159 2020 Planarity : 0.004 0.047 2235 Dihedral : 5.920 54.312 1740 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.17 % Allowed : 13.88 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.42 (0.21), residues: 1597 helix: 0.89 (0.21), residues: 650 sheet: 0.68 (0.41), residues: 187 loop : -1.62 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 502 TYR 0.012 0.001 TYR D 302 PHE 0.016 0.001 PHE K 69 TRP 0.006 0.001 TRP K 165 HIS 0.009 0.001 HIS K 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (13110) covalent geometry : angle 0.61109 / 0.32 (17718) hydrogen bonds : bond 0.03699 / 2.43 ( 534) hydrogen bonds : angle 4.72744 / 3.33 ( 1518) metal coordination : bond 0.00329 / 0.21 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: D 195 MET cc_start: 0.9150 (mmp) cc_final: 0.8921 (mmp) REVERT: D 207 HIS cc_start: 0.7153 (p90) cc_final: 0.6802 (p90) REVERT: D 319 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6896 (mtp180) REVERT: D 513 LEU cc_start: 0.6765 (mt) cc_final: 0.6348 (mp) REVERT: D 565 ARG cc_start: 0.4741 (ttm-80) cc_final: 0.4500 (tpp-160) REVERT: K 107 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7611 (ttp) REVERT: K 385 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7472 (mm-30) REVERT: K 511 MET cc_start: 0.6429 (ptp) cc_final: 0.5987 (ptm) REVERT: K 547 MET cc_start: 0.3487 (tpp) cc_final: 0.2538 (mtm) REVERT: I 279 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7597 (mm-30) REVERT: I 411 MET cc_start: 0.8331 (ttp) cc_final: 0.8010 (ttp) outliers start: 31 outliers final: 19 residues processed: 157 average time/residue: 0.6562 time to fit residues: 111.7451 Evaluate side-chains 151 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 282 MET Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 395 CYS Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 3 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 140 GLN K 496 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.175331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134224 restraints weight = 15559.968| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.19 r_work: 0.3417 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13115 Z= 0.110 Angle : 0.565 11.099 17718 Z= 0.298 Chirality : 0.044 0.186 2020 Planarity : 0.004 0.043 2235 Dihedral : 5.655 53.835 1740 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.10 % Allowed : 14.94 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.18 (0.21), residues: 1597 helix: 1.14 (0.21), residues: 646 sheet: 0.99 (0.40), residues: 190 loop : -1.59 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 502 TYR 0.010 0.001 TYR D 302 PHE 0.010 0.001 PHE K 121 TRP 0.008 0.001 TRP K 165 HIS 0.009 0.001 HIS K 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (13110) covalent geometry : angle 0.56504 / 0.30 (17718) hydrogen bonds : bond 0.03194 / 2.12 ( 534) hydrogen bonds : angle 4.55151 / 3.19 ( 1518) metal coordination : bond 0.00166 / 0.11 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.523 Fit side-chains REVERT: D 207 HIS cc_start: 0.7149 (p90) cc_final: 0.6760 (p90) REVERT: D 565 ARG cc_start: 0.4731 (ttm-80) cc_final: 0.4529 (tpp-160) REVERT: K 50 TYR cc_start: 0.8013 (t80) cc_final: 0.7657 (t80) REVERT: K 125 MET cc_start: 0.8514 (ptp) cc_final: 0.8305 (ptm) REVERT: K 385 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7499 (mm-30) REVERT: K 511 MET cc_start: 0.6512 (ptp) cc_final: 0.5854 (ptm) REVERT: K 547 MET cc_start: 0.3473 (tpp) cc_final: 0.2520 (mtm) REVERT: I 88 MET cc_start: 0.8493 (mtt) cc_final: 0.8249 (mtt) REVERT: I 279 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7559 (mm-30) REVERT: I 284 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8359 (t) REVERT: I 411 MET cc_start: 0.8086 (ttp) cc_final: 0.7794 (ttp) REVERT: I 419 SER cc_start: 0.8189 (p) cc_final: 0.7770 (m) outliers start: 30 outliers final: 14 residues processed: 160 average time/residue: 0.6300 time to fit residues: 109.6398 Evaluate side-chains 147 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 282 MET Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 395 CYS Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 157 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 0.0570 chunk 147 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 496 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.174799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126571 restraints weight = 15370.797| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.04 r_work: 0.3404 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13115 Z= 0.117 Angle : 0.574 11.116 17718 Z= 0.302 Chirality : 0.044 0.157 2020 Planarity : 0.004 0.043 2235 Dihedral : 5.592 54.455 1740 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.24 % Allowed : 16.27 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.11 (0.21), residues: 1597 helix: 1.17 (0.21), residues: 648 sheet: 0.80 (0.39), residues: 204 loop : -1.49 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 502 TYR 0.010 0.001 TYR D 302 PHE 0.012 0.001 PHE K 69 TRP 0.006 0.001 TRP K 165 HIS 0.008 0.001 HIS K 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13110) covalent geometry : angle 0.57382 / 0.30 (17718) hydrogen bonds : bond 0.03276 / 2.16 ( 534) hydrogen bonds : angle 4.50808 / 3.16 ( 1518) metal coordination : bond 0.00251 / 0.15 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.538 Fit side-chains REVERT: D 207 HIS cc_start: 0.7212 (OUTLIER) cc_final: 0.6875 (p90) REVERT: D 565 ARG cc_start: 0.4882 (ttm-80) cc_final: 0.4415 (tpp-160) REVERT: K 50 TYR cc_start: 0.7998 (t80) cc_final: 0.7640 (t80) REVERT: K 125 MET cc_start: 0.8539 (ptp) cc_final: 0.8303 (ptm) REVERT: K 385 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7549 (mm-30) REVERT: K 511 MET cc_start: 0.6551 (ptp) cc_final: 0.6209 (ptm) REVERT: K 512 ARG cc_start: 0.5991 (ttp-110) cc_final: 0.5547 (ttt180) REVERT: K 547 MET cc_start: 0.3431 (tpp) cc_final: 0.2711 (mpp) REVERT: I 88 MET cc_start: 0.8537 (mtt) cc_final: 0.8321 (mtt) REVERT: I 279 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7518 (mm-30) REVERT: I 284 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8381 (t) REVERT: I 411 MET cc_start: 0.8070 (ttp) cc_final: 0.7766 (ttp) REVERT: I 419 SER cc_start: 0.8291 (p) cc_final: 0.7848 (m) outliers start: 32 outliers final: 17 residues processed: 158 average time/residue: 0.6350 time to fit residues: 109.3185 Evaluate side-chains 153 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 395 CYS Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 10 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 122 optimal weight: 0.0370 chunk 23 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 496 ASN K 571 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.173823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132033 restraints weight = 15435.223| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.23 r_work: 0.3389 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13115 Z= 0.126 Angle : 0.581 11.179 17718 Z= 0.306 Chirality : 0.045 0.155 2020 Planarity : 0.004 0.044 2235 Dihedral : 5.612 55.711 1740 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.66 % Allowed : 16.62 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.11 (0.21), residues: 1597 helix: 1.15 (0.21), residues: 654 sheet: 0.85 (0.39), residues: 204 loop : -1.51 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 502 TYR 0.011 0.001 TYR D 302 PHE 0.014 0.001 PHE K 69 TRP 0.006 0.001 TRP K 165 HIS 0.009 0.001 HIS K 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (13110) covalent geometry : angle 0.58063 / 0.31 (17718) hydrogen bonds : bond 0.03361 / 2.21 ( 534) hydrogen bonds : angle 4.49277 / 3.15 ( 1518) metal coordination : bond 0.00243 / 0.15 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.520 Fit side-chains REVERT: D 207 HIS cc_start: 0.7222 (OUTLIER) cc_final: 0.6876 (p90) REVERT: D 473 LEU cc_start: 0.8091 (tp) cc_final: 0.7825 (mt) REVERT: D 565 ARG cc_start: 0.4896 (ttm-80) cc_final: 0.4486 (mmm160) REVERT: K 50 TYR cc_start: 0.8092 (t80) cc_final: 0.7740 (t80) REVERT: K 125 MET cc_start: 0.8568 (ptp) cc_final: 0.8338 (ptm) REVERT: K 298 ASN cc_start: 0.8036 (p0) cc_final: 0.7680 (p0) REVERT: K 385 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7610 (mm-30) REVERT: K 387 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7430 (mtp) REVERT: K 511 MET cc_start: 0.6446 (ptp) cc_final: 0.6080 (ptm) REVERT: K 512 ARG cc_start: 0.6007 (ttp-110) cc_final: 0.5522 (ttt-90) REVERT: K 547 MET cc_start: 0.3411 (tpp) cc_final: 0.2782 (mpt) REVERT: I 279 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7498 (mm-30) REVERT: I 284 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8380 (t) REVERT: I 419 SER cc_start: 0.8273 (p) cc_final: 0.7856 (m) outliers start: 38 outliers final: 27 residues processed: 166 average time/residue: 0.5902 time to fit residues: 107.2868 Evaluate side-chains 167 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 130 MET Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 157 HIS Chi-restraints excluded: chain K residue 387 MET Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 487 MET Chi-restraints excluded: chain K residue 497 LEU Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 395 CYS Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 541 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 144 optimal weight: 0.0470 chunk 109 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 496 ASN K 507 ASN I 522 GLN I 549 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.174810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126529 restraints weight = 15452.646| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.04 r_work: 0.3403 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13115 Z= 0.115 Angle : 0.571 11.127 17718 Z= 0.300 Chirality : 0.044 0.144 2020 Planarity : 0.004 0.043 2235 Dihedral : 5.535 56.239 1740 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.45 % Allowed : 16.97 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.06 (0.21), residues: 1597 helix: 1.20 (0.21), residues: 648 sheet: 0.85 (0.39), residues: 204 loop : -1.47 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 502 TYR 0.020 0.001 TYR K 386 PHE 0.011 0.001 PHE K 69 TRP 0.007 0.001 TRP K 165 HIS 0.008 0.001 HIS K 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13110) covalent geometry : angle 0.57129 / 0.30 (17718) hydrogen bonds : bond 0.03220 / 2.13 ( 534) hydrogen bonds : angle 4.44201 / 3.11 ( 1518) metal coordination : bond 0.00215 / 0.13 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.526 Fit side-chains REVERT: D 207 HIS cc_start: 0.7212 (p90) cc_final: 0.6901 (p90) REVERT: D 285 GLN cc_start: 0.7247 (tp40) cc_final: 0.6969 (tp40) REVERT: D 473 LEU cc_start: 0.8085 (tp) cc_final: 0.7832 (mt) REVERT: D 565 ARG cc_start: 0.4895 (ttm-80) cc_final: 0.4493 (mmm160) REVERT: K 50 TYR cc_start: 0.8111 (t80) cc_final: 0.7776 (t80) REVERT: K 125 MET cc_start: 0.8547 (ptp) cc_final: 0.8307 (ptm) REVERT: K 298 ASN cc_start: 0.7981 (p0) cc_final: 0.7615 (p0) REVERT: K 385 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7574 (mm-30) REVERT: K 511 MET cc_start: 0.6639 (ptp) cc_final: 0.6195 (ptm) REVERT: K 547 MET cc_start: 0.3411 (tpp) cc_final: 0.2778 (mpt) REVERT: I 279 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7501 (mm-30) REVERT: I 284 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8372 (t) REVERT: I 419 SER cc_start: 0.8242 (p) cc_final: 0.7841 (m) outliers start: 35 outliers final: 29 residues processed: 164 average time/residue: 0.6025 time to fit residues: 108.0136 Evaluate side-chains 167 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 130 MET Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 157 HIS Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 487 MET Chi-restraints excluded: chain K residue 497 LEU Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 395 CYS Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 621 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 92 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 496 ASN K 507 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.170949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129258 restraints weight = 15452.936| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.14 r_work: 0.3354 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13115 Z= 0.195 Angle : 0.668 11.600 17718 Z= 0.350 Chirality : 0.048 0.178 2020 Planarity : 0.004 0.048 2235 Dihedral : 5.938 59.424 1740 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.38 % Allowed : 17.25 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.33 (0.21), residues: 1597 helix: 0.89 (0.21), residues: 655 sheet: 0.74 (0.39), residues: 213 loop : -1.59 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 502 TYR 0.014 0.002 TYR D 302 PHE 0.021 0.002 PHE K 69 TRP 0.007 0.001 TRP I 157 HIS 0.011 0.002 HIS K 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.19 (13110) covalent geometry : angle 0.66754 / 0.35 (17718) hydrogen bonds : bond 0.04102 / 2.67 ( 534) hydrogen bonds : angle 4.64947 / 3.27 ( 1518) metal coordination : bond 0.00460 / 0.29 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.513 Fit side-chains REVERT: D 207 HIS cc_start: 0.7211 (OUTLIER) cc_final: 0.6858 (p90) REVERT: D 473 LEU cc_start: 0.8142 (tp) cc_final: 0.7858 (mt) REVERT: D 565 ARG cc_start: 0.4897 (ttm-80) cc_final: 0.4513 (mmm160) REVERT: K 50 TYR cc_start: 0.8138 (t80) cc_final: 0.7747 (t80) REVERT: K 107 MET cc_start: 0.7828 (tmm) cc_final: 0.7566 (ttp) REVERT: K 125 MET cc_start: 0.8658 (ptp) cc_final: 0.8439 (ptm) REVERT: K 216 CYS cc_start: 0.7996 (m) cc_final: 0.7526 (m) REVERT: K 298 ASN cc_start: 0.8071 (p0) cc_final: 0.7708 (p0) REVERT: K 385 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7554 (mm-30) REVERT: K 496 ASN cc_start: 0.7847 (m110) cc_final: 0.7464 (m-40) REVERT: K 511 MET cc_start: 0.6653 (ptp) cc_final: 0.6165 (ptm) REVERT: K 547 MET cc_start: 0.3549 (tpp) cc_final: 0.2816 (mpp) REVERT: I 279 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7525 (mm-30) REVERT: I 284 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8379 (t) REVERT: I 341 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7772 (mp) REVERT: I 419 SER cc_start: 0.8262 (p) cc_final: 0.7772 (m) outliers start: 34 outliers final: 26 residues processed: 157 average time/residue: 0.5964 time to fit residues: 102.4600 Evaluate side-chains 160 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 130 MET Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 487 MET Chi-restraints excluded: chain K residue 497 LEU Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 395 CYS Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 621 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 94 optimal weight: 20.0000 chunk 118 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 105 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 507 ASN I 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.174846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135641 restraints weight = 15466.148| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.32 r_work: 0.3403 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13115 Z= 0.112 Angle : 0.575 11.081 17718 Z= 0.302 Chirality : 0.044 0.146 2020 Planarity : 0.004 0.042 2235 Dihedral : 5.602 59.960 1740 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.31 % Allowed : 17.53 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -0.10 (0.21), residues: 1597 helix: 1.15 (0.21), residues: 648 sheet: 0.96 (0.39), residues: 202 loop : -1.52 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 502 TYR 0.010 0.001 TYR D 302 PHE 0.012 0.001 PHE K 69 TRP 0.010 0.001 TRP K 165 HIS 0.008 0.001 HIS K 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (13110) covalent geometry : angle 0.57491 / 0.30 (17718) hydrogen bonds : bond 0.03173 / 2.11 ( 534) hydrogen bonds : angle 4.44753 / 3.11 ( 1518) metal coordination : bond 0.00182 / 0.10 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.516 Fit side-chains REVERT: D 207 HIS cc_start: 0.7189 (OUTLIER) cc_final: 0.6832 (p90) REVERT: D 473 LEU cc_start: 0.8118 (tp) cc_final: 0.7892 (mt) REVERT: D 565 ARG cc_start: 0.4903 (ttm-80) cc_final: 0.4522 (mmm160) REVERT: K 50 TYR cc_start: 0.8108 (t80) cc_final: 0.7713 (t80) REVERT: K 125 MET cc_start: 0.8554 (ptp) cc_final: 0.8325 (ptm) REVERT: K 216 CYS cc_start: 0.7970 (m) cc_final: 0.7533 (m) REVERT: K 298 ASN cc_start: 0.8108 (p0) cc_final: 0.7736 (p0) REVERT: K 385 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7585 (mm-30) REVERT: K 511 MET cc_start: 0.6575 (ptp) cc_final: 0.6155 (ptm) REVERT: K 512 ARG cc_start: 0.6239 (ttp-110) cc_final: 0.5510 (ttt-90) REVERT: K 547 MET cc_start: 0.3392 (tpp) cc_final: 0.2769 (mpt) REVERT: I 75 ARG cc_start: 0.7453 (mtp85) cc_final: 0.7007 (mtp-110) REVERT: I 279 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7582 (mm-30) REVERT: I 284 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8360 (t) REVERT: I 419 SER cc_start: 0.8243 (p) cc_final: 0.7924 (m) outliers start: 33 outliers final: 24 residues processed: 166 average time/residue: 0.5899 time to fit residues: 107.2870 Evaluate side-chains 166 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 207 HIS Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 130 MET Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 VAL Chi-restraints excluded: chain K residue 497 LEU Chi-restraints excluded: chain K residue 510 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 395 CYS Chi-restraints excluded: chain I residue 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 621 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 5 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 113 optimal weight: 0.0370 chunk 51 optimal weight: 0.0040 chunk 56 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 154 optimal weight: 0.1980 overall best weight: 0.2870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.178598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.139324 restraints weight = 15552.079| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.44 r_work: 0.3446 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13115 Z= 0.098 Angle : 0.549 10.668 17718 Z= 0.286 Chirality : 0.043 0.147 2020 Planarity : 0.004 0.044 2235 Dihedral : 5.227 59.977 1740 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.47 % Allowed : 18.37 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.22), residues: 1597 helix: 1.34 (0.21), residues: 659 sheet: 1.07 (0.39), residues: 199 loop : -1.49 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 502 TYR 0.018 0.001 TYR K 386 PHE 0.008 0.001 PHE I 444 TRP 0.013 0.001 TRP K 165 HIS 0.008 0.001 HIS K 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (13110) covalent geometry : angle 0.54906 / 0.29 (17718) hydrogen bonds : bond 0.02788 / 1.87 ( 534) hydrogen bonds : angle 4.27672 / 2.97 ( 1518) metal coordination : bond 0.00132 / 0.07 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5573.05 seconds wall clock time: 95 minutes 55.31 seconds (5755.31 seconds total)