Starting phenix.real_space_refine on Mon Dec 30 10:54:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sn8_25214/12_2024/7sn8_25214.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sn8_25214/12_2024/7sn8_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_25214/12_2024/7sn8_25214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sn8_25214/12_2024/7sn8_25214.map" model { file = "/net/cci-nas-00/data/ceres_data/7sn8_25214/12_2024/7sn8_25214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sn8_25214/12_2024/7sn8_25214.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.65, per 1000 atoms: 0.59 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: 3.03 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.59 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: 4.26 Time building geometry restraints manager: 3.45 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: 7202 18.04 - 36.07: 685 36.07 - 54.11: 108 54.11 - 72.14: 25 72.14 - 90.18: 8 Dihedral angle restraints: 8028 sinusoidal: 3300 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 8025 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.940 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 13110 Z= 0.401 Angle : 0.911 9.751 17718 Z= 0.506 Chirality : 0.059 0.616 2020 Planarity : 0.006 0.068 2235 Dihedral : 14.483 90.175 4964 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.002 TRP K 165 HIS 0.012 0.002 HIS K 414 PHE 0.033 0.002 PHE I 181 TYR 0.019 0.002 TYR I 4 ARG 0.008 0.001 ARG I 23 *********************** 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 : 1.453 Fit side-chains REVERT: D 105 ARG cc_start: 0.7836 (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: 1.5572 time to fit residues: 278.0040 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 : 1.520 ------------------------------------------------------------------------------- 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 135 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 0.0970 chunk 93 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 329 HIS K 356 GLN K 374 ASN I 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13110 Z= 0.190 Angle : 0.635 11.787 17718 Z= 0.337 Chirality : 0.046 0.167 2020 Planarity : 0.005 0.051 2235 Dihedral : 6.667 55.723 1779 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.54 % Allowed : 7.71 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1597 helix: 0.42 (0.21), residues: 650 sheet: 0.31 (0.40), residues: 187 loop : -1.78 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 165 HIS 0.006 0.001 HIS K 414 PHE 0.013 0.001 PHE K 69 TYR 0.013 0.001 TYR D 302 ARG 0.007 0.000 ARG D 502 *********************** 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: 22 poor density : 144 time to evaluate : 1.480 Fit side-chains REVERT: D 105 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7593 (ttm170) REVERT: D 195 MET cc_start: 0.9061 (mmp) cc_final: 0.8772 (mmt) REVERT: D 565 ARG cc_start: 0.4871 (ttm-80) cc_final: 0.4460 (tpp-160) REVERT: K 125 MET cc_start: 0.8491 (ptp) cc_final: 0.8173 (ptm) REVERT: K 416 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.5981 (tm-30) REVERT: K 547 MET cc_start: 0.3097 (tpp) cc_final: 0.2613 (mpm) REVERT: I 155 ARG cc_start: 0.7524 (ptp-110) cc_final: 0.7198 (pmm-80) REVERT: I 279 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6896 (mm-30) REVERT: I 411 MET cc_start: 0.7763 (ttp) cc_final: 0.7544 (ttp) outliers start: 22 outliers final: 5 residues processed: 155 average time/residue: 1.5408 time to fit residues: 258.2688 Evaluate side-chains 135 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 534 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13110 Z= 0.199 Angle : 0.603 10.995 17718 Z= 0.321 Chirality : 0.046 0.207 2020 Planarity : 0.004 0.047 2235 Dihedral : 6.095 54.888 1776 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.03 % Allowed : 11.43 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1597 helix: 0.76 (0.21), residues: 654 sheet: 0.61 (0.41), residues: 187 loop : -1.69 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 165 HIS 0.008 0.001 HIS K 414 PHE 0.013 0.001 PHE K 69 TYR 0.012 0.001 TYR D 260 ARG 0.004 0.000 ARG D 502 *********************** 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 168 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 105 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7585 (ttm170) REVERT: D 195 MET cc_start: 0.9076 (mmp) cc_final: 0.8812 (mmt) REVERT: D 319 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6678 (mtp180) REVERT: D 443 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: K 107 MET cc_start: 0.7532 (tmm) cc_final: 0.7259 (ttp) REVERT: K 125 MET cc_start: 0.8462 (ptp) cc_final: 0.8197 (ptm) REVERT: K 511 MET cc_start: 0.6661 (ptp) cc_final: 0.6295 (ptm) REVERT: K 547 MET cc_start: 0.3472 (tpp) cc_final: 0.2346 (mtm) REVERT: I 155 ARG cc_start: 0.7635 (ptp-110) cc_final: 0.7330 (pmm-80) REVERT: I 279 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6858 (mm-30) REVERT: I 411 MET cc_start: 0.7820 (ttp) cc_final: 0.7571 (ttp) outliers start: 29 outliers final: 13 residues processed: 160 average time/residue: 1.5182 time to fit residues: 261.6572 Evaluate side-chains 144 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 D residue 443 GLU Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 344 GLU 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 266 THR Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 518 SER Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 534 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 0.0570 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 329 HIS K 496 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13110 Z= 0.269 Angle : 0.640 11.289 17718 Z= 0.338 Chirality : 0.047 0.172 2020 Planarity : 0.004 0.050 2235 Dihedral : 6.145 58.812 1776 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.24 % Allowed : 13.53 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1597 helix: 0.72 (0.21), residues: 654 sheet: 0.71 (0.42), residues: 179 loop : -1.68 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 165 HIS 0.009 0.001 HIS K 414 PHE 0.019 0.002 PHE K 69 TYR 0.013 0.001 TYR D 302 ARG 0.003 0.000 ARG D 502 *********************** 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 162 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: D 105 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7673 (ttm170) REVERT: K 50 TYR cc_start: 0.7621 (t80) cc_final: 0.7203 (t80) REVERT: K 107 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7205 (ttp) REVERT: K 125 MET cc_start: 0.8484 (ptp) cc_final: 0.8216 (ptm) REVERT: K 387 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7280 (mtt) REVERT: K 511 MET cc_start: 0.6577 (ptp) cc_final: 0.6112 (ptm) REVERT: K 547 MET cc_start: 0.3575 (tpp) cc_final: 0.2285 (mtm) REVERT: I 279 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6900 (mm-30) REVERT: I 284 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8284 (t) outliers start: 32 outliers final: 16 residues processed: 151 average time/residue: 1.3934 time to fit residues: 228.5645 Evaluate side-chains 145 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 107 MET Chi-restraints excluded: chain K residue 146 THR 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 510 VAL 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13110 Z= 0.192 Angle : 0.587 11.076 17718 Z= 0.310 Chirality : 0.045 0.162 2020 Planarity : 0.004 0.046 2235 Dihedral : 5.878 59.081 1776 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.52 % Allowed : 14.80 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1597 helix: 0.96 (0.21), residues: 647 sheet: 0.73 (0.39), residues: 206 loop : -1.60 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 165 HIS 0.008 0.001 HIS K 329 PHE 0.011 0.001 PHE K 69 TYR 0.011 0.001 TYR D 302 ARG 0.004 0.000 ARG D 502 *********************** 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 170 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.555 Fit side-chains REVERT: D 105 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7618 (ttm170) REVERT: D 319 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6632 (mtp180) REVERT: D 565 ARG cc_start: 0.5260 (tpp-160) cc_final: 0.4856 (mmm160) REVERT: K 50 TYR cc_start: 0.7679 (t80) cc_final: 0.7303 (t80) REVERT: K 107 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7204 (ttp) REVERT: K 305 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8130 (mm) REVERT: K 511 MET cc_start: 0.6782 (ptp) cc_final: 0.6324 (ptm) REVERT: K 512 ARG cc_start: 0.6092 (ttp-110) cc_final: 0.5829 (ttt-90) REVERT: K 547 MET cc_start: 0.3507 (tpp) cc_final: 0.2669 (mpt) REVERT: I 88 MET cc_start: 0.8377 (mtt) cc_final: 0.8172 (mtt) REVERT: I 279 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6849 (mm-30) REVERT: I 284 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8268 (t) REVERT: I 419 SER cc_start: 0.7853 (p) cc_final: 0.7506 (m) outliers start: 36 outliers final: 20 residues processed: 160 average time/residue: 1.3724 time to fit residues: 239.4815 Evaluate side-chains 148 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 473 LEU 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 305 ILE Chi-restraints excluded: chain K residue 344 GLU 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 510 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 147 VAL 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 140 GLN K 496 ASN K 571 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13110 Z= 0.180 Angle : 0.577 10.936 17718 Z= 0.305 Chirality : 0.044 0.146 2020 Planarity : 0.004 0.045 2235 Dihedral : 5.726 59.887 1776 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.59 % Allowed : 16.06 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1597 helix: 1.08 (0.21), residues: 647 sheet: 0.75 (0.39), residues: 206 loop : -1.55 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 165 HIS 0.009 0.001 HIS K 329 PHE 0.012 0.001 PHE K 69 TYR 0.011 0.001 TYR D 302 ARG 0.007 0.000 ARG D 502 *********************** 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 181 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 1.464 Fit side-chains REVERT: D 105 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7620 (ttm170) REVERT: D 161 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7556 (mp) REVERT: D 207 HIS cc_start: 0.7027 (p90) cc_final: 0.6711 (p90) REVERT: D 565 ARG cc_start: 0.5475 (tpp-160) cc_final: 0.4918 (mmm160) REVERT: K 50 TYR cc_start: 0.7755 (t80) cc_final: 0.7388 (t80) REVERT: K 125 MET cc_start: 0.8587 (ptp) cc_final: 0.8357 (ptm) REVERT: K 511 MET cc_start: 0.6728 (ptp) cc_final: 0.6331 (ptm) REVERT: K 512 ARG cc_start: 0.6214 (ttp-110) cc_final: 0.5792 (ttt-90) REVERT: K 547 MET cc_start: 0.3314 (tpp) cc_final: 0.2684 (mpt) REVERT: K 596 MET cc_start: 0.3337 (ppp) cc_final: 0.3109 (pp-130) REVERT: I 279 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6849 (mm-30) REVERT: I 284 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8312 (t) REVERT: I 419 SER cc_start: 0.7964 (p) cc_final: 0.7617 (m) outliers start: 37 outliers final: 19 residues processed: 170 average time/residue: 1.3249 time to fit residues: 245.7151 Evaluate side-chains 154 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 473 LEU 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 510 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 147 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 154 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13110 Z= 0.416 Angle : 0.730 11.421 17718 Z= 0.383 Chirality : 0.051 0.252 2020 Planarity : 0.005 0.053 2235 Dihedral : 6.237 54.391 1776 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.88 % Allowed : 16.83 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1597 helix: 0.69 (0.20), residues: 652 sheet: 0.64 (0.39), residues: 213 loop : -1.74 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP I 157 HIS 0.014 0.002 HIS K 414 PHE 0.025 0.002 PHE K 69 TYR 0.017 0.002 TYR D 302 ARG 0.007 0.001 ARG D 502 *********************** 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 173 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 1.503 Fit side-chains REVERT: D 105 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7701 (ttm170) REVERT: D 169 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7220 (pp30) REVERT: D 207 HIS cc_start: 0.7166 (p90) cc_final: 0.6891 (p90) REVERT: D 565 ARG cc_start: 0.5378 (tpp-160) cc_final: 0.4886 (mmm160) REVERT: K 50 TYR cc_start: 0.7768 (t80) cc_final: 0.7376 (t80) REVERT: K 107 MET cc_start: 0.7438 (tmm) cc_final: 0.7192 (ttp) REVERT: K 125 MET cc_start: 0.8717 (ptp) cc_final: 0.8515 (ptm) REVERT: K 298 ASN cc_start: 0.7920 (p0) cc_final: 0.7591 (p0) REVERT: K 496 ASN cc_start: 0.7706 (m110) cc_final: 0.7367 (m-40) REVERT: K 511 MET cc_start: 0.6847 (ptp) cc_final: 0.6370 (ptm) REVERT: K 547 MET cc_start: 0.3515 (tpp) cc_final: 0.2237 (mtt) REVERT: K 596 MET cc_start: 0.3192 (ppp) cc_final: 0.2972 (pp-130) REVERT: I 279 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6937 (mm-30) REVERT: I 284 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8333 (t) outliers start: 41 outliers final: 25 residues processed: 158 average time/residue: 1.3479 time to fit residues: 231.8391 Evaluate side-chains 157 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 169 GLN Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 560 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13110 Z= 0.205 Angle : 0.604 11.198 17718 Z= 0.320 Chirality : 0.045 0.162 2020 Planarity : 0.004 0.046 2235 Dihedral : 5.890 55.092 1776 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.38 % Allowed : 17.53 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1597 helix: 0.92 (0.21), residues: 648 sheet: 0.79 (0.39), residues: 206 loop : -1.63 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 165 HIS 0.010 0.001 HIS K 329 PHE 0.013 0.001 PHE K 69 TYR 0.012 0.001 TYR D 260 ARG 0.007 0.000 ARG D 502 *********************** 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 170 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.561 Fit side-chains REVERT: D 105 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7622 (ttm170) REVERT: D 207 HIS cc_start: 0.6994 (p90) cc_final: 0.6675 (p90) REVERT: D 565 ARG cc_start: 0.5400 (tpp-160) cc_final: 0.4852 (mmm160) REVERT: K 50 TYR cc_start: 0.7746 (t80) cc_final: 0.7323 (t80) REVERT: K 125 MET cc_start: 0.8631 (ptp) cc_final: 0.8410 (ptm) REVERT: K 298 ASN cc_start: 0.7917 (p0) cc_final: 0.7566 (p0) REVERT: K 387 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.6957 (mtp) REVERT: K 511 MET cc_start: 0.6801 (ptp) cc_final: 0.6359 (ptm) REVERT: K 547 MET cc_start: 0.3454 (tpp) cc_final: 0.2244 (mtm) REVERT: I 88 MET cc_start: 0.8458 (mtt) cc_final: 0.8240 (mtt) REVERT: I 279 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6929 (mm-30) REVERT: I 284 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8326 (t) REVERT: I 419 SER cc_start: 0.7954 (p) cc_final: 0.7659 (m) outliers start: 34 outliers final: 24 residues processed: 158 average time/residue: 1.2396 time to fit residues: 214.7754 Evaluate side-chains 159 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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 130 MET Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 363 ILE 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 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 271 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 395 CYS 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 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 140 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 112 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN I 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13110 Z= 0.167 Angle : 0.577 10.990 17718 Z= 0.304 Chirality : 0.044 0.147 2020 Planarity : 0.004 0.045 2235 Dihedral : 5.607 55.022 1776 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.31 % Allowed : 17.95 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1597 helix: 1.09 (0.21), residues: 653 sheet: 0.93 (0.39), residues: 202 loop : -1.56 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 165 HIS 0.010 0.001 HIS K 329 PHE 0.011 0.001 PHE I 444 TYR 0.011 0.001 TYR D 302 ARG 0.009 0.000 ARG D 502 *********************** 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 173 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.509 Fit side-chains REVERT: D 105 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7610 (ttm170) REVERT: D 207 HIS cc_start: 0.7014 (p90) cc_final: 0.6696 (p90) REVERT: K 50 TYR cc_start: 0.7775 (t80) cc_final: 0.7356 (t80) REVERT: K 125 MET cc_start: 0.8544 (ptp) cc_final: 0.8332 (ptm) REVERT: K 298 ASN cc_start: 0.7887 (p0) cc_final: 0.7527 (p0) REVERT: K 496 ASN cc_start: 0.7656 (m110) cc_final: 0.7351 (m-40) REVERT: K 511 MET cc_start: 0.6820 (ptp) cc_final: 0.6416 (ptm) REVERT: K 512 ARG cc_start: 0.6487 (ttp-110) cc_final: 0.5811 (ttt-90) REVERT: K 547 MET cc_start: 0.3324 (tpp) cc_final: 0.2189 (mtm) REVERT: I 75 ARG cc_start: 0.7223 (mtp85) cc_final: 0.6908 (mtp-110) REVERT: I 279 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6877 (mm-30) REVERT: I 284 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8311 (t) REVERT: I 419 SER cc_start: 0.7902 (p) cc_final: 0.7667 (m) outliers start: 33 outliers final: 24 residues processed: 162 average time/residue: 1.2263 time to fit residues: 218.5091 Evaluate side-chains 163 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 130 MET Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 146 THR 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 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 271 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 315 LEU 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 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 151 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 507 ASN I 522 GLN I 549 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13110 Z= 0.177 Angle : 0.583 10.986 17718 Z= 0.306 Chirality : 0.044 0.146 2020 Planarity : 0.004 0.052 2235 Dihedral : 5.559 53.666 1776 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.03 % Allowed : 18.30 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1597 helix: 1.13 (0.21), residues: 653 sheet: 0.86 (0.39), residues: 204 loop : -1.50 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 165 HIS 0.010 0.001 HIS K 329 PHE 0.011 0.001 PHE K 69 TYR 0.019 0.001 TYR K 386 ARG 0.010 0.000 ARG D 502 ********************** 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 168 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.558 Fit side-chains REVERT: D 105 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7662 (ttm170) REVERT: D 207 HIS cc_start: 0.6939 (p90) cc_final: 0.6619 (p90) REVERT: K 50 TYR cc_start: 0.7815 (t80) cc_final: 0.7450 (t80) REVERT: K 125 MET cc_start: 0.8544 (ptp) cc_final: 0.8336 (ptm) REVERT: K 298 ASN cc_start: 0.7933 (p0) cc_final: 0.7574 (p0) REVERT: K 511 MET cc_start: 0.6769 (ptp) cc_final: 0.6415 (ptm) REVERT: K 512 ARG cc_start: 0.6529 (ttp-110) cc_final: 0.5920 (ttt180) REVERT: K 547 MET cc_start: 0.3369 (tpp) cc_final: 0.2229 (mtm) REVERT: I 75 ARG cc_start: 0.7219 (mtp85) cc_final: 0.6884 (mtp-110) REVERT: I 88 MET cc_start: 0.8244 (mtt) cc_final: 0.7804 (mtt) REVERT: I 279 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6870 (mm-30) REVERT: I 284 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8314 (t) REVERT: I 419 SER cc_start: 0.7919 (p) cc_final: 0.7676 (m) REVERT: I 437 GLN cc_start: 0.4547 (OUTLIER) cc_final: 0.4237 (mm110) outliers start: 29 outliers final: 23 residues processed: 160 average time/residue: 1.3108 time to fit residues: 229.0770 Evaluate side-chains 163 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 130 MET Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 146 THR 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 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 160 LYS 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 315 LEU Chi-restraints excluded: chain I residue 395 CYS Chi-restraints excluded: chain I residue 437 GLN 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 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 135 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 130 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 484 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 = 0.4072 r_free = 0.4072 target = 0.174948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126646 restraints weight = 15398.864| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.04 r_work: 0.3404 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13110 Z= 0.166 Angle : 0.576 10.869 17718 Z= 0.302 Chirality : 0.044 0.146 2020 Planarity : 0.004 0.045 2235 Dihedral : 5.473 52.573 1776 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.96 % Allowed : 18.16 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1597 helix: 1.21 (0.21), residues: 651 sheet: 0.95 (0.39), residues: 202 loop : -1.51 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 165 HIS 0.010 0.001 HIS K 329 PHE 0.010 0.001 PHE I 444 TYR 0.010 0.001 TYR D 302 ARG 0.004 0.000 ARG D 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4561.76 seconds wall clock time: 82 minutes 44.22 seconds (4964.22 seconds total)