Starting phenix.real_space_refine on Thu Jul 31 01:02:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sn8_25214/07_2025/7sn8_25214.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sn8_25214/07_2025/7sn8_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_2025/7sn8_25214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sn8_25214/07_2025/7sn8_25214.map" model { file = "/net/cci-nas-00/data/ceres_data/7sn8_25214/07_2025/7sn8_25214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sn8_25214/07_2025/7sn8_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.99, per 1000 atoms: 0.54 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: 2.67 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: 1.67 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: 4.15 Time building geometry restraints manager: 3.24 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: 1.050 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.650 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.750 ------------------------------------------------------------------------------- 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 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 : 14.483 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 Details of bonding type rmsd hydrogen bonds : bond 0.15430 ( 534) hydrogen bonds : angle 6.60418 ( 1518) metal coordination : bond 0.00503 ( 5) covalent geometry : bond 0.00604 (13110) covalent geometry : angle 0.91093 (17718) *********************** 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 : 1.396 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: 1.4707 time to fit residues: 263.1652 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 : 1.393 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135200 restraints weight = 15330.481| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.34 r_work: 0.3393 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 13115 Z= 0.130 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 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 534) hydrogen bonds : angle 5.15894 ( 1518) metal coordination : bond 0.00150 ( 5) covalent geometry : bond 0.00294 (13110) covalent geometry : angle 0.63496 (17718) *********************** 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 : 1.352 Fit side-chains REVERT: D 105 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.8059 (ttm170) REVERT: D 195 MET cc_start: 0.9174 (mmp) cc_final: 0.8930 (mmt) REVERT: D 565 ARG cc_start: 0.5017 (ttm-80) cc_final: 0.4556 (tpp-160) REVERT: K 125 MET cc_start: 0.8485 (ptp) cc_final: 0.8159 (ptm) REVERT: K 385 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7351 (mm-30) REVERT: K 416 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6328 (tm-30) REVERT: K 511 MET cc_start: 0.6776 (ptp) cc_final: 0.6545 (ptp) REVERT: K 547 MET cc_start: 0.3201 (tpp) cc_final: 0.2785 (mpm) REVERT: I 155 ARG cc_start: 0.7805 (ptp-110) cc_final: 0.7509 (pmm-80) REVERT: I 279 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7594 (mm-30) REVERT: I 411 MET cc_start: 0.8340 (ttp) cc_final: 0.7918 (ttp) outliers start: 22 outliers final: 5 residues processed: 155 average time/residue: 1.4310 time to fit residues: 240.0243 Evaluate side-chains 136 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.172101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129757 restraints weight = 15450.476| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.27 r_work: 0.3356 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13115 Z= 0.151 Angle : 0.629 11.089 17718 Z= 0.335 Chirality : 0.047 0.194 2020 Planarity : 0.004 0.050 2235 Dihedral : 6.230 56.100 1776 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 1.82 % Allowed : 11.29 % Favored : 86.89 % 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: -0.65 (0.21), residues: 1597 helix: 0.66 (0.21), residues: 654 sheet: 0.56 (0.41), residues: 187 loop : -1.73 (0.21), residues: 756 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 0.016 0.001 PHE K 69 TYR 0.013 0.001 TYR D 260 ARG 0.003 0.000 ARG D 502 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 534) hydrogen bonds : angle 4.93052 ( 1518) metal coordination : bond 0.00265 ( 5) covalent geometry : bond 0.00360 (13110) covalent geometry : angle 0.62928 (17718) *********************** 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 159 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: D 105 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.8062 (ttm170) REVERT: D 195 MET cc_start: 0.9212 (mmp) cc_final: 0.8999 (mmt) REVERT: D 242 ARG cc_start: 0.8359 (ttm110) cc_final: 0.8155 (ttm110) REVERT: D 565 ARG cc_start: 0.4836 (ttm-80) cc_final: 0.4586 (tpp-160) REVERT: K 107 MET cc_start: 0.7986 (tmm) cc_final: 0.7695 (ttp) REVERT: K 385 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7413 (mm-30) REVERT: K 547 MET cc_start: 0.3509 (tpp) cc_final: 0.2552 (mtm) REVERT: I 155 ARG cc_start: 0.7913 (ptp-110) cc_final: 0.7631 (pmm-80) REVERT: I 279 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7582 (mm-30) REVERT: I 411 MET cc_start: 0.8373 (ttp) cc_final: 0.7945 (ttp) outliers start: 26 outliers final: 14 residues processed: 151 average time/residue: 1.4679 time to fit residues: 239.7980 Evaluate side-chains 145 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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 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 196 MET Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 282 MET 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 19 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 69 optimal weight: 0.0070 chunk 134 optimal weight: 2.9990 chunk 43 optimal weight: 0.0060 chunk 158 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.2018 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.172531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123890 restraints weight = 15372.321| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.04 r_work: 0.3366 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1415 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= 0.143 Angle : 0.614 11.122 17718 Z= 0.324 Chirality : 0.046 0.164 2020 Planarity : 0.004 0.048 2235 Dihedral : 6.042 58.388 1776 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.38 % Allowed : 13.04 % Favored : 84.57 % 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: -0.50 (0.21), residues: 1597 helix: 0.80 (0.21), residues: 648 sheet: 0.70 (0.42), residues: 179 loop : -1.64 (0.21), residues: 770 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 0.015 0.001 PHE K 69 TYR 0.012 0.001 TYR D 302 ARG 0.004 0.000 ARG D 502 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 534) hydrogen bonds : angle 4.75220 ( 1518) metal coordination : bond 0.00291 ( 5) covalent geometry : bond 0.00341 (13110) covalent geometry : angle 0.61401 (17718) *********************** 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 172 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.338 Fit side-chains REVERT: D 319 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6855 (mtp180) REVERT: D 443 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: D 565 ARG cc_start: 0.4731 (ttm-80) cc_final: 0.4482 (tpp-160) REVERT: K 50 TYR cc_start: 0.7979 (t80) cc_final: 0.7563 (t80) REVERT: K 125 MET cc_start: 0.8595 (ptp) cc_final: 0.8390 (ptm) REVERT: K 385 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7457 (mm-30) REVERT: K 511 MET cc_start: 0.6644 (ptp) cc_final: 0.6126 (ptm) REVERT: K 547 MET cc_start: 0.3626 (tpp) cc_final: 0.2594 (mtm) REVERT: I 279 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7628 (mm-30) REVERT: I 286 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7739 (tt) REVERT: I 411 MET cc_start: 0.8304 (ttp) cc_final: 0.8010 (ttp) outliers start: 34 outliers final: 18 residues processed: 162 average time/residue: 1.4406 time to fit residues: 252.2714 Evaluate side-chains 148 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 7 THR 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 160 LYS Chi-restraints excluded: chain I residue 196 MET Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 312 THR 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 534 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 151 optimal weight: 40.0000 chunk 122 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.173820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125387 restraints weight = 15447.518| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.04 r_work: 0.3386 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13115 Z= 0.123 Angle : 0.583 11.028 17718 Z= 0.308 Chirality : 0.045 0.162 2020 Planarity : 0.004 0.045 2235 Dihedral : 5.827 58.935 1776 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.59 % Allowed : 14.73 % 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: -0.34 (0.21), residues: 1597 helix: 0.96 (0.21), residues: 647 sheet: 0.65 (0.41), residues: 191 loop : -1.56 (0.22), residues: 759 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 0.012 0.001 PHE K 69 TYR 0.011 0.001 TYR D 302 ARG 0.006 0.000 ARG D 502 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 534) hydrogen bonds : angle 4.61901 ( 1518) metal coordination : bond 0.00229 ( 5) covalent geometry : bond 0.00286 (13110) covalent geometry : angle 0.58339 (17718) *********************** 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 177 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 1.479 Fit side-chains REVERT: D 207 HIS cc_start: 0.7161 (p90) cc_final: 0.6882 (p90) REVERT: D 319 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6968 (mtp180) REVERT: D 565 ARG cc_start: 0.4749 (ttm-80) cc_final: 0.4525 (tpp-160) REVERT: K 50 TYR cc_start: 0.8033 (t80) cc_final: 0.7646 (t80) REVERT: K 125 MET cc_start: 0.8601 (ptp) cc_final: 0.8395 (ptm) REVERT: K 385 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7483 (mm-30) REVERT: K 511 MET cc_start: 0.6873 (ptp) cc_final: 0.6294 (ptm) REVERT: K 512 ARG cc_start: 0.5959 (ttp-110) cc_final: 0.5598 (ttt-90) REVERT: K 547 MET cc_start: 0.3461 (tpp) cc_final: 0.2684 (mpp) REVERT: I 279 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7560 (mm-30) REVERT: I 284 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8388 (t) REVERT: I 411 MET cc_start: 0.8300 (ttp) cc_final: 0.8015 (ttp) REVERT: I 419 SER cc_start: 0.8180 (p) cc_final: 0.7698 (m) outliers start: 37 outliers final: 23 residues processed: 167 average time/residue: 1.2699 time to fit residues: 231.1970 Evaluate side-chains 153 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 130 MET 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 74 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 0.0270 chunk 35 optimal weight: 0.0770 chunk 42 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 30 optimal weight: 0.0570 overall best weight: 0.6316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4074 r_free = 0.4074 target = 0.175387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.127122 restraints weight = 15717.678| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.06 r_work: 0.3405 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1794 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= 0.111 Angle : 0.570 10.832 17718 Z= 0.299 Chirality : 0.044 0.146 2020 Planarity : 0.004 0.043 2235 Dihedral : 5.623 59.550 1776 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.52 % Allowed : 16.62 % Favored : 80.86 % 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: -0.19 (0.21), residues: 1597 helix: 1.13 (0.21), residues: 647 sheet: 0.81 (0.41), residues: 187 loop : -1.54 (0.22), residues: 763 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 0.010 0.001 PHE K 69 TYR 0.010 0.001 TYR D 302 ARG 0.008 0.000 ARG D 502 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 534) hydrogen bonds : angle 4.50252 ( 1518) metal coordination : bond 0.00214 ( 5) covalent geometry : bond 0.00253 (13110) covalent geometry : angle 0.57031 (17718) *********************** 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 176 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.636 Fit side-chains REVERT: D 161 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7553 (mp) REVERT: D 207 HIS cc_start: 0.7190 (p90) cc_final: 0.6846 (p90) REVERT: D 565 ARG cc_start: 0.4878 (ttm-80) cc_final: 0.4346 (tpp-160) REVERT: K 50 TYR cc_start: 0.8085 (t80) cc_final: 0.7710 (t80) REVERT: K 125 MET cc_start: 0.8568 (ptp) cc_final: 0.8357 (ptm) REVERT: K 385 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7572 (mm-30) REVERT: K 511 MET cc_start: 0.6789 (ptp) cc_final: 0.6306 (ptm) REVERT: K 512 ARG cc_start: 0.5985 (ttp-110) cc_final: 0.5522 (ttt-90) REVERT: K 547 MET cc_start: 0.3416 (tpp) cc_final: 0.2535 (mtm) REVERT: I 88 MET cc_start: 0.8485 (mtt) cc_final: 0.8240 (mtt) REVERT: I 279 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7487 (mm-30) REVERT: I 284 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8396 (t) REVERT: I 419 SER cc_start: 0.8213 (p) cc_final: 0.7743 (m) outliers start: 36 outliers final: 17 residues processed: 164 average time/residue: 1.2550 time to fit residues: 225.0903 Evaluate side-chains 155 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 K residue 7 THR Chi-restraints excluded: chain K residue 130 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 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 520 LEU Chi-restraints excluded: chain I residue 533 VAL Chi-restraints excluded: chain I residue 541 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 152 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 chunk 125 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 overall best weight: 1.5542 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.171651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123192 restraints weight = 15397.444| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.02 r_work: 0.3358 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13115 Z= 0.164 Angle : 0.628 11.252 17718 Z= 0.330 Chirality : 0.047 0.184 2020 Planarity : 0.004 0.047 2235 Dihedral : 5.837 57.365 1776 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.52 % Allowed : 17.32 % Favored : 80.15 % 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: -0.30 (0.21), residues: 1597 helix: 0.95 (0.21), residues: 654 sheet: 0.74 (0.41), residues: 191 loop : -1.54 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 157 HIS 0.010 0.001 HIS K 329 PHE 0.018 0.002 PHE K 69 TYR 0.013 0.001 TYR D 302 ARG 0.007 0.000 ARG D 502 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 534) hydrogen bonds : angle 4.61652 ( 1518) metal coordination : bond 0.00376 ( 5) covalent geometry : bond 0.00397 (13110) covalent geometry : angle 0.62806 (17718) *********************** 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: 36 poor density : 137 time to evaluate : 1.470 Fit side-chains REVERT: D 122 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6547 (m-30) REVERT: D 207 HIS cc_start: 0.7230 (p90) cc_final: 0.6902 (p90) REVERT: D 565 ARG cc_start: 0.4912 (ttm-80) cc_final: 0.4515 (mmm160) REVERT: K 50 TYR cc_start: 0.8046 (t80) cc_final: 0.7644 (t80) REVERT: K 107 MET cc_start: 0.7872 (tmm) cc_final: 0.7598 (ttp) REVERT: K 125 MET cc_start: 0.8664 (ptp) cc_final: 0.8452 (ptm) REVERT: K 298 ASN cc_start: 0.8058 (p0) cc_final: 0.7669 (p0) REVERT: K 385 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7564 (mm-30) REVERT: K 387 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7380 (mtp) REVERT: K 511 MET cc_start: 0.6833 (ptp) cc_final: 0.6306 (ptm) REVERT: K 547 MET cc_start: 0.3508 (tpp) cc_final: 0.2750 (mpp) REVERT: K 596 MET cc_start: 0.3116 (ppp) cc_final: 0.2756 (pp-130) REVERT: I 279 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7563 (mm-30) REVERT: I 284 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8391 (t) REVERT: I 419 SER cc_start: 0.8277 (p) cc_final: 0.7798 (m) outliers start: 36 outliers final: 25 residues processed: 161 average time/residue: 1.2331 time to fit residues: 217.1571 Evaluate side-chains 163 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 ASP 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 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 196 MET 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 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 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 151 optimal weight: 30.0000 chunk 63 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 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 496 ASN K 507 ASN I 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.174244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125900 restraints weight = 15571.136| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.05 r_work: 0.3392 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13115 Z= 0.117 Angle : 0.581 11.009 17718 Z= 0.305 Chirality : 0.044 0.157 2020 Planarity : 0.004 0.044 2235 Dihedral : 5.648 57.117 1776 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % 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: -0.18 (0.21), residues: 1597 helix: 1.10 (0.21), residues: 654 sheet: 0.79 (0.41), residues: 189 loop : -1.51 (0.22), residues: 754 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 0.012 0.001 PHE K 69 TYR 0.020 0.001 TYR K 386 ARG 0.008 0.000 ARG D 502 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 534) hydrogen bonds : angle 4.49026 ( 1518) metal coordination : bond 0.00211 ( 5) covalent geometry : bond 0.00271 (13110) covalent geometry : angle 0.58087 (17718) *********************** 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 172 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.524 Fit side-chains REVERT: D 122 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6604 (m-30) REVERT: D 207 HIS cc_start: 0.7199 (p90) cc_final: 0.6863 (p90) REVERT: D 473 LEU cc_start: 0.8185 (tp) cc_final: 0.7825 (mt) REVERT: D 565 ARG cc_start: 0.4909 (ttm-80) cc_final: 0.4511 (mmm160) REVERT: K 50 TYR cc_start: 0.8046 (t80) cc_final: 0.7641 (t80) REVERT: K 298 ASN cc_start: 0.8031 (p0) cc_final: 0.7672 (p0) REVERT: K 385 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7583 (mm-30) REVERT: K 511 MET cc_start: 0.6893 (ptp) cc_final: 0.6511 (ptm) REVERT: K 512 ARG cc_start: 0.6289 (ttp-110) cc_final: 0.5592 (ttt-90) REVERT: K 547 MET cc_start: 0.3433 (tpp) cc_final: 0.2659 (mpp) REVERT: K 596 MET cc_start: 0.3135 (ppp) cc_final: 0.2789 (pp-130) REVERT: I 75 ARG cc_start: 0.7451 (mtp85) cc_final: 0.7014 (mtp-110) REVERT: I 279 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7571 (mm-30) REVERT: I 284 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8368 (t) REVERT: I 419 SER cc_start: 0.8248 (p) cc_final: 0.7854 (m) outliers start: 33 outliers final: 25 residues processed: 161 average time/residue: 1.2043 time to fit residues: 212.4621 Evaluate side-chains 163 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 ASP 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 196 MET 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 421 ILE 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 128 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 77 optimal weight: 0.0980 chunk 158 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 90 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 496 ASN K 507 ASN I 549 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.176440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.135281 restraints weight = 15401.731| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.16 r_work: 0.3432 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13115 Z= 0.105 Angle : 0.559 10.800 17718 Z= 0.292 Chirality : 0.043 0.145 2020 Planarity : 0.004 0.043 2235 Dihedral : 5.427 56.819 1776 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.38 % Allowed : 17.81 % Favored : 79.80 % 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: -0.00 (0.22), residues: 1597 helix: 1.28 (0.21), residues: 646 sheet: 0.97 (0.39), residues: 202 loop : -1.49 (0.22), residues: 749 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 0.009 0.001 PHE K 69 TYR 0.009 0.001 TYR D 302 ARG 0.007 0.000 ARG D 502 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 534) hydrogen bonds : angle 4.38876 ( 1518) metal coordination : bond 0.00153 ( 5) covalent geometry : bond 0.00236 (13110) covalent geometry : angle 0.55854 (17718) *********************** 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 181 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.430 Fit side-chains REVERT: D 122 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6569 (m-30) REVERT: D 207 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6865 (p90) REVERT: D 285 GLN cc_start: 0.7225 (tp40) cc_final: 0.7007 (tp40) REVERT: D 473 LEU cc_start: 0.8159 (tp) cc_final: 0.7878 (mt) REVERT: D 565 ARG cc_start: 0.4890 (ttm-80) cc_final: 0.4518 (mmm160) REVERT: K 50 TYR cc_start: 0.8065 (t80) cc_final: 0.7670 (t80) REVERT: K 298 ASN cc_start: 0.7969 (p0) cc_final: 0.7624 (p0) REVERT: K 385 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7530 (mm-30) REVERT: K 511 MET cc_start: 0.6662 (ptp) cc_final: 0.6249 (ptm) REVERT: K 512 ARG cc_start: 0.6270 (ttp-110) cc_final: 0.5604 (ttt180) REVERT: K 547 MET cc_start: 0.3395 (tpp) cc_final: 0.2762 (mpt) REVERT: I 75 ARG cc_start: 0.7418 (mtp85) cc_final: 0.7099 (mtp-110) REVERT: I 88 MET cc_start: 0.8465 (mtt) cc_final: 0.8242 (mtt) REVERT: I 279 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7449 (mm-30) REVERT: I 284 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8394 (t) REVERT: I 419 SER cc_start: 0.8201 (p) cc_final: 0.7887 (m) outliers start: 34 outliers final: 23 residues processed: 167 average time/residue: 1.2489 time to fit residues: 227.7595 Evaluate side-chains 167 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 ASP 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 D residue 508 ILE 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 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 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 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 621 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 136 optimal weight: 0.0870 overall best weight: 2.3964 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.169809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128065 restraints weight = 15484.965| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.13 r_work: 0.3338 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 13115 Z= 0.225 Angle : 0.702 11.664 17718 Z= 0.366 Chirality : 0.050 0.204 2020 Planarity : 0.005 0.050 2235 Dihedral : 6.001 52.480 1776 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.52 % Allowed : 17.95 % Favored : 79.52 % 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: -0.41 (0.21), residues: 1597 helix: 0.87 (0.21), residues: 644 sheet: 0.67 (0.40), residues: 203 loop : -1.61 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I 157 HIS 0.013 0.002 HIS K 414 PHE 0.021 0.002 PHE K 69 TYR 0.020 0.002 TYR K 386 ARG 0.004 0.001 ARG D 462 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 534) hydrogen bonds : angle 4.70106 ( 1518) metal coordination : bond 0.00508 ( 5) covalent geometry : bond 0.00554 (13110) covalent geometry : angle 0.70217 (17718) ********************** 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: 36 poor density : 132 time to evaluate : 1.331 Fit side-chains REVERT: D 207 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.6931 (p90) REVERT: D 473 LEU cc_start: 0.8167 (tp) cc_final: 0.7832 (mt) REVERT: D 502 ARG cc_start: 0.6277 (ttm-80) cc_final: 0.5786 (mmp-170) REVERT: D 565 ARG cc_start: 0.4888 (ttm-80) cc_final: 0.4513 (mmm160) REVERT: K 50 TYR cc_start: 0.8125 (t80) cc_final: 0.7818 (t80) REVERT: K 107 MET cc_start: 0.7834 (tmm) cc_final: 0.7547 (ttp) REVERT: K 298 ASN cc_start: 0.8042 (p0) cc_final: 0.7633 (p0) REVERT: K 385 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7547 (mm-30) REVERT: K 511 MET cc_start: 0.6771 (ptp) cc_final: 0.6313 (ptm) REVERT: K 547 MET cc_start: 0.3520 (tpp) cc_final: 0.2490 (mtt) REVERT: I 279 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7565 (mm-30) REVERT: I 284 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8400 (t) outliers start: 36 outliers final: 23 residues processed: 157 average time/residue: 1.3476 time to fit residues: 233.7342 Evaluate side-chains 155 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 13 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.173046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.124259 restraints weight = 15422.848| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.05 r_work: 0.3374 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13115 Z= 0.129 Angle : 0.605 11.185 17718 Z= 0.318 Chirality : 0.045 0.148 2020 Planarity : 0.004 0.044 2235 Dihedral : 5.744 53.144 1776 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.96 % Allowed : 18.30 % Favored : 79.73 % 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: -0.27 (0.21), residues: 1597 helix: 0.99 (0.21), residues: 651 sheet: 0.81 (0.39), residues: 206 loop : -1.58 (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 0.013 0.001 PHE K 69 TYR 0.011 0.001 TYR D 302 ARG 0.008 0.000 ARG K 512 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 534) hydrogen bonds : angle 4.51069 ( 1518) metal coordination : bond 0.00264 ( 5) covalent geometry : bond 0.00299 (13110) covalent geometry : angle 0.60496 (17718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12077.44 seconds wall clock time: 209 minutes 21.34 seconds (12561.34 seconds total)