Starting phenix.real_space_refine on Thu Jul 2 12:41:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wiw_32538/07_2026/7wiw_32538.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wiw_32538/07_2026/7wiw_32538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wiw_32538/07_2026/7wiw_32538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wiw_32538/07_2026/7wiw_32538.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wiw_32538/07_2026/7wiw_32538.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wiw_32538/07_2026/7wiw_32538.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wiw_32538/07_2026/7wiw_32538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wiw_32538/07_2026/7wiw_32538.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 15 5.16 5 C 5473 2.51 5 N 1547 2.21 5 O 1559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8603 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4198 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 25, 'TRANS': 541} Chain: "A" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4340 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 25, 'TRANS': 544} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.77, per 1000 atoms: 0.21 Number of scatterers: 8603 At special positions: 0 Unit cell: (66.42, 91.02, 137.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 15 16.00 P 6 15.00 Mg 3 11.99 O 1559 8.00 N 1547 7.00 C 5473 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: 0.69 Conformation dependent library (CDL) restraints added in 509.6 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 54.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 19 through 37 removed outlier: 3.922A pdb=" N LEU B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 removed outlier: 3.696A pdb=" N LEU B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 removed outlier: 3.764A pdb=" N ARG B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP B 54 " --> pdb=" O GLN B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 83 removed outlier: 3.666A pdb=" N LEU B 60 " --> pdb=" O TRP B 56 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 97 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 107 through 119 removed outlier: 4.056A pdb=" N ALA B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 Proline residue: B 142 - end of helix Processing helix chain 'B' and resid 153 through 162 removed outlier: 3.743A pdb=" N ALA B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 202 removed outlier: 4.261A pdb=" N LEU B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ARG B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 209 removed outlier: 3.780A pdb=" N LEU B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 265 removed outlier: 3.834A pdb=" N ASN B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix Processing helix chain 'B' and resid 269 through 312 removed outlier: 3.748A pdb=" N ALA B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Proline residue: B 286 - end of helix removed outlier: 3.849A pdb=" N SER B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Proline residue: B 295 - end of helix Processing helix chain 'B' and resid 374 through 381 Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 422 through 429 Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.701A pdb=" N PHE B 439 " --> pdb=" O SER B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 471 through 485 removed outlier: 3.631A pdb=" N GLN B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 514 removed outlier: 3.520A pdb=" N ALA B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 507 " --> pdb=" O GLU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 555 removed outlier: 3.942A pdb=" N LEU B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 564 removed outlier: 3.667A pdb=" N GLN B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.631A pdb=" N GLU A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 347 removed outlier: 4.261A pdb=" N THR A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 371 removed outlier: 3.508A pdb=" N TRP A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.840A pdb=" N ARG A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 removed outlier: 3.593A pdb=" N LEU A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 408 through 418 removed outlier: 4.121A pdb=" N VAL A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 424 through 430 removed outlier: 3.671A pdb=" N VAL A 428 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 429 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.825A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 479 removed outlier: 3.561A pdb=" N GLU A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 497 through 515 removed outlier: 3.606A pdb=" N ALA A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Proline residue: A 510 - end of helix removed outlier: 3.846A pdb=" N GLY A 513 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.642A pdb=" N ALA A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 539 removed outlier: 3.569A pdb=" N PHE A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 538 " --> pdb=" O THR A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 548 Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.725A pdb=" N PHE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 568 removed outlier: 4.337A pdb=" N ARG A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 587 removed outlier: 3.628A pdb=" N LEU A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 586 " --> pdb=" O HIS A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 715 through 723 Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 734 through 738 Processing helix chain 'A' and resid 752 through 761 removed outlier: 3.516A pdb=" N ALA A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 349 through 355 removed outlier: 6.404A pdb=" N ASP B 350 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 338 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL B 352 " --> pdb=" O ASP B 336 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 336 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 337 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG B 387 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 410 through 412 removed outlier: 6.247A pdb=" N THR B 362 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 363 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 540 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 365 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU B 547 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP B 541 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL B 545 " --> pdb=" O ASP B 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 626 through 629 removed outlier: 5.522A pdb=" N VAL A 615 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 629 removed outlier: 5.522A pdb=" N VAL A 615 " --> pdb=" O ASP A 628 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 615 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG A 664 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 672 " --> pdb=" O VAL A 669 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 638 through 639 removed outlier: 6.799A pdb=" N THR A 639 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY A 687 " --> pdb=" O ILE A 768 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 813 through 817 removed outlier: 4.160A pdb=" N GLU A 823 " --> pdb=" O VAL A 815 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP A 817 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1080 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: 1.04 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1385 1.28 - 1.41: 2087 1.41 - 1.54: 5245 1.54 - 1.67: 22 1.67 - 1.81: 25 Bond restraints: 8764 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.06e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C VAL B 493 " pdb=" O VAL B 493 " ideal model delta sigma weight residual 1.238 1.152 0.085 1.17e-02 7.31e+03 5.31e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.76e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.38e+01 ... (remaining 8759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 11881 4.15 - 8.30: 96 8.30 - 12.45: 5 12.45 - 16.59: 1 16.59 - 20.74: 1 Bond angle restraints: 11984 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.13 20.74 1.00e+00 1.00e+00 4.30e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 122.08 14.75 1.00e+00 1.00e+00 2.18e+02 angle pdb=" C5 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 126.80 118.68 8.12 1.00e+00 1.00e+00 6.60e+01 angle pdb=" C5 ATP A 901 " pdb=" C4 ATP A 901 " pdb=" N3 ATP A 901 " ideal model delta sigma weight residual 126.80 118.76 8.04 1.00e+00 1.00e+00 6.46e+01 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 132.41 7.46 1.00e+00 1.00e+00 5.56e+01 ... (remaining 11979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4701 17.73 - 35.46: 361 35.46 - 53.19: 81 53.19 - 70.92: 14 70.92 - 88.65: 9 Dihedral angle restraints: 5166 sinusoidal: 1933 harmonic: 3233 Sorted by residual: dihedral pdb=" CA ALA A 711 " pdb=" C ALA A 711 " pdb=" N PRO A 712 " pdb=" CA PRO A 712 " ideal model delta harmonic sigma weight residual 180.00 -152.63 -27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA PRO A 712 " pdb=" C PRO A 712 " pdb=" N ALA A 713 " pdb=" CA ALA A 713 " ideal model delta harmonic sigma weight residual 180.00 157.75 22.25 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" N VAL B 493 " pdb=" C VAL B 493 " pdb=" CA VAL B 493 " pdb=" CB VAL B 493 " ideal model delta harmonic sigma weight residual 123.40 113.54 9.86 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 5163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1381 0.091 - 0.182: 71 0.182 - 0.272: 5 0.272 - 0.363: 1 0.363 - 0.454: 2 Chirality restraints: 1460 Sorted by residual: chirality pdb=" CB VAL B 328 " pdb=" CA VAL B 328 " pdb=" CG1 VAL B 328 " pdb=" CG2 VAL B 328 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA VAL B 493 " pdb=" N VAL B 493 " pdb=" C VAL B 493 " pdb=" CB VAL B 493 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA ASP B 325 " pdb=" N ASP B 325 " pdb=" C ASP B 325 " pdb=" CB ASP B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1457 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 827 " 0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C HIS A 827 " -0.065 2.00e-02 2.50e+03 pdb=" O HIS A 827 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 828 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 402 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C HIS A 402 " -0.064 2.00e-02 2.50e+03 pdb=" O HIS A 402 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR A 403 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 324 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ARG B 324 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG B 324 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP B 325 " -0.019 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 54 2.49 - 3.09: 6046 3.09 - 3.70: 12692 3.70 - 4.30: 18891 4.30 - 4.90: 32238 Nonbonded interactions: 69921 Sorted by model distance: nonbonded pdb=" OE1 GLN B 414 " pdb="MG MG B 602 " model vdw 1.891 2.170 nonbonded pdb=" OE1 GLN A 691 " pdb="MG MG A 902 " model vdw 1.895 2.170 nonbonded pdb=" OG SER A 650 " pdb="MG MG A 902 " model vdw 1.987 2.170 nonbonded pdb=" OG SER B 373 " pdb="MG MG B 602 " model vdw 2.110 2.170 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 2.132 2.170 ... (remaining 69916 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: 3.990 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.110 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 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 0.085 8764 Z= 0.389 Angle : 0.987 20.743 11984 Z= 0.666 Chirality : 0.049 0.454 1460 Planarity : 0.006 0.075 1522 Dihedral : 14.197 88.649 3082 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.06 % Favored : 92.32 % Rotamer: Outliers : 1.03 % Allowed : 6.86 % Favored : 92.11 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.21), residues: 1133 helix: -2.55 (0.17), residues: 701 sheet: -2.40 (0.84), residues: 33 loop : -3.70 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 574 TYR 0.010 0.001 TYR B 283 PHE 0.011 0.001 PHE B 199 TRP 0.011 0.001 TRP B 154 HIS 0.009 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.39 ( 8764) covalent geometry : angle 0.98681 / 0.67 (11984) hydrogen bonds : bond 0.20445 / 13.73 ( 368) hydrogen bonds : angle 7.37951 / 5.41 ( 1080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.278 Fit side-chains REVERT: A 407 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.8412 (p90) REVERT: A 714 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7028 (tm-30) outliers start: 9 outliers final: 3 residues processed: 101 average time/residue: 0.1129 time to fit residues: 14.9442 Evaluate side-chains 77 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 630 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 ASN B 203 GLN B 438 GLN B 476 GLN B 526 HIS A 480 GLN A 717 GLN A 752 GLN A 827 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.093872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.082180 restraints weight = 14072.225| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.78 r_work: 0.2875 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8764 Z= 0.137 Angle : 0.637 8.162 11984 Z= 0.327 Chirality : 0.042 0.177 1460 Planarity : 0.005 0.078 1522 Dihedral : 6.325 56.204 1251 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.15 % Favored : 92.59 % Rotamer: Outliers : 1.95 % Allowed : 10.98 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.24), residues: 1133 helix: -1.47 (0.20), residues: 688 sheet: -2.57 (0.76), residues: 45 loop : -2.97 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 301 TYR 0.010 0.001 TYR B 283 PHE 0.017 0.001 PHE A 612 TRP 0.010 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 8764) covalent geometry : angle 0.63658 / 0.33 (11984) hydrogen bonds : bond 0.03748 / 2.51 ( 368) hydrogen bonds : angle 4.48273 / 3.32 ( 1080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.314 Fit side-chains REVERT: B 438 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: A 286 LEU cc_start: 0.8955 (pp) cc_final: 0.8739 (pp) REVERT: A 714 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7376 (tm-30) outliers start: 17 outliers final: 8 residues processed: 94 average time/residue: 0.0871 time to fit residues: 11.5739 Evaluate side-chains 80 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 766 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.093455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.081576 restraints weight = 14035.447| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.84 r_work: 0.2858 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8764 Z= 0.147 Angle : 0.610 7.711 11984 Z= 0.312 Chirality : 0.042 0.155 1460 Planarity : 0.005 0.072 1522 Dihedral : 5.664 55.524 1247 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.80 % Favored : 92.94 % Rotamer: Outliers : 2.40 % Allowed : 13.04 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.25), residues: 1133 helix: -1.05 (0.21), residues: 700 sheet: -2.35 (0.77), residues: 32 loop : -2.70 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 753 TYR 0.010 0.001 TYR B 283 PHE 0.016 0.001 PHE A 612 TRP 0.009 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 8764) covalent geometry : angle 0.61015 / 0.31 (11984) hydrogen bonds : bond 0.03728 / 2.49 ( 368) hydrogen bonds : angle 4.17639 / 3.09 ( 1080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.370 Fit side-chains REVERT: B 425 ASP cc_start: 0.8549 (m-30) cc_final: 0.8242 (m-30) REVERT: A 376 ARG cc_start: 0.8800 (ptp90) cc_final: 0.8410 (ptt90) outliers start: 21 outliers final: 15 residues processed: 92 average time/residue: 0.1029 time to fit residues: 13.3065 Evaluate side-chains 87 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 72 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.094904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.083147 restraints weight = 14194.235| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.79 r_work: 0.2889 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8764 Z= 0.121 Angle : 0.572 7.411 11984 Z= 0.290 Chirality : 0.041 0.138 1460 Planarity : 0.005 0.071 1522 Dihedral : 5.338 54.124 1247 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.62 % Favored : 93.12 % Rotamer: Outliers : 2.86 % Allowed : 13.04 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.25), residues: 1133 helix: -0.73 (0.21), residues: 703 sheet: -2.01 (0.80), residues: 32 loop : -2.51 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 753 TYR 0.009 0.001 TYR B 283 PHE 0.013 0.001 PHE A 612 TRP 0.009 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 8764) covalent geometry : angle 0.57246 / 0.29 (11984) hydrogen bonds : bond 0.03302 / 2.20 ( 368) hydrogen bonds : angle 3.95572 / 2.94 ( 1080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.330 Fit side-chains REVERT: B 425 ASP cc_start: 0.8510 (m-30) cc_final: 0.8184 (m-30) REVERT: A 376 ARG cc_start: 0.8746 (ptp90) cc_final: 0.8350 (ptt90) outliers start: 25 outliers final: 16 residues processed: 98 average time/residue: 0.1028 time to fit residues: 14.0358 Evaluate side-chains 88 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.094513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.082573 restraints weight = 14038.184| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.83 r_work: 0.2883 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8764 Z= 0.125 Angle : 0.570 7.379 11984 Z= 0.288 Chirality : 0.041 0.138 1460 Planarity : 0.004 0.069 1522 Dihedral : 5.249 54.548 1247 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.27 % Favored : 93.47 % Rotamer: Outliers : 2.63 % Allowed : 14.42 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.25), residues: 1133 helix: -0.49 (0.21), residues: 695 sheet: -1.86 (0.81), residues: 32 loop : -2.40 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 753 TYR 0.009 0.001 TYR B 283 PHE 0.014 0.001 PHE A 612 TRP 0.007 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8764) covalent geometry : angle 0.56969 / 0.29 (11984) hydrogen bonds : bond 0.03325 / 2.22 ( 368) hydrogen bonds : angle 3.89938 / 2.89 ( 1080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.332 Fit side-chains REVERT: B 425 ASP cc_start: 0.8514 (m-30) cc_final: 0.8185 (m-30) REVERT: A 376 ARG cc_start: 0.8762 (ptp90) cc_final: 0.8354 (ptt90) REVERT: A 714 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7695 (pp20) outliers start: 23 outliers final: 15 residues processed: 98 average time/residue: 0.1091 time to fit residues: 14.6535 Evaluate side-chains 92 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 73 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 71 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 96 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.084416 restraints weight = 13939.539| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.83 r_work: 0.2913 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8764 Z= 0.105 Angle : 0.546 7.303 11984 Z= 0.274 Chirality : 0.040 0.137 1460 Planarity : 0.004 0.067 1522 Dihedral : 5.044 55.864 1247 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.18 % Favored : 93.56 % Rotamer: Outliers : 2.75 % Allowed : 15.10 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.25), residues: 1133 helix: -0.20 (0.22), residues: 686 sheet: -1.45 (0.82), residues: 38 loop : -2.37 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 753 TYR 0.010 0.001 TYR B 283 PHE 0.012 0.001 PHE A 612 TRP 0.009 0.001 TRP B 154 HIS 0.002 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 8764) covalent geometry : angle 0.54572 / 0.27 (11984) hydrogen bonds : bond 0.02968 / 1.98 ( 368) hydrogen bonds : angle 3.76763 / 2.79 ( 1080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.338 Fit side-chains REVERT: B 372 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8389 (mtmm) REVERT: B 425 ASP cc_start: 0.8476 (m-30) cc_final: 0.8131 (m-30) REVERT: A 376 ARG cc_start: 0.8693 (ptp90) cc_final: 0.8275 (ptt90) REVERT: A 714 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7759 (tm-30) outliers start: 24 outliers final: 16 residues processed: 94 average time/residue: 0.1054 time to fit residues: 13.7970 Evaluate side-chains 89 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 108 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.095329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.083247 restraints weight = 14125.392| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.86 r_work: 0.2896 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8764 Z= 0.122 Angle : 0.561 8.838 11984 Z= 0.280 Chirality : 0.041 0.141 1460 Planarity : 0.004 0.066 1522 Dihedral : 5.067 56.372 1247 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.18 % Favored : 93.56 % Rotamer: Outliers : 2.52 % Allowed : 16.02 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.25), residues: 1133 helix: -0.08 (0.22), residues: 686 sheet: -1.28 (0.84), residues: 38 loop : -2.34 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.010 0.001 TYR B 283 PHE 0.014 0.001 PHE A 612 TRP 0.007 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8764) covalent geometry : angle 0.56052 / 0.28 (11984) hydrogen bonds : bond 0.03163 / 2.11 ( 368) hydrogen bonds : angle 3.76935 / 2.79 ( 1080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.367 Fit side-chains REVERT: B 425 ASP cc_start: 0.8510 (m-30) cc_final: 0.8177 (m-30) REVERT: A 714 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7793 (tm-30) outliers start: 22 outliers final: 20 residues processed: 85 average time/residue: 0.0925 time to fit residues: 11.1900 Evaluate side-chains 90 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.096108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.084315 restraints weight = 13927.204| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.81 r_work: 0.2897 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8764 Z= 0.121 Angle : 0.557 8.594 11984 Z= 0.277 Chirality : 0.041 0.143 1460 Planarity : 0.004 0.062 1522 Dihedral : 5.068 57.136 1247 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.00 % Favored : 93.73 % Rotamer: Outliers : 2.75 % Allowed : 16.02 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.26), residues: 1133 helix: 0.04 (0.22), residues: 685 sheet: -1.22 (0.84), residues: 38 loop : -2.28 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.010 0.001 TYR B 283 PHE 0.013 0.001 PHE A 612 TRP 0.007 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8764) covalent geometry : angle 0.55732 / 0.28 (11984) hydrogen bonds : bond 0.03172 / 2.12 ( 368) hydrogen bonds : angle 3.76159 / 2.79 ( 1080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.331 Fit side-chains REVERT: B 425 ASP cc_start: 0.8504 (m-30) cc_final: 0.8166 (m-30) REVERT: A 714 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7788 (tm-30) outliers start: 24 outliers final: 19 residues processed: 89 average time/residue: 0.0924 time to fit residues: 11.7839 Evaluate side-chains 90 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 88 optimal weight: 0.0170 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.084054 restraints weight = 13966.802| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.85 r_work: 0.2907 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8764 Z= 0.109 Angle : 0.554 8.476 11984 Z= 0.275 Chirality : 0.041 0.139 1460 Planarity : 0.004 0.060 1522 Dihedral : 4.992 57.354 1247 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.09 % Favored : 93.65 % Rotamer: Outliers : 2.63 % Allowed : 16.36 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.26), residues: 1133 helix: 0.17 (0.22), residues: 685 sheet: -1.14 (0.85), residues: 38 loop : -2.24 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.010 0.001 TYR B 283 PHE 0.012 0.001 PHE A 612 TRP 0.008 0.001 TRP B 154 HIS 0.002 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8764) covalent geometry : angle 0.55377 / 0.27 (11984) hydrogen bonds : bond 0.03014 / 2.01 ( 368) hydrogen bonds : angle 3.71545 / 2.76 ( 1080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.351 Fit side-chains REVERT: B 372 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8452 (mtmm) REVERT: B 425 ASP cc_start: 0.8505 (m-30) cc_final: 0.8172 (m-30) outliers start: 23 outliers final: 20 residues processed: 92 average time/residue: 0.0940 time to fit residues: 12.2918 Evaluate side-chains 91 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 HIS B 420 HIS B 438 GLN A 752 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.093055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.081117 restraints weight = 14064.057| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.83 r_work: 0.2863 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8764 Z= 0.162 Angle : 0.601 8.691 11984 Z= 0.299 Chirality : 0.043 0.158 1460 Planarity : 0.004 0.056 1522 Dihedral : 5.211 58.445 1247 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.44 % Favored : 93.29 % Rotamer: Outliers : 2.29 % Allowed : 16.93 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.26), residues: 1133 helix: 0.13 (0.22), residues: 686 sheet: -1.26 (0.82), residues: 38 loop : -2.26 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.010 0.001 TYR B 283 PHE 0.015 0.001 PHE A 612 TRP 0.009 0.001 TRP A 507 HIS 0.004 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 8764) covalent geometry : angle 0.60068 / 0.30 (11984) hydrogen bonds : bond 0.03612 / 2.41 ( 368) hydrogen bonds : angle 3.83992 / 2.85 ( 1080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.329 Fit side-chains REVERT: B 425 ASP cc_start: 0.8540 (m-30) cc_final: 0.8227 (m-30) REVERT: A 376 ARG cc_start: 0.8795 (ptp90) cc_final: 0.8350 (ptt90) outliers start: 20 outliers final: 18 residues processed: 86 average time/residue: 0.0991 time to fit residues: 11.9419 Evaluate side-chains 87 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 2.9990 chunk 92 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 109 optimal weight: 0.0770 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.083770 restraints weight = 13863.767| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.84 r_work: 0.2902 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8764 Z= 0.111 Angle : 0.559 9.081 11984 Z= 0.278 Chirality : 0.041 0.143 1460 Planarity : 0.004 0.056 1522 Dihedral : 5.024 58.381 1247 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.27 % Favored : 93.47 % Rotamer: Outliers : 2.17 % Allowed : 16.82 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.26), residues: 1133 helix: 0.29 (0.22), residues: 684 sheet: -1.09 (0.85), residues: 38 loop : -2.26 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.009 0.001 TYR B 283 PHE 0.011 0.001 PHE A 612 TRP 0.008 0.001 TRP B 154 HIS 0.002 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 8764) covalent geometry : angle 0.55943 / 0.28 (11984) hydrogen bonds : bond 0.03034 / 2.02 ( 368) hydrogen bonds : angle 3.73566 / 2.77 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2097.94 seconds wall clock time: 36 minutes 43.27 seconds (2203.27 seconds total)