Starting phenix.real_space_refine on Sat Jun 7 12:24:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wiw_32538/06_2025/7wiw_32538.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wiw_32538/06_2025/7wiw_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_32538/06_2025/7wiw_32538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wiw_32538/06_2025/7wiw_32538.map" model { file = "/net/cci-nas-00/data/ceres_data/7wiw_32538/06_2025/7wiw_32538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wiw_32538/06_2025/7wiw_32538.cif" } resolution = 3.12 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= 0.057 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.58, per 1000 atoms: 0.65 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: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.85 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: 2.58 Time building geometry restraints manager: 2.88 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: 4719 17.73 - 35.46: 390 35.46 - 53.19: 92 53.19 - 70.92: 17 70.92 - 88.65: 10 Dihedral angle restraints: 5228 sinusoidal: 1995 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 5225 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: 4.160 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.570 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: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 : 14.745 88.649 3144 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 (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: -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 TRP 0.011 0.001 TRP B 154 HIS 0.009 0.001 HIS A 407 PHE 0.011 0.001 PHE B 199 TYR 0.010 0.001 TYR B 283 ARG 0.002 0.000 ARG A 574 Details of bonding type rmsd hydrogen bonds : bond 0.20445 ( 368) hydrogen bonds : angle 7.37951 ( 1080) covalent geometry : bond 0.00603 ( 8764) covalent geometry : angle 0.98681 (11984) *********************** 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 : 0.866 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: 0.2868 time to fit residues: 37.3979 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 : 0.866 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 88 optimal weight: 0.0000 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 203 GLN B 438 GLN B 476 GLN B 526 HIS A 480 GLN A 582 HIS A 717 GLN A 752 GLN A 827 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.083821 restraints weight = 13772.307| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.78 r_work: 0.2903 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8764 Z= 0.118 Angle : 0.619 8.119 11984 Z= 0.318 Chirality : 0.041 0.168 1460 Planarity : 0.005 0.078 1522 Dihedral : 9.369 88.606 1313 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.06 % Favored : 92.67 % Rotamer: Outliers : 1.83 % Allowed : 10.64 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.10 (0.24), residues: 1133 helix: -1.44 (0.20), residues: 689 sheet: -2.22 (0.85), residues: 33 loop : -2.98 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.015 0.001 PHE A 612 TYR 0.009 0.001 TYR B 283 ARG 0.003 0.000 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 368) hydrogen bonds : angle 4.45475 ( 1080) covalent geometry : bond 0.00255 ( 8764) covalent geometry : angle 0.61878 (11984) *********************** 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 103 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.856 Fit side-chains REVERT: B 372 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8325 (mtmm) REVERT: B 425 ASP cc_start: 0.8521 (m-30) cc_final: 0.8244 (m-30) REVERT: B 438 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7877 (pt0) REVERT: A 286 LEU cc_start: 0.8854 (pp) cc_final: 0.8641 (pp) REVERT: A 714 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7293 (tm-30) outliers start: 16 outliers final: 7 residues processed: 99 average time/residue: 0.2436 time to fit residues: 33.0871 Evaluate side-chains 82 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 88 optimal weight: 0.0040 chunk 5 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 83 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.084841 restraints weight = 13979.840| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.86 r_work: 0.2915 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8764 Z= 0.108 Angle : 0.576 7.857 11984 Z= 0.294 Chirality : 0.041 0.148 1460 Planarity : 0.005 0.074 1522 Dihedral : 8.691 87.111 1309 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.27 % Favored : 93.47 % Rotamer: Outliers : 1.95 % Allowed : 13.39 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.47 (0.25), residues: 1133 helix: -0.94 (0.21), residues: 698 sheet: -2.40 (0.72), residues: 39 loop : -2.70 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.002 0.001 HIS A 407 PHE 0.013 0.001 PHE A 612 TYR 0.009 0.001 TYR B 283 ARG 0.002 0.000 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 368) hydrogen bonds : angle 4.03323 ( 1080) covalent geometry : bond 0.00237 ( 8764) covalent geometry : angle 0.57637 (11984) *********************** 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 99 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.930 Fit side-chains REVERT: B 48 GLU cc_start: 0.7743 (mp0) cc_final: 0.7456 (pm20) REVERT: B 372 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8388 (mtmm) REVERT: B 425 ASP cc_start: 0.8491 (m-30) cc_final: 0.8169 (m-30) outliers start: 17 outliers final: 9 residues processed: 95 average time/residue: 0.2218 time to fit residues: 28.9945 Evaluate side-chains 84 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain B residue 250 LEU 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 422 VAL Chi-restraints excluded: chain A residue 766 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.0170 chunk 25 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.2620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 HIS B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.092879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.080979 restraints weight = 14176.337| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.84 r_work: 0.2844 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8764 Z= 0.177 Angle : 0.617 7.507 11984 Z= 0.314 Chirality : 0.043 0.145 1460 Planarity : 0.005 0.068 1522 Dihedral : 8.890 89.312 1309 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.80 % Favored : 92.94 % Rotamer: Outliers : 3.20 % Allowed : 13.16 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.21 (0.25), residues: 1133 helix: -0.82 (0.21), residues: 707 sheet: -1.63 (0.87), residues: 33 loop : -2.51 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 841 HIS 0.003 0.001 HIS A 407 PHE 0.018 0.001 PHE A 612 TYR 0.011 0.001 TYR B 283 ARG 0.002 0.000 ARG A 376 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 368) hydrogen bonds : angle 4.05332 ( 1080) covalent geometry : bond 0.00420 ( 8764) covalent geometry : angle 0.61733 (11984) *********************** 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: 28 poor density : 75 time to evaluate : 0.960 Fit side-chains REVERT: B 425 ASP cc_start: 0.8547 (m-30) cc_final: 0.8225 (m-30) outliers start: 28 outliers final: 16 residues processed: 95 average time/residue: 0.2230 time to fit residues: 29.1622 Evaluate side-chains 91 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 662 VAL 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 88 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.094976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.083018 restraints weight = 13978.083| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.83 r_work: 0.2889 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1924 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= 0.120 Angle : 0.571 7.340 11984 Z= 0.288 Chirality : 0.041 0.137 1460 Planarity : 0.004 0.069 1522 Dihedral : 8.593 89.232 1309 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.18 % Favored : 93.56 % Rotamer: Outliers : 2.63 % Allowed : 14.30 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.85 (0.25), residues: 1133 helix: -0.48 (0.21), residues: 695 sheet: -1.72 (0.76), residues: 38 loop : -2.41 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.013 0.001 PHE A 612 TYR 0.010 0.001 TYR B 283 ARG 0.002 0.000 ARG A 376 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 368) hydrogen bonds : angle 3.90496 ( 1080) covalent geometry : bond 0.00274 ( 8764) covalent geometry : angle 0.57065 (11984) *********************** 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 101 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.941 Fit side-chains REVERT: B 372 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8432 (mtmm) REVERT: B 425 ASP cc_start: 0.8522 (m-30) cc_final: 0.8187 (m-30) REVERT: A 714 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7755 (tm-30) outliers start: 23 outliers final: 13 residues processed: 96 average time/residue: 0.2181 time to fit residues: 29.0326 Evaluate side-chains 88 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 443 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain A residue 291 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 105 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 48 optimal weight: 0.0770 chunk 42 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 109 optimal weight: 0.0470 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.085884 restraints weight = 13788.985| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.80 r_work: 0.2923 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8764 Z= 0.104 Angle : 0.547 7.263 11984 Z= 0.275 Chirality : 0.040 0.138 1460 Planarity : 0.004 0.067 1522 Dihedral : 8.252 84.398 1309 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.09 % Favored : 93.65 % Rotamer: Outliers : 3.20 % Allowed : 14.19 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.25), residues: 1133 helix: -0.15 (0.22), residues: 686 sheet: -1.38 (0.81), residues: 38 loop : -2.32 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.002 0.001 HIS A 407 PHE 0.011 0.001 PHE A 612 TYR 0.011 0.001 TYR B 283 ARG 0.002 0.000 ARG A 376 Details of bonding type rmsd hydrogen bonds : bond 0.02943 ( 368) hydrogen bonds : angle 3.75778 ( 1080) covalent geometry : bond 0.00229 ( 8764) covalent geometry : angle 0.54652 (11984) *********************** 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 107 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: B 372 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8460 (mtmm) REVERT: A 714 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7776 (tm-30) outliers start: 28 outliers final: 21 residues processed: 98 average time/residue: 0.2299 time to fit residues: 30.9511 Evaluate side-chains 96 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 45 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 250 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 397 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 A residue 286 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 ARG 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 75 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 52 optimal weight: 0.0060 chunk 86 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.083602 restraints weight = 13914.401| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.83 r_work: 0.2901 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2174 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= 0.123 Angle : 0.563 8.789 11984 Z= 0.281 Chirality : 0.041 0.141 1460 Planarity : 0.004 0.066 1522 Dihedral : 8.325 86.516 1309 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.09 % Favored : 93.65 % Rotamer: Outliers : 2.63 % Allowed : 14.99 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.34 (0.25), residues: 1133 helix: -0.04 (0.22), residues: 685 sheet: -1.21 (0.84), residues: 38 loop : -2.29 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.014 0.001 PHE A 612 TYR 0.011 0.001 TYR B 283 ARG 0.002 0.000 ARG A 376 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 368) hydrogen bonds : angle 3.75595 ( 1080) covalent geometry : bond 0.00284 ( 8764) covalent geometry : angle 0.56282 (11984) *********************** 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 99 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.739 Fit side-chains REVERT: B 372 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8432 (mtmm) REVERT: B 425 ASP cc_start: 0.8512 (m-30) cc_final: 0.8179 (m-30) REVERT: A 714 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7800 (tm-30) outliers start: 23 outliers final: 19 residues processed: 92 average time/residue: 0.2735 time to fit residues: 35.5555 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 : 1.408 ------------------------------------------------------------------------------- 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 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 A residue 286 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 ARG 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 15 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.0970 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 HIS B 438 GLN A 752 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.093332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.081339 restraints weight = 14270.773| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.84 r_work: 0.2859 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8764 Z= 0.163 Angle : 0.596 8.576 11984 Z= 0.298 Chirality : 0.043 0.158 1460 Planarity : 0.005 0.064 1522 Dihedral : 8.620 88.382 1309 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.62 % Favored : 93.12 % Rotamer: Outliers : 2.86 % Allowed : 15.56 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.34 (0.25), residues: 1133 helix: -0.04 (0.22), residues: 688 sheet: -1.34 (0.82), residues: 38 loop : -2.26 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 507 HIS 0.004 0.001 HIS A 407 PHE 0.016 0.001 PHE A 612 TYR 0.011 0.001 TYR B 283 ARG 0.003 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 368) hydrogen bonds : angle 3.85727 ( 1080) covalent geometry : bond 0.00385 ( 8764) covalent geometry : angle 0.59580 (11984) *********************** 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 100 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.865 Fit side-chains REVERT: B 425 ASP cc_start: 0.8560 (m-30) cc_final: 0.8251 (m-30) REVERT: A 714 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7851 (tm-30) outliers start: 25 outliers final: 20 residues processed: 93 average time/residue: 0.2386 time to fit residues: 30.8025 Evaluate side-chains 94 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 319 ARG 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 7 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.094725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.082729 restraints weight = 14017.266| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.83 r_work: 0.2884 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8764 Z= 0.127 Angle : 0.573 8.398 11984 Z= 0.286 Chirality : 0.041 0.148 1460 Planarity : 0.004 0.061 1522 Dihedral : 8.471 89.223 1309 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.91 % Favored : 93.82 % Rotamer: Outliers : 2.63 % Allowed : 16.02 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.17 (0.26), residues: 1133 helix: 0.12 (0.22), residues: 685 sheet: -1.23 (0.84), residues: 38 loop : -2.24 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.013 0.001 PHE A 612 TYR 0.010 0.001 TYR B 283 ARG 0.003 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 368) hydrogen bonds : angle 3.79975 ( 1080) covalent geometry : bond 0.00295 ( 8764) covalent geometry : angle 0.57259 (11984) *********************** 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 : 0.880 Fit side-chains REVERT: B 372 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8475 (mtmm) REVERT: B 425 ASP cc_start: 0.8543 (m-30) cc_final: 0.8214 (m-30) REVERT: A 714 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7787 (tm-30) outliers start: 23 outliers final: 21 residues processed: 91 average time/residue: 0.2079 time to fit residues: 26.6114 Evaluate side-chains 95 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 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 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 319 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.095920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.083897 restraints weight = 13924.255| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.83 r_work: 0.2906 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8764 Z= 0.110 Angle : 0.557 8.287 11984 Z= 0.278 Chirality : 0.041 0.142 1460 Planarity : 0.004 0.061 1522 Dihedral : 8.276 85.943 1309 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.18 % Favored : 93.56 % Rotamer: Outliers : 2.29 % Allowed : 16.48 % 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 (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: -1.00 (0.26), residues: 1133 helix: 0.26 (0.22), residues: 685 sheet: -1.08 (0.85), residues: 38 loop : -2.21 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.002 0.001 HIS A 407 PHE 0.012 0.001 PHE A 612 TYR 0.010 0.001 TYR B 283 ARG 0.003 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 368) hydrogen bonds : angle 3.73476 ( 1080) covalent geometry : bond 0.00250 ( 8764) covalent geometry : angle 0.55694 (11984) ********************** 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 93 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 1.034 Fit side-chains REVERT: B 372 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8489 (mtmm) REVERT: B 425 ASP cc_start: 0.8525 (m-30) cc_final: 0.8196 (m-30) outliers start: 20 outliers final: 18 residues processed: 86 average time/residue: 0.2271 time to fit residues: 27.6271 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 : 1.186 ------------------------------------------------------------------------------- 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 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 512 LEU 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 319 ARG 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 103 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 87 optimal weight: 0.0270 chunk 111 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.095772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.083736 restraints weight = 14082.714| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.84 r_work: 0.2906 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8764 Z= 0.115 Angle : 0.568 8.340 11984 Z= 0.282 Chirality : 0.041 0.144 1460 Planarity : 0.004 0.061 1522 Dihedral : 8.242 85.741 1309 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.00 % Favored : 93.73 % Rotamer: Outliers : 2.29 % Allowed : 16.59 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.26), residues: 1133 helix: 0.32 (0.22), residues: 688 sheet: -1.04 (0.86), residues: 38 loop : -2.22 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.012 0.001 PHE A 612 TYR 0.010 0.001 TYR B 283 ARG 0.003 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.03074 ( 368) hydrogen bonds : angle 3.71470 ( 1080) covalent geometry : bond 0.00265 ( 8764) covalent geometry : angle 0.56758 (11984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4511.71 seconds wall clock time: 79 minutes 55.74 seconds (4795.74 seconds total)