Starting phenix.real_space_refine on Sun Jun 15 06:05:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j6x_61188/06_2025/9j6x_61188.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j6x_61188/06_2025/9j6x_61188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j6x_61188/06_2025/9j6x_61188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j6x_61188/06_2025/9j6x_61188.map" model { file = "/net/cci-nas-00/data/ceres_data/9j6x_61188/06_2025/9j6x_61188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j6x_61188/06_2025/9j6x_61188.cif" } resolution = 2.4 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= -0.001 sd= 0.076 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 10825 2.51 5 N 2896 2.21 5 O 3143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16969 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5637 Classifications: {'peptide': 709} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 667} Chain breaks: 1 Chain: "B" Number of atoms: 5649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5649 Classifications: {'peptide': 710} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 668} Chain breaks: 1 Chain: "C" Number of atoms: 5683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5683 Classifications: {'peptide': 737} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 695} Chain breaks: 5 Time building chain proxies: 10.91, per 1000 atoms: 0.64 Number of scatterers: 16969 At special positions: 0 Unit cell: (113.4, 93.24, 228.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3143 8.00 N 2896 7.00 C 10825 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: 4.05 Conformation dependent library (CDL) restraints added in 2.4 seconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3920 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 25 sheets defined 29.9% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 131 through 138 removed outlier: 4.256A pdb=" N GLU A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.737A pdb=" N ASP A 214 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.529A pdb=" N LEU A 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 removed outlier: 4.417A pdb=" N THR A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 removed outlier: 3.795A pdb=" N SER A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.600A pdb=" N ILE A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 406 through 424 Processing helix chain 'A' and resid 433 through 439 removed outlier: 3.691A pdb=" N ARG A 439 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.542A pdb=" N TRP A 444 " --> pdb=" O CYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 477 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.836A pdb=" N VAL A 483 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 524 removed outlier: 3.861A pdb=" N LYS A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.701A pdb=" N TYR A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 566 through 570 Processing helix chain 'A' and resid 603 through 623 Processing helix chain 'A' and resid 651 through 655 Processing helix chain 'A' and resid 664 through 681 Processing helix chain 'A' and resid 770 through 777 Processing helix chain 'A' and resid 778 through 783 Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.543A pdb=" N GLU B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 183 Processing helix chain 'B' and resid 241 through 245 Processing helix chain 'B' and resid 251 through 257 removed outlier: 4.444A pdb=" N THR B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.610A pdb=" N ASN B 262 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.677A pdb=" N ILE B 273 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 removed outlier: 3.570A pdb=" N LEU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 333 through 350 removed outlier: 3.511A pdb=" N ARG B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 384 removed outlier: 4.067A pdb=" N ASN B 380 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N SER B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR B 382 " --> pdb=" O ILE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 425 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 441 through 445 removed outlier: 3.613A pdb=" N TRP B 444 " --> pdb=" O CYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 479 through 483 Processing helix chain 'B' and resid 511 through 524 removed outlier: 3.561A pdb=" N ARG B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 523 " --> pdb=" O ARG B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 537 Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 564 through 569 removed outlier: 3.875A pdb=" N VAL B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 580 Processing helix chain 'B' and resid 603 through 623 Processing helix chain 'B' and resid 651 through 655 Processing helix chain 'B' and resid 657 through 663 removed outlier: 3.872A pdb=" N GLU B 662 " --> pdb=" O TRP B 658 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 Processing helix chain 'B' and resid 770 through 777 Processing helix chain 'B' and resid 778 through 783 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.634A pdb=" N LEU C 287 " --> pdb=" O LEU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 removed outlier: 4.340A pdb=" N THR C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 312 through 318 Processing helix chain 'C' and resid 319 through 327 removed outlier: 3.815A pdb=" N PHE C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 363 through 381 Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 410 through 415 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.572A pdb=" N GLU C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 531 removed outlier: 4.280A pdb=" N SER C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 524 " --> pdb=" O THR C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 544 removed outlier: 3.717A pdb=" N LEU C 539 " --> pdb=" O LEU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 556 No H-bonds generated for 'chain 'C' and resid 554 through 556' Processing helix chain 'C' and resid 571 through 575 Processing helix chain 'C' and resid 581 through 585 removed outlier: 3.797A pdb=" N SER C 585 " --> pdb=" O LEU C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 617 removed outlier: 3.539A pdb=" N GLN C 602 " --> pdb=" O SER C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 643 removed outlier: 3.606A pdb=" N ARG C 643 " --> pdb=" O TYR C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 673 Processing helix chain 'C' and resid 673 through 678 Processing helix chain 'C' and resid 684 through 686 No H-bonds generated for 'chain 'C' and resid 684 through 686' Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.572A pdb=" N ALA A 124 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 179 Processing sheet with id=AA5, first strand: chain 'A' and resid 484 through 487 removed outlier: 6.905A pdb=" N VAL A 354 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ARG A 430 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N MET A 356 " --> pdb=" O ARG A 430 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 357 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 630 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER A 553 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N MET A 629 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN A 555 " --> pdb=" O MET A 629 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N TYR A 631 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU A 509 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N PHE A 556 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN A 511 " --> pdb=" O PHE A 556 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 293 through 294 removed outlier: 7.642A pdb=" N SER A 319 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 695 through 698 removed outlier: 3.632A pdb=" N ALA A 715 " --> pdb=" O HIS A 698 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLU A 725 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER A 794 " --> pdb=" O ASP A 754 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP A 754 " --> pdb=" O SER A 794 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 796 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 737 through 740 Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.684A pdb=" N ARG B 95 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.684A pdb=" N ARG B 95 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.559A pdb=" N ALA B 124 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 220 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 178 through 179 Processing sheet with id=AB4, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.286A pdb=" N VAL B 287 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP B 357 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU B 289 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 428 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 485 " --> pdb=" O SER B 508 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TRP B 510 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA B 487 " --> pdb=" O TRP B 510 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU B 509 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N PHE B 556 " --> pdb=" O GLU B 509 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER B 553 " --> pdb=" O VAL B 627 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N MET B 629 " --> pdb=" O SER B 553 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASN B 555 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N TYR B 631 " --> pdb=" O ASN B 555 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 293 through 295 removed outlier: 7.371A pdb=" N GLU B 294 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 695 through 698 removed outlier: 3.723A pdb=" N ALA B 715 " --> pdb=" O HIS B 698 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU B 725 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER B 794 " --> pdb=" O ASP B 754 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP B 754 " --> pdb=" O SER B 794 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE B 796 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 737 through 740 Processing sheet with id=AB8, first strand: chain 'C' and resid 37 through 43 removed outlier: 5.326A pdb=" N VAL C 49 " --> pdb=" O PRO C 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AC1, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 154 through 157 Processing sheet with id=AC3, first strand: chain 'C' and resid 194 through 197 Processing sheet with id=AC4, first strand: chain 'C' and resid 289 through 292 removed outlier: 6.303A pdb=" N TYR C 290 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 385 " --> pdb=" O GLY C 454 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N CYS C 456 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU C 387 " --> pdb=" O CYS C 456 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 458 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C 389 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU C 517 " --> pdb=" O PHE C 559 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER C 558 " --> pdb=" O VAL C 621 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL C 623 " --> pdb=" O SER C 558 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN C 560 " --> pdb=" O VAL C 623 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASN C 625 " --> pdb=" O ASN C 560 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 289 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 393 through 394 removed outlier: 4.485A pdb=" N SER C 426 " --> pdb=" O THR C 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 688 through 691 removed outlier: 6.769A pdb=" N CYS C 790 " --> pdb=" O ASP C 757 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP C 757 " --> pdb=" O CYS C 790 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU C 792 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 739 through 742 583 hydrogen bonds defined for protein. 1512 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: 6.31 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5556 1.34 - 1.46: 4318 1.46 - 1.58: 7432 1.58 - 1.70: 0 1.70 - 1.82: 157 Bond restraints: 17463 Sorted by residual: bond pdb=" C ALA C 115 " pdb=" N PRO C 116 " ideal model delta sigma weight residual 1.330 1.347 -0.017 1.19e-02 7.06e+03 1.97e+00 bond pdb=" C ALA B 387 " pdb=" N PRO B 388 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.38e-02 5.25e+03 1.51e+00 bond pdb=" CB ASN A 583 " pdb=" CG ASN A 583 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.26e+00 bond pdb=" CB ASP A 244 " pdb=" CG ASP A 244 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.23e+00 bond pdb=" CB GLU A 281 " pdb=" CG GLU A 281 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.16e+00 ... (remaining 17458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 23509 2.27 - 4.53: 194 4.53 - 6.80: 5 6.80 - 9.06: 2 9.06 - 11.33: 2 Bond angle restraints: 23712 Sorted by residual: angle pdb=" C ASP C 307 " pdb=" N ASP C 308 " pdb=" CA ASP C 308 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C PRO C 112 " pdb=" N THR C 113 " pdb=" CA THR C 113 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 angle pdb=" CB MET A 290 " pdb=" CG MET A 290 " pdb=" SD MET A 290 " ideal model delta sigma weight residual 112.70 121.95 -9.25 3.00e+00 1.11e-01 9.50e+00 angle pdb=" CA GLU A 281 " pdb=" CB GLU A 281 " pdb=" CG GLU A 281 " ideal model delta sigma weight residual 114.10 119.84 -5.74 2.00e+00 2.50e-01 8.22e+00 angle pdb=" CB GLU A 281 " pdb=" CG GLU A 281 " pdb=" CD GLU A 281 " ideal model delta sigma weight residual 112.60 116.97 -4.37 1.70e+00 3.46e-01 6.61e+00 ... (remaining 23707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8788 17.99 - 35.99: 1018 35.99 - 53.98: 278 53.98 - 71.98: 49 71.98 - 89.97: 22 Dihedral angle restraints: 10155 sinusoidal: 3996 harmonic: 6159 Sorted by residual: dihedral pdb=" CA PHE B 130 " pdb=" C PHE B 130 " pdb=" N THR B 131 " pdb=" CA THR B 131 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA SER B 374 " pdb=" C SER B 374 " pdb=" N PHE B 375 " pdb=" CA PHE B 375 " ideal model delta harmonic sigma weight residual -180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA GLU B 488 " pdb=" C GLU B 488 " pdb=" N ALA B 489 " pdb=" CA ALA B 489 " ideal model delta harmonic sigma weight residual -180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 10152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1824 0.045 - 0.090: 494 0.090 - 0.135: 145 0.135 - 0.180: 2 0.180 - 0.225: 1 Chirality restraints: 2466 Sorted by residual: chirality pdb=" CB THR C 75 " pdb=" CA THR C 75 " pdb=" OG1 THR C 75 " pdb=" CG2 THR C 75 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ASN A 583 " pdb=" N ASN A 583 " pdb=" C ASN A 583 " pdb=" CB ASN A 583 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE B 223 " pdb=" N ILE B 223 " pdb=" C ILE B 223 " pdb=" CB ILE B 223 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2463 not shown) Planarity restraints: 3110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 445 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO B 446 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 446 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 446 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 308 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" CG ASP C 308 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP C 308 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP C 308 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 96 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO C 97 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 97 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 97 " -0.025 5.00e-02 4.00e+02 ... (remaining 3107 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 8321 3.00 - 3.47: 15666 3.47 - 3.95: 28110 3.95 - 4.42: 33678 4.42 - 4.90: 52909 Nonbonded interactions: 138684 Sorted by model distance: nonbonded pdb=" O ASP C 307 " pdb=" OD1 ASP C 308 " model vdw 2.520 3.040 nonbonded pdb=" O SER C 705 " pdb=" OG SER C 705 " model vdw 2.556 3.040 nonbonded pdb=" O ASP C 47 " pdb=" OD2 ASP C 47 " model vdw 2.561 3.040 nonbonded pdb=" N ASP A 666 " pdb=" OD1 ASP A 666 " model vdw 2.565 3.120 nonbonded pdb=" N THR B 460 " pdb=" OG1 THR B 460 " model vdw 2.568 2.496 ... (remaining 138679 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 86 through 449 or resid 459 through 803)) } 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: 5.380 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: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 42.120 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.003 0.040 17463 Z= 0.127 Angle : 0.538 11.331 23712 Z= 0.296 Chirality : 0.043 0.225 2466 Planarity : 0.004 0.047 3110 Dihedral : 16.822 89.971 6235 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.87 % Allowed : 21.46 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.35 (0.18), residues: 2136 helix: 1.37 (0.26), residues: 434 sheet: 0.56 (0.23), residues: 486 loop : -0.28 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 515 HIS 0.004 0.001 HIS B 651 PHE 0.015 0.001 PHE C 765 TYR 0.012 0.001 TYR A 655 ARG 0.006 0.000 ARG C 680 Details of bonding type rmsd hydrogen bonds : bond 0.19266 ( 572) hydrogen bonds : angle 7.36336 ( 1512) covalent geometry : bond 0.00268 (17463) covalent geometry : angle 0.53844 (23712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 1.789 Fit side-chains REVERT: A 250 MET cc_start: 0.6927 (tpp) cc_final: 0.6665 (tmm) REVERT: A 281 GLU cc_start: 0.6063 (tm-30) cc_final: 0.5737 (tt0) REVERT: A 290 MET cc_start: 0.6326 (mmp) cc_final: 0.5926 (mmm) REVERT: A 706 ASP cc_start: 0.7321 (t0) cc_final: 0.6746 (t0) REVERT: B 460 THR cc_start: 0.7364 (OUTLIER) cc_final: 0.6994 (p) REVERT: B 534 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: B 662 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7678 (mm-30) REVERT: C 83 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8381 (p) REVERT: C 171 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.7789 (p0) REVERT: C 260 MET cc_start: 0.2797 (tpt) cc_final: 0.2384 (mmm) REVERT: C 299 LYS cc_start: 0.8575 (tptp) cc_final: 0.8093 (ttmm) REVERT: C 651 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7056 (mtt) outliers start: 34 outliers final: 23 residues processed: 199 average time/residue: 1.5395 time to fit residues: 337.6304 Evaluate side-chains 191 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 124 optimal weight: 0.0050 chunk 194 optimal weight: 5.9990 overall best weight: 2.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 693 GLN A 800 GLN B 541 HIS B 654 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.174179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108289 restraints weight = 18490.252| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.99 r_work: 0.3061 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17463 Z= 0.211 Angle : 0.615 12.265 23712 Z= 0.331 Chirality : 0.048 0.176 2466 Planarity : 0.005 0.048 3110 Dihedral : 5.910 58.947 2391 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.24 % Allowed : 19.15 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.26 (0.18), residues: 2136 helix: 1.14 (0.25), residues: 450 sheet: 0.59 (0.23), residues: 478 loop : -0.32 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 216 HIS 0.006 0.001 HIS B 406 PHE 0.020 0.002 PHE C 483 TYR 0.013 0.002 TYR A 787 ARG 0.007 0.001 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.06295 ( 572) hydrogen bonds : angle 5.88256 ( 1512) covalent geometry : bond 0.00502 (17463) covalent geometry : angle 0.61543 (23712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 163 time to evaluate : 1.827 Fit side-chains REVERT: A 169 LEU cc_start: 0.4940 (OUTLIER) cc_final: 0.4527 (mt) REVERT: A 250 MET cc_start: 0.6360 (tpp) cc_final: 0.6135 (tmm) REVERT: A 307 MET cc_start: 0.5423 (OUTLIER) cc_final: 0.4541 (tpp) REVERT: A 337 ILE cc_start: 0.5479 (mm) cc_final: 0.5239 (mt) REVERT: A 385 MET cc_start: 0.0950 (OUTLIER) cc_final: 0.0519 (pp-130) REVERT: A 622 MET cc_start: 0.8324 (mmt) cc_final: 0.7548 (mmm) REVERT: B 161 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8666 (mm) REVERT: B 600 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: C 260 MET cc_start: 0.2845 (OUTLIER) cc_final: 0.2338 (mmm) REVERT: C 753 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8015 (tm) outliers start: 77 outliers final: 34 residues processed: 225 average time/residue: 1.4476 time to fit residues: 362.3248 Evaluate side-chains 202 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 551 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 785 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 158 optimal weight: 0.0980 chunk 71 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 800 GLN B 541 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.176034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110618 restraints weight = 18551.338| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.12 r_work: 0.3083 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17463 Z= 0.122 Angle : 0.511 11.764 23712 Z= 0.272 Chirality : 0.044 0.151 2466 Planarity : 0.004 0.042 3110 Dihedral : 5.040 52.285 2366 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.52 % Allowed : 19.48 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.46 (0.18), residues: 2136 helix: 1.40 (0.25), residues: 456 sheet: 0.69 (0.23), residues: 478 loop : -0.25 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 446 HIS 0.005 0.001 HIS B 651 PHE 0.016 0.001 PHE C 765 TYR 0.010 0.001 TYR B 761 ARG 0.006 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 572) hydrogen bonds : angle 5.46094 ( 1512) covalent geometry : bond 0.00281 (17463) covalent geometry : angle 0.51113 (23712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 164 time to evaluate : 1.807 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.2957 (tpp) cc_final: 0.2278 (mpt) REVERT: A 168 MET cc_start: 0.5270 (OUTLIER) cc_final: 0.5056 (tpp) REVERT: A 169 LEU cc_start: 0.4834 (OUTLIER) cc_final: 0.4353 (mt) REVERT: A 247 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7570 (mp) REVERT: A 250 MET cc_start: 0.6491 (tpp) cc_final: 0.6245 (tmm) REVERT: A 307 MET cc_start: 0.5494 (OUTLIER) cc_final: 0.4552 (tpp) REVERT: A 337 ILE cc_start: 0.5426 (mm) cc_final: 0.5186 (mt) REVERT: A 622 MET cc_start: 0.8240 (mmt) cc_final: 0.8033 (mmt) REVERT: A 750 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: B 161 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8638 (mm) REVERT: B 460 THR cc_start: 0.7529 (OUTLIER) cc_final: 0.7168 (p) REVERT: B 662 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7815 (mm-30) REVERT: C 244 PHE cc_start: 0.4107 (m-80) cc_final: 0.3442 (m-80) REVERT: C 287 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9006 (mp) REVERT: C 404 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8454 (mt) REVERT: C 686 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: C 753 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7928 (tm) outliers start: 64 outliers final: 34 residues processed: 213 average time/residue: 1.6396 time to fit residues: 387.9280 Evaluate side-chains 203 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 551 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 124 optimal weight: 0.0770 chunk 71 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN B 541 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.174859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109366 restraints weight = 18396.107| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.07 r_work: 0.3068 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17463 Z= 0.163 Angle : 0.557 11.951 23712 Z= 0.297 Chirality : 0.045 0.152 2466 Planarity : 0.005 0.040 3110 Dihedral : 5.097 56.998 2361 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.40 % Allowed : 18.93 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.43 (0.18), residues: 2136 helix: 1.42 (0.25), residues: 450 sheet: 0.68 (0.24), residues: 479 loop : -0.28 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 446 HIS 0.005 0.001 HIS B 406 PHE 0.016 0.002 PHE C 765 TYR 0.014 0.002 TYR A 278 ARG 0.005 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 572) hydrogen bonds : angle 5.49991 ( 1512) covalent geometry : bond 0.00383 (17463) covalent geometry : angle 0.55716 (23712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 163 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.2967 (tpp) cc_final: 0.2314 (mpt) REVERT: A 168 MET cc_start: 0.5118 (OUTLIER) cc_final: 0.4872 (tpp) REVERT: A 169 LEU cc_start: 0.4839 (OUTLIER) cc_final: 0.4329 (mp) REVERT: A 205 GLU cc_start: 0.4693 (OUTLIER) cc_final: 0.4064 (mp0) REVERT: A 247 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7505 (mp) REVERT: A 250 MET cc_start: 0.6536 (tpp) cc_final: 0.6294 (tmm) REVERT: A 307 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.4685 (tpp) REVERT: A 337 ILE cc_start: 0.5397 (mm) cc_final: 0.5162 (mt) REVERT: A 427 ASP cc_start: 0.4741 (OUTLIER) cc_final: 0.4474 (m-30) REVERT: A 622 MET cc_start: 0.8230 (mmt) cc_final: 0.7429 (mmm) REVERT: A 750 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: B 161 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8642 (mm) REVERT: B 460 THR cc_start: 0.7566 (OUTLIER) cc_final: 0.7211 (p) REVERT: B 600 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: B 748 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8143 (ptp-170) REVERT: C 287 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9026 (mp) REVERT: C 305 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7951 (mm) REVERT: C 753 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7949 (tm) outliers start: 80 outliers final: 48 residues processed: 222 average time/residue: 2.0119 time to fit residues: 502.7841 Evaluate side-chains 225 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 163 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 551 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 52 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 205 optimal weight: 0.0000 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 168 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 211 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110195 restraints weight = 18677.020| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.11 r_work: 0.3079 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17463 Z= 0.131 Angle : 0.519 11.652 23712 Z= 0.276 Chirality : 0.044 0.150 2466 Planarity : 0.004 0.041 3110 Dihedral : 4.818 52.555 2360 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.07 % Allowed : 19.54 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.54 (0.18), residues: 2136 helix: 1.56 (0.25), residues: 449 sheet: 0.76 (0.24), residues: 478 loop : -0.23 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 446 HIS 0.004 0.001 HIS B 651 PHE 0.016 0.001 PHE C 765 TYR 0.012 0.001 TYR A 278 ARG 0.008 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 572) hydrogen bonds : angle 5.34052 ( 1512) covalent geometry : bond 0.00305 (17463) covalent geometry : angle 0.51895 (23712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 162 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.3002 (tpp) cc_final: 0.2250 (mpt) REVERT: A 168 MET cc_start: 0.5253 (OUTLIER) cc_final: 0.4968 (tpp) REVERT: A 169 LEU cc_start: 0.4971 (OUTLIER) cc_final: 0.4464 (mp) REVERT: A 250 MET cc_start: 0.6628 (tpp) cc_final: 0.6308 (tmm) REVERT: A 257 LYS cc_start: 0.6030 (tptt) cc_final: 0.5814 (tptp) REVERT: A 307 MET cc_start: 0.5602 (OUTLIER) cc_final: 0.4759 (tpp) REVERT: A 337 ILE cc_start: 0.5435 (mm) cc_final: 0.5191 (mt) REVERT: A 495 LEU cc_start: 0.2022 (OUTLIER) cc_final: 0.1653 (mt) REVERT: A 622 MET cc_start: 0.8283 (mmt) cc_final: 0.7502 (mmm) REVERT: A 750 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: B 161 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8637 (mm) REVERT: B 460 THR cc_start: 0.7565 (OUTLIER) cc_final: 0.7215 (p) REVERT: B 600 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7606 (tp30) REVERT: B 748 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8207 (ptp-170) REVERT: C 51 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8105 (m-30) REVERT: C 244 PHE cc_start: 0.4259 (m-80) cc_final: 0.3481 (m-80) REVERT: C 287 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9026 (mp) REVERT: C 305 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7884 (mm) outliers start: 74 outliers final: 44 residues processed: 218 average time/residue: 1.3632 time to fit residues: 330.8747 Evaluate side-chains 212 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 156 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 551 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 179 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 109 optimal weight: 0.4980 chunk 155 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 overall best weight: 1.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.174831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109085 restraints weight = 18486.280| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.99 r_work: 0.3068 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17463 Z= 0.161 Angle : 0.556 12.273 23712 Z= 0.296 Chirality : 0.045 0.149 2466 Planarity : 0.005 0.045 3110 Dihedral : 4.965 53.198 2360 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.68 % Allowed : 19.43 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.48 (0.18), residues: 2136 helix: 1.43 (0.25), residues: 451 sheet: 0.80 (0.24), residues: 467 loop : -0.27 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 446 HIS 0.005 0.001 HIS B 406 PHE 0.018 0.002 PHE A 528 TYR 0.014 0.002 TYR A 278 ARG 0.008 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.05332 ( 572) hydrogen bonds : angle 5.41942 ( 1512) covalent geometry : bond 0.00381 (17463) covalent geometry : angle 0.55595 (23712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 164 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.3176 (tpp) cc_final: 0.2495 (mpt) REVERT: A 168 MET cc_start: 0.5212 (OUTLIER) cc_final: 0.4920 (tpp) REVERT: A 169 LEU cc_start: 0.4942 (OUTLIER) cc_final: 0.4460 (mp) REVERT: A 205 GLU cc_start: 0.4907 (OUTLIER) cc_final: 0.4203 (mp0) REVERT: A 247 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7583 (mp) REVERT: A 250 MET cc_start: 0.6491 (tpp) cc_final: 0.6156 (tmm) REVERT: A 257 LYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5774 (tptp) REVERT: A 307 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.4824 (tpp) REVERT: A 337 ILE cc_start: 0.5429 (mm) cc_final: 0.5170 (mt) REVERT: A 495 LEU cc_start: 0.2048 (OUTLIER) cc_final: 0.1685 (mt) REVERT: A 622 MET cc_start: 0.8360 (mmt) cc_final: 0.7573 (mmm) REVERT: A 651 HIS cc_start: 0.4050 (OUTLIER) cc_final: 0.3351 (m-70) REVERT: A 750 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7676 (mm-30) REVERT: A 771 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6488 (ttt180) REVERT: B 161 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8660 (mm) REVERT: B 460 THR cc_start: 0.7651 (OUTLIER) cc_final: 0.7293 (p) REVERT: B 600 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: B 748 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8221 (ptp-170) REVERT: C 51 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: C 132 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.6993 (mtp180) REVERT: C 244 PHE cc_start: 0.4237 (m-80) cc_final: 0.3458 (m-80) REVERT: C 287 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9011 (mp) REVERT: C 305 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7985 (mm) outliers start: 85 outliers final: 50 residues processed: 229 average time/residue: 1.3520 time to fit residues: 345.3308 Evaluate side-chains 224 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 156 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 551 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 130 optimal weight: 0.0980 chunk 146 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN A 800 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.175242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109359 restraints weight = 18399.518| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.98 r_work: 0.3100 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17463 Z= 0.163 Angle : 0.559 12.148 23712 Z= 0.297 Chirality : 0.045 0.148 2466 Planarity : 0.005 0.047 3110 Dihedral : 4.976 53.186 2360 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.57 % Allowed : 19.59 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.48 (0.18), residues: 2136 helix: 1.44 (0.25), residues: 450 sheet: 0.82 (0.24), residues: 466 loop : -0.27 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 446 HIS 0.005 0.001 HIS B 406 PHE 0.017 0.002 PHE C 765 TYR 0.013 0.002 TYR A 278 ARG 0.009 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.05262 ( 572) hydrogen bonds : angle 5.40266 ( 1512) covalent geometry : bond 0.00384 (17463) covalent geometry : angle 0.55900 (23712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 160 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.3216 (tpp) cc_final: 0.2555 (mpt) REVERT: A 168 MET cc_start: 0.5265 (OUTLIER) cc_final: 0.4980 (tpp) REVERT: A 205 GLU cc_start: 0.4898 (OUTLIER) cc_final: 0.4204 (mp0) REVERT: A 247 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7542 (mp) REVERT: A 257 LYS cc_start: 0.6007 (OUTLIER) cc_final: 0.5784 (tptp) REVERT: A 296 ASN cc_start: 0.6570 (t0) cc_final: 0.6295 (t0) REVERT: A 337 ILE cc_start: 0.5480 (mm) cc_final: 0.5201 (mt) REVERT: A 495 LEU cc_start: 0.2031 (OUTLIER) cc_final: 0.1679 (mt) REVERT: A 515 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6097 (ttp-110) REVERT: A 622 MET cc_start: 0.8323 (mmt) cc_final: 0.7525 (mmm) REVERT: A 651 HIS cc_start: 0.3902 (OUTLIER) cc_final: 0.3168 (m-70) REVERT: A 750 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: A 771 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6534 (ttt180) REVERT: B 161 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8632 (mm) REVERT: B 600 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7669 (tp30) REVERT: C 51 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8026 (m-30) REVERT: C 132 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.6985 (mtp180) REVERT: C 260 MET cc_start: 0.4404 (OUTLIER) cc_final: 0.3554 (ptp) REVERT: C 287 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9018 (mp) REVERT: C 305 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8018 (mm) REVERT: C 651 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7306 (mtt) outliers start: 83 outliers final: 54 residues processed: 225 average time/residue: 1.3932 time to fit residues: 352.4952 Evaluate side-chains 228 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 157 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 551 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 107 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.176699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111217 restraints weight = 18469.063| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.15 r_work: 0.3101 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17463 Z= 0.111 Angle : 0.506 11.487 23712 Z= 0.268 Chirality : 0.043 0.146 2466 Planarity : 0.004 0.046 3110 Dihedral : 4.709 52.094 2360 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.13 % Allowed : 20.09 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.61 (0.19), residues: 2136 helix: 1.63 (0.25), residues: 452 sheet: 0.78 (0.24), residues: 477 loop : -0.17 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 446 HIS 0.004 0.001 HIS B 651 PHE 0.016 0.001 PHE C 765 TYR 0.012 0.001 TYR A 278 ARG 0.010 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 572) hydrogen bonds : angle 5.19001 ( 1512) covalent geometry : bond 0.00253 (17463) covalent geometry : angle 0.50585 (23712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 160 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5222 (OUTLIER) cc_final: 0.4916 (tpp) REVERT: A 205 GLU cc_start: 0.4681 (OUTLIER) cc_final: 0.4244 (mp0) REVERT: A 247 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7573 (mp) REVERT: A 257 LYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5761 (tptp) REVERT: A 281 GLU cc_start: 0.6092 (tm-30) cc_final: 0.5713 (tt0) REVERT: A 337 ILE cc_start: 0.5409 (mm) cc_final: 0.5145 (mt) REVERT: A 385 MET cc_start: 0.0946 (OUTLIER) cc_final: 0.0698 (pp-130) REVERT: A 477 ASP cc_start: 0.4519 (OUTLIER) cc_final: 0.4175 (t0) REVERT: A 495 LEU cc_start: 0.1974 (OUTLIER) cc_final: 0.1619 (mt) REVERT: A 622 MET cc_start: 0.8308 (mmt) cc_final: 0.8044 (mmt) REVERT: A 651 HIS cc_start: 0.3773 (OUTLIER) cc_final: 0.3019 (m-70) REVERT: A 682 GLU cc_start: 0.6983 (pp20) cc_final: 0.6747 (pp20) REVERT: A 750 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: B 161 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8653 (mm) REVERT: B 460 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.7243 (p) REVERT: B 600 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: B 748 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8223 (ptp-170) REVERT: C 51 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8095 (m-30) REVERT: C 132 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7003 (mtp180) REVERT: C 171 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.7919 (p0) REVERT: C 244 PHE cc_start: 0.4256 (m-80) cc_final: 0.3480 (m-80) REVERT: C 260 MET cc_start: 0.4307 (mmm) cc_final: 0.3975 (ptp) REVERT: C 651 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7295 (mtt) REVERT: C 753 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7860 (mm) outliers start: 75 outliers final: 44 residues processed: 219 average time/residue: 1.2908 time to fit residues: 315.6779 Evaluate side-chains 219 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 157 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 551 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 10 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.174708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108933 restraints weight = 18512.983| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.06 r_work: 0.3064 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17463 Z= 0.192 Angle : 0.592 12.608 23712 Z= 0.316 Chirality : 0.047 0.150 2466 Planarity : 0.005 0.049 3110 Dihedral : 5.054 53.451 2360 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.02 % Allowed : 20.25 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2136 helix: 1.36 (0.25), residues: 456 sheet: 0.70 (0.24), residues: 477 loop : -0.29 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 446 HIS 0.005 0.001 HIS B 406 PHE 0.017 0.002 PHE B 521 TYR 0.015 0.002 TYR A 278 ARG 0.009 0.001 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.05681 ( 572) hydrogen bonds : angle 5.43953 ( 1512) covalent geometry : bond 0.00459 (17463) covalent geometry : angle 0.59245 (23712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.3222 (tpp) cc_final: 0.2586 (mpt) REVERT: A 168 MET cc_start: 0.5146 (OUTLIER) cc_final: 0.4867 (tpp) REVERT: A 205 GLU cc_start: 0.4768 (OUTLIER) cc_final: 0.4104 (mp0) REVERT: A 247 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7469 (mp) REVERT: A 257 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5872 (tptp) REVERT: A 296 ASN cc_start: 0.6561 (t0) cc_final: 0.6273 (t0) REVERT: A 385 MET cc_start: 0.0923 (OUTLIER) cc_final: 0.0637 (pp-130) REVERT: A 477 ASP cc_start: 0.4642 (OUTLIER) cc_final: 0.4285 (t0) REVERT: A 495 LEU cc_start: 0.2070 (OUTLIER) cc_final: 0.1733 (mt) REVERT: A 622 MET cc_start: 0.8401 (mmt) cc_final: 0.7623 (mmm) REVERT: A 629 MET cc_start: 0.6827 (tmm) cc_final: 0.6567 (mmm) REVERT: A 750 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7714 (mm-30) REVERT: A 771 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6516 (ttt180) REVERT: B 460 THR cc_start: 0.7644 (OUTLIER) cc_final: 0.7304 (p) REVERT: B 600 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7681 (tp30) REVERT: B 748 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8250 (ptp-170) REVERT: C 51 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: C 132 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7055 (mtp180) REVERT: C 244 PHE cc_start: 0.4510 (m-80) cc_final: 0.3512 (m-80) REVERT: C 260 MET cc_start: 0.4484 (mmm) cc_final: 0.4139 (ptp) REVERT: C 651 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7310 (mtt) outliers start: 73 outliers final: 52 residues processed: 218 average time/residue: 1.3241 time to fit residues: 322.5268 Evaluate side-chains 221 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 154 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 551 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 68 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.175440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109179 restraints weight = 18447.235| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.94 r_work: 0.3105 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17463 Z= 0.151 Angle : 0.555 11.924 23712 Z= 0.295 Chirality : 0.045 0.147 2466 Planarity : 0.005 0.048 3110 Dihedral : 4.943 53.019 2360 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.80 % Allowed : 20.58 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.49 (0.18), residues: 2136 helix: 1.49 (0.25), residues: 450 sheet: 0.74 (0.24), residues: 476 loop : -0.25 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 446 HIS 0.005 0.001 HIS A 265 PHE 0.017 0.002 PHE C 765 TYR 0.014 0.001 TYR A 278 ARG 0.009 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 572) hydrogen bonds : angle 5.34640 ( 1512) covalent geometry : bond 0.00355 (17463) covalent geometry : angle 0.55542 (23712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 159 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.3293 (tpp) cc_final: 0.2610 (mpt) REVERT: A 168 MET cc_start: 0.5311 (OUTLIER) cc_final: 0.5017 (tpp) REVERT: A 205 GLU cc_start: 0.4652 (OUTLIER) cc_final: 0.4232 (mp0) REVERT: A 247 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7421 (mp) REVERT: A 257 LYS cc_start: 0.6059 (OUTLIER) cc_final: 0.5828 (tptp) REVERT: A 281 GLU cc_start: 0.6111 (tm-30) cc_final: 0.5752 (tt0) REVERT: A 307 MET cc_start: 0.5540 (OUTLIER) cc_final: 0.4562 (tpp) REVERT: A 321 MET cc_start: 0.6053 (tpt) cc_final: 0.5618 (tpp) REVERT: A 337 ILE cc_start: 0.5532 (mm) cc_final: 0.5283 (mt) REVERT: A 385 MET cc_start: 0.1007 (OUTLIER) cc_final: 0.0698 (pp-130) REVERT: A 477 ASP cc_start: 0.4742 (OUTLIER) cc_final: 0.4366 (t0) REVERT: A 495 LEU cc_start: 0.2064 (OUTLIER) cc_final: 0.1715 (mt) REVERT: A 515 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6107 (ttp-110) REVERT: A 622 MET cc_start: 0.8341 (mmt) cc_final: 0.7554 (mmm) REVERT: A 629 MET cc_start: 0.6731 (tmm) cc_final: 0.6466 (mmm) REVERT: A 682 GLU cc_start: 0.6962 (pp20) cc_final: 0.6677 (pp20) REVERT: A 750 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: A 771 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6518 (ttt180) REVERT: B 460 THR cc_start: 0.7630 (OUTLIER) cc_final: 0.7303 (p) REVERT: B 600 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: B 748 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8213 (ptp-170) REVERT: C 51 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: C 132 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.6985 (mtp180) REVERT: C 244 PHE cc_start: 0.4411 (m-80) cc_final: 0.3553 (m-80) REVERT: C 260 MET cc_start: 0.4519 (mmm) cc_final: 0.4145 (ptp) REVERT: C 651 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7307 (mtt) REVERT: C 753 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7914 (mm) outliers start: 69 outliers final: 50 residues processed: 213 average time/residue: 1.3608 time to fit residues: 322.0227 Evaluate side-chains 225 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 157 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 551 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 94 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 161 optimal weight: 0.0370 chunk 178 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.175359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108967 restraints weight = 18422.791| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.97 r_work: 0.3100 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17463 Z= 0.153 Angle : 0.559 12.213 23712 Z= 0.297 Chirality : 0.045 0.146 2466 Planarity : 0.005 0.046 3110 Dihedral : 4.939 53.090 2360 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.96 % Allowed : 20.47 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.49 (0.18), residues: 2136 helix: 1.48 (0.25), residues: 450 sheet: 0.74 (0.24), residues: 476 loop : -0.25 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 446 HIS 0.005 0.001 HIS B 651 PHE 0.017 0.002 PHE C 765 TYR 0.013 0.001 TYR A 278 ARG 0.009 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.05122 ( 572) hydrogen bonds : angle 5.35575 ( 1512) covalent geometry : bond 0.00358 (17463) covalent geometry : angle 0.55855 (23712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18744.78 seconds wall clock time: 323 minutes 56.79 seconds (19436.79 seconds total)