Starting phenix.real_space_refine on Thu Sep 18 13:10:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j6x_61188/09_2025/9j6x_61188.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j6x_61188/09_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_61188/09_2025/9j6x_61188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j6x_61188/09_2025/9j6x_61188.map" model { file = "/net/cci-nas-00/data/ceres_data/9j6x_61188/09_2025/9j6x_61188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j6x_61188/09_2025/9j6x_61188.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.25, per 1000 atoms: 0.19 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: 1.18 Conformation dependent library (CDL) restraints added in 673.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.70 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: 3.23 Time building geometry restraints manager: 1.61 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: 8.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.180 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- 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 : 3.29 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG C 680 TYR 0.012 0.001 TYR A 655 PHE 0.015 0.001 PHE C 765 TRP 0.009 0.001 TRP C 515 HIS 0.004 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00268 (17463) covalent geometry : angle 0.53844 (23712) hydrogen bonds : bond 0.19266 ( 572) hydrogen bonds : angle 7.36336 ( 1512) *********************** 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 : 0.788 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: 0.8006 time to fit residues: 174.3065 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 : 0.666 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.0870 chunk 212 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 616 ASN A 693 GLN A 800 GLN B 541 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.178161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113691 restraints weight = 18686.395| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.11 r_work: 0.3116 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17463 Z= 0.090 Angle : 0.470 11.022 23712 Z= 0.250 Chirality : 0.042 0.151 2466 Planarity : 0.004 0.043 3110 Dihedral : 5.094 58.381 2391 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.42 % Allowed : 20.25 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.19), residues: 2136 helix: 1.66 (0.26), residues: 444 sheet: 0.76 (0.23), residues: 478 loop : -0.16 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 584 TYR 0.010 0.001 TYR A 655 PHE 0.015 0.001 PHE C 765 TRP 0.009 0.001 TRP C 446 HIS 0.004 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00194 (17463) covalent geometry : angle 0.47026 (23712) hydrogen bonds : bond 0.03868 ( 572) hydrogen bonds : angle 5.54843 ( 1512) *********************** 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 217 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.664 Fit side-chains REVERT: A 100 MET cc_start: 0.2968 (tpp) cc_final: 0.2347 (mpt) REVERT: A 250 MET cc_start: 0.6312 (tpp) cc_final: 0.6023 (tmm) REVERT: A 281 GLU cc_start: 0.5965 (tm-30) cc_final: 0.5617 (tt0) REVERT: A 307 MET cc_start: 0.5281 (OUTLIER) cc_final: 0.4412 (tpp) REVERT: A 337 ILE cc_start: 0.5501 (mm) cc_final: 0.5253 (mt) REVERT: A 622 MET cc_start: 0.8207 (mmt) cc_final: 0.7432 (mmm) REVERT: A 706 ASP cc_start: 0.6767 (t0) cc_final: 0.6314 (t0) REVERT: B 460 THR cc_start: 0.7444 (OUTLIER) cc_final: 0.7056 (p) REVERT: B 662 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7702 (mm-30) REVERT: C 171 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.7875 (p0) REVERT: C 244 PHE cc_start: 0.4084 (m-80) cc_final: 0.3457 (m-80) REVERT: C 299 LYS cc_start: 0.8550 (tptp) cc_final: 0.8127 (ttmm) outliers start: 44 outliers final: 17 residues processed: 206 average time/residue: 0.7503 time to fit residues: 169.9245 Evaluate side-chains 185 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 307 MET Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 177 MET 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 718 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 452 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 212 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 166 optimal weight: 0.3980 chunk 185 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 163 optimal weight: 0.0070 chunk 176 optimal weight: 3.9990 overall best weight: 1.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 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 = 0.4037 r_free = 0.4037 target = 0.176149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109818 restraints weight = 18645.885| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.13 r_work: 0.3077 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17463 Z= 0.133 Angle : 0.523 11.696 23712 Z= 0.277 Chirality : 0.044 0.151 2466 Planarity : 0.004 0.042 3110 Dihedral : 4.720 51.445 2360 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.63 % Rotamer: Outliers : 3.47 % Allowed : 19.43 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 2136 helix: 1.48 (0.25), residues: 455 sheet: 0.75 (0.23), residues: 479 loop : -0.18 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 680 TYR 0.011 0.001 TYR A 278 PHE 0.017 0.002 PHE A 528 TRP 0.010 0.001 TRP B 216 HIS 0.004 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00307 (17463) covalent geometry : angle 0.52267 (23712) hydrogen bonds : bond 0.04956 ( 572) hydrogen bonds : angle 5.45464 ( 1512) *********************** 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 230 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 167 time to evaluate : 0.684 Fit side-chains REVERT: A 100 MET cc_start: 0.3029 (tpp) cc_final: 0.2314 (mpt) REVERT: A 168 MET cc_start: 0.5345 (OUTLIER) cc_final: 0.5122 (tpp) REVERT: A 169 LEU cc_start: 0.4889 (OUTLIER) cc_final: 0.4395 (mt) REVERT: A 249 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6218 (tt0) REVERT: A 250 MET cc_start: 0.6549 (tpp) cc_final: 0.6312 (tmm) REVERT: A 307 MET cc_start: 0.5431 (OUTLIER) cc_final: 0.4535 (tpp) REVERT: A 337 ILE cc_start: 0.5441 (mm) cc_final: 0.5200 (mt) REVERT: A 706 ASP cc_start: 0.6830 (t0) cc_final: 0.6589 (t0) REVERT: A 720 ASP cc_start: 0.5695 (OUTLIER) cc_final: 0.5308 (m-30) REVERT: A 750 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7812 (mp0) REVERT: B 161 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8687 (mm) REVERT: B 460 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.7182 (p) REVERT: C 171 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.7879 (p0) REVERT: C 287 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9026 (mp) REVERT: C 299 LYS cc_start: 0.8561 (tptp) cc_final: 0.8169 (ttmm) REVERT: C 651 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7238 (mtt) REVERT: C 753 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7969 (tm) outliers start: 63 outliers final: 28 residues processed: 212 average time/residue: 0.7394 time to fit residues: 173.2252 Evaluate side-chains 200 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 177 MET Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 307 MET 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 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 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 704 LYS Chi-restraints excluded: chain B residue 726 ILE 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 366 SER Chi-restraints excluded: chain C residue 399 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 14 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 162 optimal weight: 0.0870 chunk 67 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 211 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 92 optimal weight: 4.9990 chunk 5 optimal weight: 0.0270 overall best weight: 0.8338 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.177164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111718 restraints weight = 18628.556| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.01 r_work: 0.3113 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17463 Z= 0.104 Angle : 0.483 11.459 23712 Z= 0.256 Chirality : 0.042 0.149 2466 Planarity : 0.004 0.041 3110 Dihedral : 4.539 51.161 2359 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 3.69 % Allowed : 19.37 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.19), residues: 2136 helix: 1.60 (0.25), residues: 456 sheet: 0.81 (0.24), residues: 479 loop : -0.13 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 584 TYR 0.011 0.001 TYR A 278 PHE 0.015 0.001 PHE C 765 TRP 0.009 0.001 TRP C 446 HIS 0.004 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00234 (17463) covalent geometry : angle 0.48308 (23712) hydrogen bonds : bond 0.04126 ( 572) hydrogen bonds : angle 5.23649 ( 1512) *********************** 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 233 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 166 time to evaluate : 0.673 Fit side-chains REVERT: A 100 MET cc_start: 0.2998 (tpp) cc_final: 0.2328 (mpt) REVERT: A 168 MET cc_start: 0.5294 (OUTLIER) cc_final: 0.5040 (tpp) REVERT: A 169 LEU cc_start: 0.4875 (OUTLIER) cc_final: 0.4392 (mt) REVERT: A 249 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6181 (tt0) REVERT: A 250 MET cc_start: 0.6405 (tpp) cc_final: 0.6125 (tmm) REVERT: A 307 MET cc_start: 0.5430 (OUTLIER) cc_final: 0.4546 (tpp) REVERT: A 337 ILE cc_start: 0.5451 (mm) cc_final: 0.5211 (mt) REVERT: A 622 MET cc_start: 0.8174 (mmt) cc_final: 0.7966 (mmm) REVERT: A 706 ASP cc_start: 0.6614 (t0) cc_final: 0.6350 (t0) REVERT: A 720 ASP cc_start: 0.5748 (OUTLIER) cc_final: 0.5158 (m-30) REVERT: A 750 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: B 161 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8703 (mm) REVERT: B 460 THR cc_start: 0.7504 (OUTLIER) cc_final: 0.7131 (p) REVERT: B 600 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7509 (tp30) REVERT: B 748 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7999 (ptp-170) REVERT: C 171 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.7864 (p0) REVERT: C 287 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9002 (mp) REVERT: C 753 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7933 (tm) outliers start: 67 outliers final: 32 residues processed: 216 average time/residue: 0.7102 time to fit residues: 169.3781 Evaluate side-chains 205 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 249 GLU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 436 ILE 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 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 250 MET 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 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 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 598 SER 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 791 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 41 optimal weight: 9.9990 chunk 49 optimal weight: 0.1980 chunk 29 optimal weight: 20.0000 chunk 44 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.176174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109008 restraints weight = 18428.203| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.73 r_work: 0.3125 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17463 Z= 0.132 Angle : 0.519 11.993 23712 Z= 0.276 Chirality : 0.044 0.147 2466 Planarity : 0.004 0.041 3110 Dihedral : 4.559 51.859 2356 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 3.74 % Allowed : 19.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.19), residues: 2136 helix: 1.53 (0.25), residues: 456 sheet: 0.82 (0.24), residues: 478 loop : -0.14 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 584 TYR 0.014 0.001 TYR A 278 PHE 0.016 0.001 PHE C 765 TRP 0.010 0.001 TRP C 446 HIS 0.004 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00305 (17463) covalent geometry : angle 0.51911 (23712) hydrogen bonds : bond 0.04729 ( 572) hydrogen bonds : angle 5.28875 ( 1512) *********************** 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 232 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 164 time to evaluate : 0.872 Fit side-chains REVERT: A 100 MET cc_start: 0.3035 (tpp) cc_final: 0.2279 (mpt) REVERT: A 168 MET cc_start: 0.5434 (OUTLIER) cc_final: 0.5197 (tpp) REVERT: A 169 LEU cc_start: 0.4986 (OUTLIER) cc_final: 0.4519 (mt) REVERT: A 249 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6145 (tt0) REVERT: A 250 MET cc_start: 0.6477 (tpp) cc_final: 0.6216 (tmm) REVERT: A 307 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.4667 (tpp) REVERT: A 337 ILE cc_start: 0.5494 (mm) cc_final: 0.5245 (mt) REVERT: A 427 ASP cc_start: 0.4659 (OUTLIER) cc_final: 0.4432 (m-30) REVERT: A 495 LEU cc_start: 0.2218 (OUTLIER) cc_final: 0.1840 (mt) REVERT: A 622 MET cc_start: 0.8261 (mmt) cc_final: 0.7492 (mmm) REVERT: A 706 ASP cc_start: 0.6730 (t0) cc_final: 0.6459 (t0) REVERT: A 750 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: B 161 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8672 (mm) REVERT: B 460 THR cc_start: 0.7599 (OUTLIER) cc_final: 0.7233 (p) REVERT: B 600 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: B 748 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8154 (ptp-170) REVERT: C 171 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.7852 (p0) REVERT: C 287 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8969 (mp) REVERT: C 651 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.7219 (mtt) outliers start: 68 outliers final: 37 residues processed: 213 average time/residue: 0.6630 time to fit residues: 156.4685 Evaluate side-chains 214 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 163 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 177 MET Chi-restraints excluded: chain A residue 249 GLU 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 495 LEU 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 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 604 LEU 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 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 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 730 ILE Chi-restraints excluded: chain C residue 753 LEU 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 178 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 B 541 HIS B 654 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.173635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108324 restraints weight = 18436.452| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.08 r_work: 0.3028 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 17463 Z= 0.252 Angle : 0.646 12.165 23712 Z= 0.347 Chirality : 0.050 0.162 2466 Planarity : 0.005 0.049 3110 Dihedral : 5.063 53.986 2356 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 4.29 % Allowed : 18.99 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.18), residues: 2136 helix: 1.13 (0.24), residues: 464 sheet: 0.81 (0.24), residues: 447 loop : -0.32 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 673 TYR 0.018 0.002 TYR A 278 PHE 0.021 0.003 PHE C 483 TRP 0.012 0.002 TRP B 216 HIS 0.007 0.002 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00605 (17463) covalent geometry : angle 0.64602 (23712) hydrogen bonds : bond 0.06484 ( 572) hydrogen bonds : angle 5.62416 ( 1512) *********************** 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 238 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 160 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5262 (OUTLIER) cc_final: 0.4955 (tpp) REVERT: A 205 GLU cc_start: 0.4927 (OUTLIER) cc_final: 0.4217 (mp0) REVERT: A 247 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7616 (mp) REVERT: A 250 MET cc_start: 0.6578 (tpp) cc_final: 0.5947 (tpp) REVERT: A 307 MET cc_start: 0.5658 (OUTLIER) cc_final: 0.4679 (tpp) REVERT: A 337 ILE cc_start: 0.5421 (mm) cc_final: 0.5157 (mt) REVERT: A 495 LEU cc_start: 0.2119 (OUTLIER) cc_final: 0.1776 (mt) REVERT: A 622 MET cc_start: 0.8378 (mmt) cc_final: 0.7635 (mmm) REVERT: A 706 ASP cc_start: 0.6803 (t0) cc_final: 0.6547 (t0) REVERT: A 750 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7825 (mm-30) REVERT: B 161 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8670 (mm) REVERT: B 600 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7775 (tp30) REVERT: B 748 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8268 (ptp-170) REVERT: C 260 MET cc_start: 0.4465 (OUTLIER) cc_final: 0.3411 (ptp) REVERT: C 287 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9048 (mp) REVERT: C 305 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7985 (mm) REVERT: C 651 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7283 (mtt) outliers start: 78 outliers final: 43 residues processed: 219 average time/residue: 0.6803 time to fit residues: 165.6420 Evaluate side-chains 215 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 205 GLU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 436 ILE 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 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 604 LEU 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 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 260 MET 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 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 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 192 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 112 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.175634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114563 restraints weight = 18461.652| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.02 r_work: 0.3095 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17463 Z= 0.144 Angle : 0.536 11.682 23712 Z= 0.286 Chirality : 0.044 0.145 2466 Planarity : 0.004 0.043 3110 Dihedral : 4.752 52.958 2356 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 3.63 % Allowed : 19.65 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.18), residues: 2136 helix: 1.54 (0.25), residues: 448 sheet: 0.75 (0.24), residues: 478 loop : -0.22 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 680 TYR 0.012 0.001 TYR A 278 PHE 0.016 0.002 PHE C 765 TRP 0.010 0.001 TRP C 446 HIS 0.005 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00338 (17463) covalent geometry : angle 0.53586 (23712) hydrogen bonds : bond 0.04903 ( 572) hydrogen bonds : angle 5.35574 ( 1512) *********************** 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 228 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 162 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5429 (OUTLIER) cc_final: 0.5135 (tpp) REVERT: A 250 MET cc_start: 0.6508 (tpp) cc_final: 0.5820 (tpp) REVERT: A 307 MET cc_start: 0.5770 (OUTLIER) cc_final: 0.4734 (tpp) REVERT: A 337 ILE cc_start: 0.5487 (mm) cc_final: 0.5206 (mt) REVERT: A 495 LEU cc_start: 0.2140 (OUTLIER) cc_final: 0.1807 (mt) REVERT: A 706 ASP cc_start: 0.6673 (t0) cc_final: 0.6443 (t0) REVERT: A 750 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: B 161 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8648 (mm) REVERT: B 600 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: C 132 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.6923 (mtp180) REVERT: C 260 MET cc_start: 0.4265 (OUTLIER) cc_final: 0.3547 (ptp) REVERT: C 287 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8989 (mp) outliers start: 66 outliers final: 45 residues processed: 211 average time/residue: 0.6957 time to fit residues: 162.8675 Evaluate side-chains 213 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 307 MET Chi-restraints excluded: chain A residue 436 ILE 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 138 ASP 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 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 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 365 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 399 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 74 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 134 optimal weight: 0.0030 chunk 18 optimal weight: 8.9990 chunk 2 optimal weight: 30.0000 chunk 161 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 88 optimal weight: 0.0670 chunk 184 optimal weight: 2.9990 overall best weight: 1.6132 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.180760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119439 restraints weight = 19399.704| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.61 r_work: 0.3274 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1155 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= 0.156 Angle : 0.556 12.128 23712 Z= 0.296 Chirality : 0.045 0.146 2466 Planarity : 0.005 0.042 3110 Dihedral : 4.799 53.143 2356 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.52 % Allowed : 19.98 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.18), residues: 2136 helix: 1.50 (0.25), residues: 449 sheet: 0.82 (0.24), residues: 466 loop : -0.24 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 680 TYR 0.014 0.002 TYR A 278 PHE 0.016 0.002 PHE C 765 TRP 0.010 0.001 TRP C 446 HIS 0.005 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00365 (17463) covalent geometry : angle 0.55592 (23712) hydrogen bonds : bond 0.05186 ( 572) hydrogen bonds : angle 5.38081 ( 1512) *********************** 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 227 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5520 (OUTLIER) cc_final: 0.5231 (tpp) REVERT: A 205 GLU cc_start: 0.4939 (OUTLIER) cc_final: 0.4236 (mp0) REVERT: A 250 MET cc_start: 0.6554 (tpp) cc_final: 0.5871 (tpp) REVERT: A 337 ILE cc_start: 0.5552 (mm) cc_final: 0.5260 (mt) REVERT: A 495 LEU cc_start: 0.2183 (OUTLIER) cc_final: 0.1811 (mt) REVERT: A 706 ASP cc_start: 0.6739 (t0) cc_final: 0.6504 (t0) REVERT: A 750 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: B 161 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8638 (mm) REVERT: B 600 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7499 (tp30) REVERT: B 748 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8065 (ptp-170) REVERT: C 132 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.6930 (mtp180) REVERT: C 260 MET cc_start: 0.4447 (mmm) cc_final: 0.3572 (ptp) REVERT: C 287 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9004 (mp) REVERT: C 404 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8512 (mt) outliers start: 64 outliers final: 44 residues processed: 213 average time/residue: 0.7102 time to fit residues: 167.7574 Evaluate side-chains 212 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain A residue 205 GLU 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 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 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 365 VAL 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 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 192 optimal weight: 0.0370 chunk 20 optimal weight: 10.0000 chunk 128 optimal weight: 0.5980 chunk 213 optimal weight: 0.9980 chunk 199 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 190 optimal weight: 0.0270 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.183616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121296 restraints weight = 19507.899| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.99 r_work: 0.3304 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17463 Z= 0.088 Angle : 0.474 10.873 23712 Z= 0.249 Chirality : 0.042 0.144 2466 Planarity : 0.004 0.043 3110 Dihedral : 4.304 50.698 2356 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.53 % Allowed : 21.02 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.19), residues: 2136 helix: 1.83 (0.25), residues: 449 sheet: 0.91 (0.24), residues: 470 loop : -0.10 (0.19), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 584 TYR 0.016 0.001 TYR B 652 PHE 0.015 0.001 PHE C 765 TRP 0.009 0.001 TRP B 420 HIS 0.004 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00194 (17463) covalent geometry : angle 0.47359 (23712) hydrogen bonds : bond 0.03378 ( 572) hydrogen bonds : angle 4.99387 ( 1512) *********************** 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 207 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.3972 (tpt) cc_final: 0.3275 (mpt) REVERT: A 168 MET cc_start: 0.5552 (OUTLIER) cc_final: 0.5266 (tpp) REVERT: A 247 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7604 (mp) REVERT: A 250 MET cc_start: 0.6553 (tpp) cc_final: 0.5916 (tpp) REVERT: A 281 GLU cc_start: 0.6129 (tm-30) cc_final: 0.5693 (tt0) REVERT: A 296 ASN cc_start: 0.6620 (t0) cc_final: 0.6168 (t0) REVERT: A 651 HIS cc_start: 0.4024 (OUTLIER) cc_final: 0.3258 (m-70) REVERT: A 706 ASP cc_start: 0.6728 (t0) cc_final: 0.6508 (t0) REVERT: B 161 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8656 (mm) REVERT: B 460 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.7235 (p) REVERT: B 600 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: C 171 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.7824 (p0) REVERT: C 244 PHE cc_start: 0.4008 (m-80) cc_final: 0.3469 (m-80) REVERT: C 260 MET cc_start: 0.4476 (mmm) cc_final: 0.3940 (ptp) REVERT: C 404 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8347 (mt) REVERT: C 719 MET cc_start: 0.4218 (ptt) cc_final: 0.3653 (pmm) REVERT: C 753 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.8003 (mm) outliers start: 46 outliers final: 25 residues processed: 198 average time/residue: 0.7369 time to fit residues: 161.5501 Evaluate side-chains 193 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 177 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 436 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 722 THR 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 304 SER 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 777 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 404 ILE 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 730 ILE Chi-restraints excluded: chain C residue 753 LEU 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 188 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.180262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120199 restraints weight = 19327.235| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.90 r_work: 0.3239 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17463 Z= 0.196 Angle : 0.598 12.427 23712 Z= 0.318 Chirality : 0.047 0.151 2466 Planarity : 0.005 0.045 3110 Dihedral : 4.841 53.142 2356 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.42 % Allowed : 21.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.18), residues: 2136 helix: 1.51 (0.25), residues: 449 sheet: 0.80 (0.24), residues: 467 loop : -0.23 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 584 TYR 0.013 0.002 TYR A 278 PHE 0.018 0.002 PHE C 483 TRP 0.013 0.002 TRP C 446 HIS 0.005 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00465 (17463) covalent geometry : angle 0.59810 (23712) hydrogen bonds : bond 0.05679 ( 572) hydrogen bonds : angle 5.40346 ( 1512) ********************** 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 205 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.5150 (tpp) REVERT: A 219 MET cc_start: 0.6397 (mmt) cc_final: 0.6034 (mmp) REVERT: A 247 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7642 (mp) REVERT: A 250 MET cc_start: 0.6563 (tpp) cc_final: 0.5894 (tpp) REVERT: A 281 GLU cc_start: 0.6289 (tm-30) cc_final: 0.5910 (tt0) REVERT: A 651 HIS cc_start: 0.3984 (OUTLIER) cc_final: 0.3160 (m-70) REVERT: A 706 ASP cc_start: 0.6797 (t0) cc_final: 0.6553 (t0) REVERT: B 161 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8655 (mm) REVERT: B 600 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: C 260 MET cc_start: 0.4505 (mmm) cc_final: 0.3546 (ptp) REVERT: C 686 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7711 (mp0) outliers start: 44 outliers final: 32 residues processed: 197 average time/residue: 0.7246 time to fit residues: 158.1336 Evaluate side-chains 195 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 247 ILE Chi-restraints excluded: chain A residue 436 ILE 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 722 THR 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 304 SER 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 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 365 VAL 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 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 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 791 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 209 optimal weight: 5.9990 chunk 106 optimal weight: 0.3980 chunk 177 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 117 optimal weight: 0.4980 chunk 201 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.182527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120224 restraints weight = 19406.507| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.01 r_work: 0.3287 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17463 Z= 0.099 Angle : 0.495 11.283 23712 Z= 0.260 Chirality : 0.042 0.144 2466 Planarity : 0.004 0.042 3110 Dihedral : 4.442 51.450 2356 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.09 % Allowed : 21.79 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.19), residues: 2136 helix: 1.72 (0.25), residues: 456 sheet: 0.81 (0.24), residues: 477 loop : -0.13 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 584 TYR 0.009 0.001 TYR A 278 PHE 0.016 0.001 PHE C 765 TRP 0.008 0.001 TRP C 752 HIS 0.005 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00222 (17463) covalent geometry : angle 0.49461 (23712) hydrogen bonds : bond 0.03825 ( 572) hydrogen bonds : angle 5.06923 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9752.76 seconds wall clock time: 166 minutes 10.30 seconds (9970.30 seconds total)