Starting phenix.real_space_refine on Sun Aug 24 03:51:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yuv_34112/08_2025/7yuv_34112.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yuv_34112/08_2025/7yuv_34112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yuv_34112/08_2025/7yuv_34112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yuv_34112/08_2025/7yuv_34112.map" model { file = "/net/cci-nas-00/data/ceres_data/7yuv_34112/08_2025/7yuv_34112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yuv_34112/08_2025/7yuv_34112.cif" } resolution = 3.8 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= 0.002 sd= 0.040 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 60 5.16 5 C 10510 2.51 5 N 2919 2.21 5 O 3162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16657 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "B" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "C" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "D" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.08, per 1000 atoms: 0.24 Number of scatterers: 16657 At special positions: 0 Unit cell: (113.98, 106.6, 141.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 6 15.00 O 3162 8.00 N 2919 7.00 C 10510 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: 1.24 Conformation dependent library (CDL) restraints added in 673.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3904 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 18 sheets defined 46.0% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 245 through 256 removed outlier: 4.850A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.800A pdb=" N THR A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.554A pdb=" N ARG A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 403 through 412 removed outlier: 3.625A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.651A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.850A pdb=" N ASP A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 506 removed outlier: 3.949A pdb=" N LEU A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 3.614A pdb=" N SER A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.875A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 Processing helix chain 'A' and resid 570 through 573 removed outlier: 3.612A pdb=" N ASP A 573 " --> pdb=" O ASP A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 570 through 573' Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 630 through 647 removed outlier: 3.702A pdb=" N LYS A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.527A pdb=" N ARG A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 Processing helix chain 'A' and resid 739 through 745 removed outlier: 3.750A pdb=" N GLU A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 768 removed outlier: 3.762A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 284 through 296 Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.165A pdb=" N THR B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 339 removed outlier: 4.284A pdb=" N ARG B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 424 through 427 removed outlier: 3.639A pdb=" N MET B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 424 through 427' Processing helix chain 'B' and resid 435 through 444 removed outlier: 3.679A pdb=" N ASP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.765A pdb=" N ASP B 483 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 removed outlier: 3.526A pdb=" N GLN B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 514 removed outlier: 3.509A pdb=" N LYS B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 540 through 560 removed outlier: 3.541A pdb=" N GLU B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 545 " --> pdb=" O ARG B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.774A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 4.009A pdb=" N GLU B 589 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.759A pdb=" N LYS B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 719 through 728 removed outlier: 3.945A pdb=" N ALA B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 747 through 753 removed outlier: 4.015A pdb=" N GLY B 753 " --> pdb=" O GLU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 769 removed outlier: 3.822A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 767 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 768 " --> pdb=" O GLU B 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 removed outlier: 3.692A pdb=" N VAL C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 271 removed outlier: 3.790A pdb=" N LYS C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 309 through 319 Processing helix chain 'C' and resid 324 through 339 Processing helix chain 'C' and resid 361 through 372 Processing helix chain 'C' and resid 386 through 391 removed outlier: 4.182A pdb=" N ILE C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 391' Processing helix chain 'C' and resid 403 through 412 removed outlier: 3.867A pdb=" N HIS C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 427 removed outlier: 3.733A pdb=" N MET C 427 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 444 removed outlier: 4.303A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 449 removed outlier: 3.709A pdb=" N ASN C 449 " --> pdb=" O PRO C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 515 Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.635A pdb=" N THR C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 removed outlier: 3.530A pdb=" N GLU C 560 " --> pdb=" O LYS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.578A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 591 removed outlier: 3.782A pdb=" N GLU C 589 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU C 591 " --> pdb=" O ALA C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.997A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 651 Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 Processing helix chain 'C' and resid 738 through 740 No H-bonds generated for 'chain 'C' and resid 738 through 740' Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.578A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 769 " --> pdb=" O VAL C 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 254 Processing helix chain 'D' and resid 259 through 273 Processing helix chain 'D' and resid 283 through 295 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.630A pdb=" N ILE D 329 " --> pdb=" O VAL D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 338 No H-bonds generated for 'chain 'D' and resid 337 through 338' Processing helix chain 'D' and resid 339 through 343 removed outlier: 3.742A pdb=" N ASP D 343 " --> pdb=" O GLN D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 373 removed outlier: 3.534A pdb=" N LEU D 364 " --> pdb=" O GLY D 360 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 411 removed outlier: 3.817A pdb=" N GLN D 411 " --> pdb=" O HIS D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 444 Processing helix chain 'D' and resid 478 through 483 removed outlier: 3.611A pdb=" N ASP D 483 " --> pdb=" O ARG D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.747A pdb=" N LYS D 509 " --> pdb=" O TYR D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 534 Processing helix chain 'D' and resid 540 through 560 Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 630 through 647 removed outlier: 3.716A pdb=" N HIS D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 728 removed outlier: 3.531A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 746 removed outlier: 3.517A pdb=" N ASN D 739 " --> pdb=" O PRO D 736 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D 745 " --> pdb=" O GLN D 742 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 746 " --> pdb=" O LEU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 removed outlier: 3.539A pdb=" N LEU D 751 " --> pdb=" O PRO D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 768 removed outlier: 3.653A pdb=" N VAL D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 421 removed outlier: 6.553A pdb=" N LEU A 353 " --> pdb=" O ALA A 471 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 7.116A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 597 through 603 removed outlier: 3.730A pdb=" N THR A 608 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 613 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 615 " --> pdb=" O HIS A 664 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS A 664 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.711A pdb=" N ALA A 701 " --> pdb=" O VAL A 734 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 705 through 706 removed outlier: 3.670A pdb=" N GLU A 705 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 376 through 380 removed outlier: 6.729A pdb=" N HIS B 377 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP B 422 " --> pdb=" O HIS B 377 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 379 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE B 419 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR B 470 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 421 " --> pdb=" O THR B 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 599 through 603 removed outlier: 3.850A pdb=" N THR B 603 " --> pdb=" O GLY B 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 613 through 615 Processing sheet with id=AA9, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.384A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 379 through 380 removed outlier: 3.507A pdb=" N ILE C 379 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP C 422 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE C 419 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR C 470 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 421 " --> pdb=" O THR C 470 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU C 351 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 471 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 486 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 520 through 522 Processing sheet with id=AB3, first strand: chain 'C' and resid 601 through 603 removed outlier: 3.528A pdb=" N ALA C 601 " --> pdb=" O THR C 608 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 608 " --> pdb=" O ALA C 601 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 603 " --> pdb=" O GLY C 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 613 through 618 removed outlier: 3.694A pdb=" N HIS C 664 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 617 " --> pdb=" O ASP C 662 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 700 through 702 removed outlier: 6.786A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 376 through 378 removed outlier: 7.362A pdb=" N HIS D 377 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE D 419 " --> pdb=" O ILE D 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 520 through 522 removed outlier: 3.665A pdb=" N ILE D 569 " --> pdb=" O GLU D 521 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 596 through 603 removed outlier: 3.528A pdb=" N ALA D 597 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR D 603 " --> pdb=" O GLY D 606 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 622 " --> pdb=" O VAL D 661 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 700 through 702 removed outlier: 3.809A pdb=" N VAL D 734 " --> pdb=" O ALA D 701 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.67 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: 5591 1.34 - 1.46: 2678 1.46 - 1.58: 8573 1.58 - 1.69: 9 1.69 - 1.81: 120 Bond restraints: 16971 Sorted by residual: bond pdb=" N LYS B 323 " pdb=" CA LYS B 323 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.76e+00 bond pdb=" C THR B 672 " pdb=" N PRO B 673 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.03e+00 bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C4 ADP C 801 " pdb=" C5 ADP C 801 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C THR A 672 " pdb=" O THR A 672 " ideal model delta sigma weight residual 1.234 1.240 -0.005 5.00e-03 4.00e+04 1.08e+00 ... (remaining 16966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 22346 1.67 - 3.34: 514 3.34 - 5.02: 113 5.02 - 6.69: 37 6.69 - 8.36: 9 Bond angle restraints: 23019 Sorted by residual: angle pdb=" N VAL A 605 " pdb=" CA VAL A 605 " pdb=" C VAL A 605 " ideal model delta sigma weight residual 111.91 106.84 5.07 8.90e-01 1.26e+00 3.24e+01 angle pdb=" C LEU A 322 " pdb=" CA LEU A 322 " pdb=" CB LEU A 322 " ideal model delta sigma weight residual 117.23 109.86 7.37 1.36e+00 5.41e-01 2.94e+01 angle pdb=" CA LEU A 322 " pdb=" C LEU A 322 " pdb=" N LYS A 323 " ideal model delta sigma weight residual 119.98 116.23 3.75 8.50e-01 1.38e+00 1.95e+01 angle pdb=" C LYS C 556 " pdb=" CA LYS C 556 " pdb=" CB LYS C 556 " ideal model delta sigma weight residual 110.92 105.12 5.80 1.59e+00 3.96e-01 1.33e+01 angle pdb=" N GLY C 539 " pdb=" CA GLY C 539 " pdb=" C GLY C 539 " ideal model delta sigma weight residual 111.21 114.99 -3.78 1.04e+00 9.25e-01 1.32e+01 ... (remaining 23014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.90: 10081 28.90 - 57.80: 303 57.80 - 86.70: 28 86.70 - 115.59: 4 115.59 - 144.49: 5 Dihedral angle restraints: 10421 sinusoidal: 4333 harmonic: 6088 Sorted by residual: dihedral pdb=" C2' ADP B 801 " pdb=" C1' ADP B 801 " pdb=" N9 ADP B 801 " pdb=" C4 ADP B 801 " ideal model delta sinusoidal sigma weight residual 91.55 -123.96 -144.49 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 171.53 128.47 1 2.00e+01 2.50e-03 3.89e+01 dihedral pdb=" O1B ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " pdb=" PA ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 65.30 -125.30 1 2.00e+01 2.50e-03 3.79e+01 ... (remaining 10418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1860 0.043 - 0.086: 553 0.086 - 0.130: 186 0.130 - 0.173: 16 0.173 - 0.216: 1 Chirality restraints: 2616 Sorted by residual: chirality pdb=" CB ILE A 424 " pdb=" CA ILE A 424 " pdb=" CG1 ILE A 424 " pdb=" CG2 ILE A 424 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CG LEU C 743 " pdb=" CB LEU C 743 " pdb=" CD1 LEU C 743 " pdb=" CD2 LEU C 743 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 2613 not shown) Planarity restraints: 2975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 617 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO B 618 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 618 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 618 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 557 " 0.009 2.00e-02 2.50e+03 1.29e-02 2.89e+00 pdb=" CG PHE D 557 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE D 557 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE D 557 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 557 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 557 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 557 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 558 " 0.013 2.00e-02 2.50e+03 9.69e-03 2.35e+00 pdb=" CG TRP B 558 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP B 558 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 558 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 558 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 558 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 558 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 558 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 558 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 558 " 0.000 2.00e-02 2.50e+03 ... (remaining 2972 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 413 2.69 - 3.24: 17129 3.24 - 3.80: 26839 3.80 - 4.35: 35403 4.35 - 4.90: 56140 Nonbonded interactions: 135924 Sorted by model distance: nonbonded pdb=" NE2 GLN A 510 " pdb=" O GLU A 544 " model vdw 2.141 3.120 nonbonded pdb=" OE1 GLN C 277 " pdb=" OG1 THR C 284 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR B 603 " pdb=" O GLY B 606 " model vdw 2.154 3.040 nonbonded pdb=" O LYS C 587 " pdb=" OG1 THR C 590 " model vdw 2.170 3.040 nonbonded pdb=" O ARG C 512 " pdb=" NE2 GLN D 340 " model vdw 2.177 3.120 ... (remaining 135919 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' and resid 243 through 774) selection = (chain 'B' and resid 243 through 774) selection = (chain 'C' and resid 243 through 774) selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.690 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 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 16971 Z= 0.128 Angle : 0.672 8.362 23019 Z= 0.337 Chirality : 0.045 0.216 2616 Planarity : 0.004 0.054 2975 Dihedral : 13.834 144.492 6517 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.19), residues: 2120 helix: 0.43 (0.19), residues: 838 sheet: -2.04 (0.32), residues: 260 loop : -1.67 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 552 TYR 0.018 0.001 TYR C 643 PHE 0.029 0.002 PHE D 557 TRP 0.026 0.002 TRP B 558 HIS 0.007 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00273 (16971) covalent geometry : angle 0.67161 (23019) hydrogen bonds : bond 0.17142 ( 621) hydrogen bonds : angle 6.63349 ( 1791) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LEU cc_start: 0.6089 (mt) cc_final: 0.5871 (mt) REVERT: C 568 THR cc_start: 0.8142 (m) cc_final: 0.7558 (p) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.1173 time to fit residues: 45.1362 Evaluate side-chains 183 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.2980 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 377 HIS ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 GLN C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.163752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.136069 restraints weight = 39336.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.134972 restraints weight = 27708.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.136038 restraints weight = 23498.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.136525 restraints weight = 18292.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.136750 restraints weight = 16510.183| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16971 Z= 0.129 Angle : 0.658 8.624 23019 Z= 0.319 Chirality : 0.045 0.157 2616 Planarity : 0.004 0.051 2975 Dihedral : 8.163 152.387 2357 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.79 % Allowed : 7.90 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.19), residues: 2120 helix: 0.28 (0.18), residues: 881 sheet: -1.85 (0.32), residues: 258 loop : -1.79 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 645 TYR 0.014 0.001 TYR B 658 PHE 0.023 0.002 PHE D 557 TRP 0.023 0.002 TRP B 558 HIS 0.009 0.001 HIS C 726 Details of bonding type rmsd covalent geometry : bond 0.00284 (16971) covalent geometry : angle 0.65752 (23019) hydrogen bonds : bond 0.04342 ( 621) hydrogen bonds : angle 5.28852 ( 1791) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 359 VAL cc_start: 0.7934 (m) cc_final: 0.7711 (t) REVERT: C 603 THR cc_start: 0.8390 (m) cc_final: 0.8080 (p) REVERT: D 666 HIS cc_start: 0.5844 (OUTLIER) cc_final: 0.5131 (m-70) outliers start: 14 outliers final: 9 residues processed: 225 average time/residue: 0.1317 time to fit residues: 44.4858 Evaluate side-chains 198 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 659 ASN Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 104 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 173 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.162739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.135096 restraints weight = 41037.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.134625 restraints weight = 33031.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.135720 restraints weight = 27670.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.136186 restraints weight = 19743.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.136396 restraints weight = 19366.920| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16971 Z= 0.146 Angle : 0.656 10.466 23019 Z= 0.314 Chirality : 0.045 0.150 2616 Planarity : 0.004 0.056 2975 Dihedral : 7.973 153.203 2357 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.07 % Allowed : 11.46 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.19), residues: 2120 helix: 0.40 (0.18), residues: 871 sheet: -1.91 (0.31), residues: 259 loop : -1.68 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 529 TYR 0.028 0.002 TYR B 768 PHE 0.019 0.002 PHE D 557 TRP 0.018 0.001 TRP B 558 HIS 0.006 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00334 (16971) covalent geometry : angle 0.65608 (23019) hydrogen bonds : bond 0.03574 ( 621) hydrogen bonds : angle 5.04129 ( 1791) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8883 (m) REVERT: C 603 THR cc_start: 0.8421 (m) cc_final: 0.8174 (p) REVERT: D 258 MET cc_start: 0.2128 (mmt) cc_final: 0.1566 (mmm) REVERT: D 633 MET cc_start: 0.2931 (mmt) cc_final: 0.2719 (mmt) REVERT: D 666 HIS cc_start: 0.5551 (OUTLIER) cc_final: 0.4923 (m-70) outliers start: 19 outliers final: 13 residues processed: 219 average time/residue: 0.1414 time to fit residues: 45.7528 Evaluate side-chains 198 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 126 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 209 optimal weight: 0.1980 chunk 205 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 142 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 GLN B 726 HIS ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS C 726 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.162960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.135472 restraints weight = 40398.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.133242 restraints weight = 33129.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.134482 restraints weight = 27486.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.134970 restraints weight = 21912.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.135133 restraints weight = 19359.053| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16971 Z= 0.130 Angle : 0.637 10.564 23019 Z= 0.306 Chirality : 0.044 0.147 2616 Planarity : 0.004 0.055 2975 Dihedral : 7.715 154.948 2357 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.35 % Allowed : 13.43 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.19), residues: 2120 helix: 0.49 (0.18), residues: 873 sheet: -1.85 (0.32), residues: 251 loop : -1.73 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 529 TYR 0.020 0.001 TYR C 768 PHE 0.021 0.002 PHE D 467 TRP 0.016 0.001 TRP A 431 HIS 0.010 0.001 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00298 (16971) covalent geometry : angle 0.63675 (23019) hydrogen bonds : bond 0.03289 ( 621) hydrogen bonds : angle 4.86435 ( 1791) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6732 (mtt) cc_final: 0.5793 (mtt) REVERT: B 702 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.6660 (ptp) REVERT: C 255 GLU cc_start: 0.7693 (pm20) cc_final: 0.7485 (pm20) REVERT: C 262 VAL cc_start: 0.5270 (OUTLIER) cc_final: 0.5066 (t) REVERT: C 421 LEU cc_start: 0.8812 (mt) cc_final: 0.8482 (mt) REVERT: C 702 MET cc_start: 0.7796 (ptp) cc_final: 0.7485 (ptp) REVERT: D 258 MET cc_start: 0.2318 (mmt) cc_final: 0.1457 (mmm) REVERT: D 633 MET cc_start: 0.2884 (mmt) cc_final: 0.2580 (mmt) REVERT: D 666 HIS cc_start: 0.5808 (OUTLIER) cc_final: 0.5055 (m-70) outliers start: 24 outliers final: 14 residues processed: 219 average time/residue: 0.1425 time to fit residues: 46.3090 Evaluate side-chains 201 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 62 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 137 optimal weight: 0.3980 chunk 191 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS B 472 ASN ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.160918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.132847 restraints weight = 40689.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.131180 restraints weight = 33298.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.132454 restraints weight = 29163.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.132690 restraints weight = 21321.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.132915 restraints weight = 20604.939| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16971 Z= 0.175 Angle : 0.675 10.315 23019 Z= 0.323 Chirality : 0.045 0.183 2616 Planarity : 0.005 0.058 2975 Dihedral : 7.614 156.123 2357 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.75 % Allowed : 14.79 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.19), residues: 2120 helix: 0.39 (0.18), residues: 878 sheet: -2.10 (0.30), residues: 268 loop : -1.68 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 541 TYR 0.014 0.002 TYR B 658 PHE 0.014 0.002 PHE C 466 TRP 0.012 0.002 TRP C 563 HIS 0.014 0.001 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00403 (16971) covalent geometry : angle 0.67522 (23019) hydrogen bonds : bond 0.03366 ( 621) hydrogen bonds : angle 4.89535 ( 1791) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6753 (mtt) cc_final: 0.5831 (mtt) REVERT: B 472 ASN cc_start: 0.7916 (m-40) cc_final: 0.7189 (t0) REVERT: B 702 MET cc_start: 0.7859 (ptp) cc_final: 0.6813 (ptp) REVERT: C 262 VAL cc_start: 0.5403 (OUTLIER) cc_final: 0.5187 (t) REVERT: D 633 MET cc_start: 0.3129 (mmt) cc_final: 0.2786 (mmt) REVERT: D 666 HIS cc_start: 0.5711 (OUTLIER) cc_final: 0.5006 (m-70) outliers start: 31 outliers final: 20 residues processed: 212 average time/residue: 0.1356 time to fit residues: 43.3418 Evaluate side-chains 203 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 46 optimal weight: 20.0000 chunk 42 optimal weight: 0.3980 chunk 56 optimal weight: 0.5980 chunk 198 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 67 optimal weight: 0.0470 chunk 122 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 HIS ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.163299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.134747 restraints weight = 39338.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.133783 restraints weight = 28158.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.135099 restraints weight = 23236.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.135392 restraints weight = 17773.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.135613 restraints weight = 16620.415| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16971 Z= 0.114 Angle : 0.633 12.032 23019 Z= 0.301 Chirality : 0.044 0.315 2616 Planarity : 0.004 0.054 2975 Dihedral : 7.417 159.562 2357 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.69 % Allowed : 15.74 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.19), residues: 2120 helix: 0.59 (0.18), residues: 879 sheet: -1.98 (0.31), residues: 259 loop : -1.68 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 541 TYR 0.014 0.001 TYR A 658 PHE 0.011 0.001 PHE D 557 TRP 0.014 0.001 TRP D 292 HIS 0.018 0.001 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00264 (16971) covalent geometry : angle 0.63349 (23019) hydrogen bonds : bond 0.03020 ( 621) hydrogen bonds : angle 4.64055 ( 1791) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6924 (mtt) cc_final: 0.6103 (mtt) REVERT: A 422 ASP cc_start: 0.6775 (t0) cc_final: 0.6556 (t0) REVERT: A 423 GLU cc_start: 0.7922 (tt0) cc_final: 0.7714 (mt-10) REVERT: A 698 MET cc_start: 0.7547 (tpp) cc_final: 0.7218 (mmm) REVERT: B 702 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7164 (ptp) REVERT: C 262 VAL cc_start: 0.5278 (OUTLIER) cc_final: 0.5071 (t) REVERT: D 258 MET cc_start: 0.2242 (mmt) cc_final: 0.1629 (mmm) REVERT: D 276 MET cc_start: 0.3541 (mmm) cc_final: 0.3323 (mmm) REVERT: D 633 MET cc_start: 0.3349 (mmt) cc_final: 0.3017 (mmt) REVERT: D 666 HIS cc_start: 0.5809 (OUTLIER) cc_final: 0.5198 (m-70) outliers start: 30 outliers final: 14 residues processed: 225 average time/residue: 0.1429 time to fit residues: 47.5205 Evaluate side-chains 199 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 103 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 64 optimal weight: 0.0070 chunk 3 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 HIS D 310 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.159739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.131858 restraints weight = 40728.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.130446 restraints weight = 36927.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.131961 restraints weight = 33608.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.131949 restraints weight = 22612.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.132407 restraints weight = 21485.812| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 16971 Z= 0.206 Angle : 0.722 10.835 23019 Z= 0.347 Chirality : 0.046 0.191 2616 Planarity : 0.005 0.061 2975 Dihedral : 7.523 155.239 2357 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.37 % Allowed : 16.48 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.18), residues: 2120 helix: 0.37 (0.18), residues: 876 sheet: -2.08 (0.31), residues: 265 loop : -1.73 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 479 TYR 0.018 0.002 TYR A 332 PHE 0.030 0.003 PHE A 657 TRP 0.015 0.002 TRP C 563 HIS 0.019 0.002 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00476 (16971) covalent geometry : angle 0.72222 (23019) hydrogen bonds : bond 0.03430 ( 621) hydrogen bonds : angle 4.96612 ( 1791) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6683 (mtt) cc_final: 0.5820 (mtt) REVERT: B 702 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7200 (ptp) REVERT: B 708 LEU cc_start: 0.7742 (tt) cc_final: 0.7490 (mp) REVERT: C 262 VAL cc_start: 0.5455 (OUTLIER) cc_final: 0.5201 (t) REVERT: D 258 MET cc_start: 0.2348 (mmt) cc_final: 0.1412 (mmm) REVERT: D 633 MET cc_start: 0.3302 (mmt) cc_final: 0.2982 (mmt) REVERT: D 666 HIS cc_start: 0.5530 (OUTLIER) cc_final: 0.4879 (m-70) outliers start: 42 outliers final: 29 residues processed: 216 average time/residue: 0.1325 time to fit residues: 43.3913 Evaluate side-chains 211 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 195 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 HIS ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.163006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.135014 restraints weight = 40087.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.133665 restraints weight = 32529.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.135026 restraints weight = 26456.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.135226 restraints weight = 20270.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.135454 restraints weight = 19381.575| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16971 Z= 0.122 Angle : 0.671 13.064 23019 Z= 0.318 Chirality : 0.045 0.181 2616 Planarity : 0.004 0.059 2975 Dihedral : 7.375 158.399 2357 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.58 % Allowed : 17.66 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.19), residues: 2120 helix: 0.62 (0.18), residues: 874 sheet: -1.99 (0.31), residues: 265 loop : -1.68 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 541 TYR 0.010 0.001 TYR C 768 PHE 0.029 0.002 PHE A 657 TRP 0.016 0.001 TRP C 563 HIS 0.015 0.001 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00282 (16971) covalent geometry : angle 0.67116 (23019) hydrogen bonds : bond 0.03048 ( 621) hydrogen bonds : angle 4.68835 ( 1791) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6709 (mtt) cc_final: 0.5926 (mtt) REVERT: A 645 ARG cc_start: 0.6845 (mtt90) cc_final: 0.6473 (mtt90) REVERT: B 702 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7320 (ptp) REVERT: C 262 VAL cc_start: 0.5322 (OUTLIER) cc_final: 0.5112 (t) REVERT: C 702 MET cc_start: 0.7812 (ptp) cc_final: 0.7602 (ptp) REVERT: D 258 MET cc_start: 0.2307 (mmt) cc_final: 0.1487 (mmm) REVERT: D 505 TYR cc_start: 0.1905 (m-80) cc_final: -0.1237 (m-10) REVERT: D 633 MET cc_start: 0.3440 (mmt) cc_final: 0.3158 (mmt) REVERT: D 666 HIS cc_start: 0.5664 (OUTLIER) cc_final: 0.5083 (m-70) outliers start: 28 outliers final: 18 residues processed: 222 average time/residue: 0.1418 time to fit residues: 46.7868 Evaluate side-chains 208 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 180 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 185 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 140 optimal weight: 0.0370 chunk 115 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.162239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.133870 restraints weight = 39584.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.132841 restraints weight = 30313.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.134160 restraints weight = 25307.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.134380 restraints weight = 18774.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.134604 restraints weight = 18119.189| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16971 Z= 0.139 Angle : 0.677 13.010 23019 Z= 0.322 Chirality : 0.045 0.218 2616 Planarity : 0.005 0.060 2975 Dihedral : 7.361 157.826 2357 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.03 % Allowed : 17.27 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.19), residues: 2120 helix: 0.64 (0.18), residues: 872 sheet: -1.93 (0.31), residues: 262 loop : -1.69 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 541 TYR 0.018 0.002 TYR A 320 PHE 0.028 0.002 PHE A 657 TRP 0.019 0.002 TRP B 602 HIS 0.004 0.001 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00327 (16971) covalent geometry : angle 0.67731 (23019) hydrogen bonds : bond 0.03062 ( 621) hydrogen bonds : angle 4.67839 ( 1791) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6744 (mtt) cc_final: 0.5954 (mtt) REVERT: A 645 ARG cc_start: 0.6907 (mtt90) cc_final: 0.6562 (mtt90) REVERT: A 658 TYR cc_start: 0.7480 (p90) cc_final: 0.7249 (p90) REVERT: B 485 MET cc_start: 0.6565 (tpp) cc_final: 0.6291 (tpp) REVERT: B 702 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7328 (ptp) REVERT: C 262 VAL cc_start: 0.5339 (OUTLIER) cc_final: 0.5126 (t) REVERT: C 702 MET cc_start: 0.7829 (ptp) cc_final: 0.7619 (ptp) REVERT: D 258 MET cc_start: 0.2203 (mmt) cc_final: 0.1396 (mmm) REVERT: D 505 TYR cc_start: 0.2008 (m-80) cc_final: -0.1070 (m-10) REVERT: D 633 MET cc_start: 0.3496 (mmt) cc_final: 0.3195 (mmt) REVERT: D 666 HIS cc_start: 0.5764 (OUTLIER) cc_final: 0.5209 (m-70) outliers start: 36 outliers final: 28 residues processed: 216 average time/residue: 0.1473 time to fit residues: 47.2442 Evaluate side-chains 217 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 121 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.158488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.130526 restraints weight = 40695.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.128523 restraints weight = 35407.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.129686 restraints weight = 34578.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.130621 restraints weight = 23817.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.130755 restraints weight = 22073.992| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 16971 Z= 0.249 Angle : 0.782 12.040 23019 Z= 0.377 Chirality : 0.048 0.229 2616 Planarity : 0.005 0.066 2975 Dihedral : 7.601 156.623 2357 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.43 % Allowed : 17.21 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.18), residues: 2120 helix: 0.18 (0.18), residues: 880 sheet: -2.18 (0.30), residues: 268 loop : -1.76 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 479 TYR 0.019 0.002 TYR A 332 PHE 0.027 0.003 PHE A 657 TRP 0.022 0.002 TRP B 602 HIS 0.018 0.002 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00569 (16971) covalent geometry : angle 0.78195 (23019) hydrogen bonds : bond 0.03666 ( 621) hydrogen bonds : angle 5.07505 ( 1791) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6634 (mtt) cc_final: 0.5787 (mtt) REVERT: B 323 LYS cc_start: 0.6138 (mtmm) cc_final: 0.5852 (mtmm) REVERT: B 528 LEU cc_start: 0.8108 (pp) cc_final: 0.7850 (tt) REVERT: B 702 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7320 (ptp) REVERT: B 708 LEU cc_start: 0.7889 (tt) cc_final: 0.7661 (mp) REVERT: C 262 VAL cc_start: 0.5458 (OUTLIER) cc_final: 0.5221 (t) REVERT: C 331 GLU cc_start: 0.7549 (pt0) cc_final: 0.7274 (pt0) REVERT: D 505 TYR cc_start: 0.1888 (m-80) cc_final: -0.1019 (m-10) REVERT: D 633 MET cc_start: 0.3378 (mmt) cc_final: 0.2995 (mmt) REVERT: D 666 HIS cc_start: 0.5566 (OUTLIER) cc_final: 0.4924 (m-70) outliers start: 43 outliers final: 35 residues processed: 213 average time/residue: 0.1383 time to fit residues: 44.2803 Evaluate side-chains 215 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 32 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 68 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 147 optimal weight: 0.0010 chunk 115 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.163280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.135376 restraints weight = 40101.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.134672 restraints weight = 31652.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.136066 restraints weight = 24488.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.136301 restraints weight = 19100.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.136390 restraints weight = 18054.732| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16971 Z= 0.122 Angle : 0.701 13.165 23019 Z= 0.331 Chirality : 0.046 0.187 2616 Planarity : 0.004 0.060 2975 Dihedral : 7.370 160.043 2357 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.69 % Allowed : 18.28 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.19), residues: 2120 helix: 0.56 (0.18), residues: 874 sheet: -2.02 (0.31), residues: 266 loop : -1.70 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 541 TYR 0.038 0.001 TYR A 768 PHE 0.026 0.002 PHE A 657 TRP 0.019 0.002 TRP C 563 HIS 0.012 0.001 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00280 (16971) covalent geometry : angle 0.70101 (23019) hydrogen bonds : bond 0.03152 ( 621) hydrogen bonds : angle 4.64864 ( 1791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2585.16 seconds wall clock time: 45 minutes 47.94 seconds (2747.94 seconds total)