Starting phenix.real_space_refine on Tue Dec 31 21:50:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yuv_34112/12_2024/7yuv_34112.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yuv_34112/12_2024/7yuv_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_34112/12_2024/7yuv_34112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yuv_34112/12_2024/7yuv_34112.map" model { file = "/net/cci-nas-00/data/ceres_data/7yuv_34112/12_2024/7yuv_34112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yuv_34112/12_2024/7yuv_34112.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 10.37, per 1000 atoms: 0.62 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: 4.42 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.88 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: 5.07 Time building geometry restraints manager: 4.93 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: 2.690 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 38.150 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- 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= 0.182 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (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 TRP 0.026 0.002 TRP B 558 HIS 0.007 0.001 HIS C 377 PHE 0.029 0.002 PHE D 557 TYR 0.018 0.001 TYR C 643 ARG 0.008 0.000 ARG C 552 *********************** 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 : 2.074 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: 0.5870 (mt) REVERT: C 568 THR cc_start: 0.8142 (m) cc_final: 0.7559 (p) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.2827 time to fit residues: 108.0697 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 : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 7.9990 chunk 160 optimal weight: 0.0370 chunk 89 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 166 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 0.0050 chunk 192 optimal weight: 20.0000 overall best weight: 1.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 377 HIS ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16971 Z= 0.212 Angle : 0.671 9.982 23019 Z= 0.325 Chirality : 0.046 0.162 2616 Planarity : 0.005 0.054 2975 Dihedral : 8.224 152.924 2357 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.96 % Allowed : 8.41 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 2120 helix: 0.26 (0.18), residues: 875 sheet: -1.92 (0.31), residues: 274 loop : -1.69 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 558 HIS 0.010 0.001 HIS C 726 PHE 0.023 0.002 PHE D 557 TYR 0.017 0.002 TYR B 658 ARG 0.007 0.000 ARG B 645 *********************** 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 226 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.3560 (mpp) cc_final: 0.3332 (mpp) REVERT: D 485 MET cc_start: 0.6535 (tpp) cc_final: 0.6318 (tpp) REVERT: D 666 HIS cc_start: 0.5059 (OUTLIER) cc_final: 0.4502 (m-70) outliers start: 17 outliers final: 11 residues processed: 217 average time/residue: 0.3218 time to fit residues: 103.9471 Evaluate side-chains 195 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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 623 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS 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 106 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 171 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16971 Z= 0.240 Angle : 0.669 10.012 23019 Z= 0.323 Chirality : 0.045 0.158 2616 Planarity : 0.005 0.056 2975 Dihedral : 8.024 153.998 2357 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.35 % Allowed : 11.91 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.18), residues: 2120 helix: 0.29 (0.18), residues: 877 sheet: -1.99 (0.31), residues: 267 loop : -1.69 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 558 HIS 0.006 0.001 HIS B 377 PHE 0.019 0.002 PHE D 557 TYR 0.021 0.002 TYR B 768 ARG 0.006 0.000 ARG C 529 *********************** 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 229 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.5626 (mmt90) cc_final: 0.5326 (mtt90) REVERT: A 611 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8559 (m) REVERT: C 255 GLU cc_start: 0.7414 (pm20) cc_final: 0.7153 (pm20) REVERT: C 439 MET cc_start: 0.6559 (mtt) cc_final: 0.6310 (mtt) REVERT: D 666 HIS cc_start: 0.4901 (OUTLIER) cc_final: 0.4407 (m-70) outliers start: 24 outliers final: 18 residues processed: 220 average time/residue: 0.3156 time to fit residues: 103.5707 Evaluate side-chains 206 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 1.985 ------------------------------------------------------------------------------- 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 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 468 ILE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain D residue 483 ASP 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 190 optimal weight: 0.1980 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 129 optimal weight: 0.3980 chunk 193 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN B 726 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16971 Z= 0.204 Angle : 0.647 10.634 23019 Z= 0.311 Chirality : 0.044 0.153 2616 Planarity : 0.004 0.057 2975 Dihedral : 7.763 156.413 2357 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.58 % Allowed : 13.94 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 2120 helix: 0.39 (0.18), residues: 880 sheet: -1.96 (0.31), residues: 261 loop : -1.69 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 431 HIS 0.013 0.001 HIS B 726 PHE 0.022 0.002 PHE D 467 TYR 0.018 0.001 TYR C 768 ARG 0.006 0.000 ARG C 529 *********************** 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 233 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6605 (mtt) cc_final: 0.5711 (mtt) REVERT: A 427 MET cc_start: 0.3159 (mpp) cc_final: 0.2829 (mpp) REVERT: A 611 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8528 (m) REVERT: B 702 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.6833 (ptp) REVERT: C 262 VAL cc_start: 0.5511 (OUTLIER) cc_final: 0.5274 (t) REVERT: D 258 MET cc_start: 0.2212 (mmt) cc_final: 0.1740 (mmm) REVERT: D 666 HIS cc_start: 0.5030 (OUTLIER) cc_final: 0.4544 (m-70) outliers start: 28 outliers final: 17 residues processed: 224 average time/residue: 0.3128 time to fit residues: 105.4093 Evaluate side-chains 204 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 1.917 ------------------------------------------------------------------------------- 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 611 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 439 MET 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 412 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 483 ASP 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 170 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16971 Z= 0.275 Angle : 0.694 10.780 23019 Z= 0.332 Chirality : 0.046 0.236 2616 Planarity : 0.005 0.059 2975 Dihedral : 7.671 157.137 2357 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.14 % Allowed : 15.41 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2120 helix: 0.32 (0.18), residues: 876 sheet: -2.16 (0.30), residues: 265 loop : -1.71 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 507 HIS 0.013 0.001 HIS B 726 PHE 0.014 0.002 PHE C 466 TYR 0.016 0.002 TYR B 768 ARG 0.014 0.000 ARG A 541 *********************** 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 235 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6575 (mtt) cc_final: 0.5751 (mtt) REVERT: A 611 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8479 (m) REVERT: B 472 ASN cc_start: 0.7917 (m-40) cc_final: 0.7267 (t0) REVERT: B 702 MET cc_start: 0.7850 (ptp) cc_final: 0.6851 (ptp) REVERT: C 262 VAL cc_start: 0.5586 (OUTLIER) cc_final: 0.5345 (t) REVERT: D 258 MET cc_start: 0.2162 (mmt) cc_final: 0.1390 (mmm) REVERT: D 666 HIS cc_start: 0.5003 (OUTLIER) cc_final: 0.4480 (m-70) outliers start: 38 outliers final: 24 residues processed: 220 average time/residue: 0.3067 time to fit residues: 101.8100 Evaluate side-chains 211 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 2.016 ------------------------------------------------------------------------------- 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 611 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 683 MET 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 531 ILE Chi-restraints excluded: chain B residue 682 THR 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 468 ILE Chi-restraints excluded: chain C residue 568 THR 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 483 ASP 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 68 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 170 optimal weight: 0.3980 chunk 94 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 HIS ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 16971 Z= 0.369 Angle : 0.761 10.982 23019 Z= 0.368 Chirality : 0.047 0.170 2616 Planarity : 0.005 0.062 2975 Dihedral : 7.768 157.239 2357 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.22 % Allowed : 15.80 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.18), residues: 2120 helix: 0.09 (0.18), residues: 869 sheet: -2.35 (0.29), residues: 270 loop : -1.81 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 563 HIS 0.020 0.002 HIS B 726 PHE 0.020 0.003 PHE B 467 TYR 0.015 0.002 TYR B 658 ARG 0.012 0.001 ARG C 479 *********************** 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 246 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 189 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6615 (mtt) cc_final: 0.5873 (mtt) REVERT: A 427 MET cc_start: 0.3589 (mpp) cc_final: 0.3378 (mpp) REVERT: A 698 MET cc_start: 0.7258 (tpp) cc_final: 0.6821 (tpp) REVERT: B 472 ASN cc_start: 0.8149 (m-40) cc_final: 0.7481 (t0) REVERT: B 486 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6409 (pm20) REVERT: B 493 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.6047 (m-10) REVERT: B 702 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7298 (ptp) REVERT: B 708 LEU cc_start: 0.7709 (tt) cc_final: 0.7456 (mp) REVERT: C 262 VAL cc_start: 0.5664 (OUTLIER) cc_final: 0.5396 (t) REVERT: D 666 HIS cc_start: 0.4893 (OUTLIER) cc_final: 0.4404 (m-70) outliers start: 57 outliers final: 35 residues processed: 229 average time/residue: 0.2950 time to fit residues: 101.5093 Evaluate side-chains 218 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 2.034 ------------------------------------------------------------------------------- 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 494 THR 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 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 482 LEU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 493 TYR 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 568 THR 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 731 HIS Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 666 HIS Chi-restraints excluded: chain D residue 769 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 204 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 HIS C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16971 Z= 0.232 Angle : 0.692 12.125 23019 Z= 0.331 Chirality : 0.045 0.151 2616 Planarity : 0.005 0.059 2975 Dihedral : 7.614 159.506 2357 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.65 % Allowed : 16.82 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.19), residues: 2120 helix: 0.34 (0.18), residues: 875 sheet: -2.31 (0.29), residues: 277 loop : -1.74 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 563 HIS 0.022 0.001 HIS B 726 PHE 0.030 0.002 PHE A 657 TYR 0.011 0.001 TYR B 658 ARG 0.011 0.000 ARG A 541 *********************** 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 252 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6695 (mtt) cc_final: 0.5956 (mtt) REVERT: A 427 MET cc_start: 0.3546 (mpp) cc_final: 0.3332 (mpp) REVERT: A 698 MET cc_start: 0.7294 (tpp) cc_final: 0.6956 (mmm) REVERT: B 472 ASN cc_start: 0.7963 (m-40) cc_final: 0.7411 (t0) REVERT: B 493 TYR cc_start: 0.6336 (OUTLIER) cc_final: 0.5888 (m-10) REVERT: B 702 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7345 (ptp) REVERT: B 708 LEU cc_start: 0.7561 (tt) cc_final: 0.7328 (mp) REVERT: C 262 VAL cc_start: 0.5596 (OUTLIER) cc_final: 0.5357 (t) REVERT: C 528 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8231 (mp) REVERT: D 258 MET cc_start: 0.2463 (mmt) cc_final: 0.1529 (mmm) REVERT: D 666 HIS cc_start: 0.4964 (OUTLIER) cc_final: 0.4536 (m-70) outliers start: 47 outliers final: 35 residues processed: 237 average time/residue: 0.2937 time to fit residues: 105.8495 Evaluate side-chains 228 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 1.866 ------------------------------------------------------------------------------- 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 513 GLU 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 318 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 493 TYR 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 296 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 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 364 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 666 HIS Chi-restraints excluded: chain D residue 769 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 160 optimal weight: 0.0870 chunk 185 optimal weight: 20.0000 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 HIS C 472 ASN C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16971 Z= 0.193 Angle : 0.677 10.598 23019 Z= 0.323 Chirality : 0.045 0.164 2616 Planarity : 0.004 0.059 2975 Dihedral : 7.474 160.925 2357 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.54 % Allowed : 17.61 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 2120 helix: 0.53 (0.18), residues: 870 sheet: -2.02 (0.31), residues: 264 loop : -1.73 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 292 HIS 0.017 0.001 HIS B 726 PHE 0.029 0.002 PHE A 657 TYR 0.037 0.001 TYR A 768 ARG 0.010 0.000 ARG A 541 *********************** 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 246 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 2.057 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: 0.6702 (mtt) cc_final: 0.6039 (mtt) REVERT: A 698 MET cc_start: 0.7308 (tpp) cc_final: 0.6930 (tpp) REVERT: B 472 ASN cc_start: 0.7885 (m-40) cc_final: 0.7329 (t0) REVERT: B 493 TYR cc_start: 0.6257 (OUTLIER) cc_final: 0.5719 (m-10) REVERT: B 702 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7288 (ptp) REVERT: C 262 VAL cc_start: 0.5568 (OUTLIER) cc_final: 0.5351 (t) REVERT: C 421 LEU cc_start: 0.8899 (mt) cc_final: 0.8627 (mt) REVERT: C 528 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8163 (mp) REVERT: D 258 MET cc_start: 0.2488 (mmt) cc_final: 0.1545 (mmm) REVERT: D 666 HIS cc_start: 0.4957 (OUTLIER) cc_final: 0.4595 (m-70) outliers start: 45 outliers final: 33 residues processed: 233 average time/residue: 0.3095 time to fit residues: 107.0217 Evaluate side-chains 224 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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 454 HIS Chi-restraints excluded: chain A residue 513 GLU 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 B residue 319 HIS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 493 TYR 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 296 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 528 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 310 HIS Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 483 ASP 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 195 optimal weight: 30.0000 chunk 178 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 149 optimal weight: 0.0270 chunk 58 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 overall best weight: 3.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS B 649 GLN ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 16971 Z= 0.370 Angle : 0.771 10.580 23019 Z= 0.373 Chirality : 0.048 0.231 2616 Planarity : 0.005 0.063 2975 Dihedral : 7.611 157.309 2357 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.48 % Allowed : 18.00 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.18), residues: 2120 helix: 0.14 (0.18), residues: 876 sheet: -2.22 (0.30), residues: 259 loop : -1.81 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 563 HIS 0.010 0.002 HIS D 310 PHE 0.026 0.003 PHE A 657 TYR 0.015 0.002 TYR C 534 ARG 0.011 0.001 ARG B 479 *********************** 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 230 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6788 (mtt) cc_final: 0.6140 (mtt) REVERT: A 338 LEU cc_start: 0.4442 (OUTLIER) cc_final: 0.3109 (tt) REVERT: B 472 ASN cc_start: 0.8177 (m-40) cc_final: 0.7555 (t0) REVERT: B 493 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.6022 (m-10) REVERT: B 702 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7380 (ptp) REVERT: B 708 LEU cc_start: 0.7688 (tt) cc_final: 0.7452 (mp) REVERT: C 262 VAL cc_start: 0.5709 (OUTLIER) cc_final: 0.5436 (t) REVERT: C 528 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8236 (mp) REVERT: D 258 MET cc_start: 0.2486 (mmt) cc_final: 0.1558 (mmm) REVERT: D 666 HIS cc_start: 0.4965 (OUTLIER) cc_final: 0.4499 (m-70) outliers start: 44 outliers final: 36 residues processed: 213 average time/residue: 0.3059 time to fit residues: 97.6926 Evaluate side-chains 224 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 338 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 454 HIS 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 B residue 319 HIS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 493 TYR 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 296 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 528 LEU 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 731 HIS Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 483 ASP 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 201 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 211 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 129 optimal weight: 0.0870 chunk 103 optimal weight: 0.0000 chunk 133 optimal weight: 1.9990 overall best weight: 0.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2494 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= 0.202 Angle : 0.698 10.919 23019 Z= 0.331 Chirality : 0.045 0.169 2616 Planarity : 0.004 0.062 2975 Dihedral : 7.472 161.451 2357 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.20 % Allowed : 18.85 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 2120 helix: 0.46 (0.18), residues: 873 sheet: -2.05 (0.31), residues: 264 loop : -1.76 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 563 HIS 0.008 0.001 HIS C 726 PHE 0.027 0.002 PHE A 657 TYR 0.017 0.001 TYR A 320 ARG 0.010 0.000 ARG A 541 ********************** 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 239 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 2.152 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: 0.6610 (mtt) cc_final: 0.5962 (mtt) REVERT: A 338 LEU cc_start: 0.4334 (OUTLIER) cc_final: 0.3058 (tt) REVERT: A 698 MET cc_start: 0.7445 (tpp) cc_final: 0.7206 (tpp) REVERT: B 472 ASN cc_start: 0.8014 (m-40) cc_final: 0.7420 (t0) REVERT: B 493 TYR cc_start: 0.6267 (OUTLIER) cc_final: 0.5728 (m-10) REVERT: B 702 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7370 (ptp) REVERT: C 262 VAL cc_start: 0.5581 (OUTLIER) cc_final: 0.5345 (t) REVERT: C 516 MET cc_start: 0.5162 (tpp) cc_final: 0.4961 (tpp) REVERT: C 528 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8194 (mp) REVERT: D 258 MET cc_start: 0.2445 (mmt) cc_final: 0.1546 (mmm) REVERT: D 505 TYR cc_start: 0.2092 (m-80) cc_final: -0.0792 (m-10) REVERT: D 666 HIS cc_start: 0.5020 (OUTLIER) cc_final: 0.4669 (m-70) outliers start: 39 outliers final: 32 residues processed: 228 average time/residue: 0.3081 time to fit residues: 105.2181 Evaluate side-chains 224 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 338 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 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 322 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 493 TYR 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 296 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 528 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 310 HIS Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 483 ASP 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 179 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 155 optimal weight: 0.0770 chunk 24 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 172 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 overall best weight: 0.7938 ------------------------------------------------------------------------------- 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** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS ** C 726 HIS ** 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 = 0.4499 r_free = 0.4499 target = 0.162399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.132279 restraints weight = 39926.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.131895 restraints weight = 26310.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.133273 restraints weight = 21428.278| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16971 Z= 0.205 Angle : 0.696 11.123 23019 Z= 0.330 Chirality : 0.045 0.188 2616 Planarity : 0.005 0.081 2975 Dihedral : 7.429 160.911 2357 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.54 % Allowed : 18.85 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.19), residues: 2120 helix: 0.49 (0.18), residues: 874 sheet: -1.93 (0.32), residues: 254 loop : -1.76 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 602 HIS 0.022 0.001 HIS D 310 PHE 0.027 0.002 PHE A 657 TYR 0.040 0.002 TYR A 768 ARG 0.022 0.000 ARG C 552 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3383.11 seconds wall clock time: 62 minutes 49.28 seconds (3769.28 seconds total)