Starting phenix.real_space_refine on Sun Jun 15 02:06:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yuv_34112/06_2025/7yuv_34112.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yuv_34112/06_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_34112/06_2025/7yuv_34112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yuv_34112/06_2025/7yuv_34112.map" model { file = "/net/cci-nas-00/data/ceres_data/7yuv_34112/06_2025/7yuv_34112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yuv_34112/06_2025/7yuv_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.33, 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: 4.45 Conformation dependent library (CDL) restraints added in 2.3 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: 2.00 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: 4.99 Time building geometry restraints manager: 5.24 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 39.230 Find NCS groups from input model: 0.850 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.630 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.17142 ( 621) hydrogen bonds : angle 6.63349 ( 1791) covalent geometry : bond 0.00273 (16971) covalent geometry : angle 0.67161 (23019) *********************** 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 : 1.832 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: 0.2755 time to fit residues: 105.8147 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 : 1.768 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.162815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.135652 restraints weight = 40676.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.134136 restraints weight = 34420.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.135587 restraints weight = 26903.058| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 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= 0.143 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 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 621) hydrogen bonds : angle 5.31543 ( 1791) covalent geometry : bond 0.00320 (16971) covalent geometry : angle 0.67127 (23019) *********************** 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 : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 359 VAL cc_start: 0.7908 (m) cc_final: 0.7663 (t) REVERT: D 485 MET cc_start: 0.6671 (tpp) cc_final: 0.6397 (tpp) REVERT: D 633 MET cc_start: 0.2819 (mmt) cc_final: 0.2583 (mmt) REVERT: D 666 HIS cc_start: 0.5816 (OUTLIER) cc_final: 0.5074 (m-70) outliers start: 17 outliers final: 11 residues processed: 217 average time/residue: 0.2940 time to fit residues: 95.1527 Evaluate side-chains 196 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 149 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 100 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4515 r_free = 0.4515 target = 0.163475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.135987 restraints weight = 40265.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.134281 restraints weight = 33581.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.135378 restraints weight = 26878.911| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16971 Z= 0.126 Angle : 0.641 10.950 23019 Z= 0.308 Chirality : 0.045 0.152 2616 Planarity : 0.004 0.052 2975 Dihedral : 8.003 154.552 2357 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.02 % Allowed : 11.74 % Favored : 87.25 % 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: 0.43 (0.18), residues: 874 sheet: -1.87 (0.32), residues: 259 loop : -1.69 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 558 HIS 0.006 0.001 HIS B 726 PHE 0.018 0.002 PHE D 557 TYR 0.017 0.001 TYR B 658 ARG 0.006 0.000 ARG C 529 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 621) hydrogen bonds : angle 4.97389 ( 1791) covalent geometry : bond 0.00281 (16971) covalent geometry : angle 0.64138 (23019) *********************** 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 231 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6724 (mtt) cc_final: 0.5729 (mtt) REVERT: A 611 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8834 (m) REVERT: C 255 GLU cc_start: 0.7712 (pm20) cc_final: 0.7452 (pm20) REVERT: C 359 VAL cc_start: 0.7941 (m) cc_final: 0.7673 (t) REVERT: C 439 MET cc_start: 0.6790 (mtt) cc_final: 0.6525 (mtt) REVERT: D 258 MET cc_start: 0.2078 (mmt) cc_final: 0.1536 (mmm) REVERT: D 633 MET cc_start: 0.2945 (mmt) cc_final: 0.2597 (mmt) REVERT: D 666 HIS cc_start: 0.5733 (OUTLIER) cc_final: 0.5113 (m-70) outliers start: 18 outliers final: 12 residues processed: 224 average time/residue: 0.3094 time to fit residues: 103.3577 Evaluate side-chains 198 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 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 175 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 171 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN B 598 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.163578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.135899 restraints weight = 40223.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.134461 restraints weight = 32406.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.135510 restraints weight = 27437.798| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16971 Z= 0.123 Angle : 0.638 10.775 23019 Z= 0.305 Chirality : 0.044 0.157 2616 Planarity : 0.004 0.054 2975 Dihedral : 7.853 156.069 2357 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.75 % Allowed : 13.26 % Favored : 84.99 % 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: -1.25 (0.19), residues: 2120 helix: 0.46 (0.18), residues: 882 sheet: -1.90 (0.31), residues: 261 loop : -1.72 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 431 HIS 0.012 0.001 HIS B 726 PHE 0.021 0.002 PHE D 467 TYR 0.017 0.001 TYR C 768 ARG 0.006 0.000 ARG C 529 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 621) hydrogen bonds : angle 4.83838 ( 1791) covalent geometry : bond 0.00283 (16971) covalent geometry : angle 0.63760 (23019) *********************** 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 240 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6692 (mtt) cc_final: 0.5790 (mtt) REVERT: B 702 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.6676 (ptp) REVERT: C 262 VAL cc_start: 0.5292 (OUTLIER) cc_final: 0.5074 (t) REVERT: C 439 MET cc_start: 0.6864 (mtt) cc_final: 0.6563 (mtt) REVERT: C 528 LEU cc_start: 0.8713 (tp) cc_final: 0.8494 (mp) REVERT: D 258 MET cc_start: 0.2323 (mmt) cc_final: 0.1459 (mmm) REVERT: D 633 MET cc_start: 0.2974 (mmt) cc_final: 0.2626 (mmt) REVERT: D 666 HIS cc_start: 0.5650 (OUTLIER) cc_final: 0.5010 (m-70) outliers start: 31 outliers final: 18 residues processed: 229 average time/residue: 0.3149 time to fit residues: 107.9680 Evaluate side-chains 207 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 1.940 ------------------------------------------------------------------------------- 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 494 THR 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 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 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 63 optimal weight: 0.0370 chunk 7 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 78 optimal weight: 0.0570 chunk 5 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 201 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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** B 726 HIS ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.164658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.136450 restraints weight = 40350.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.135544 restraints weight = 29940.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.136934 restraints weight = 24336.670| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16971 Z= 0.111 Angle : 0.636 11.343 23019 Z= 0.303 Chirality : 0.044 0.178 2616 Planarity : 0.004 0.051 2975 Dihedral : 7.578 159.106 2357 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.64 % Allowed : 14.84 % Favored : 83.52 % 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: -1.14 (0.19), residues: 2120 helix: 0.54 (0.18), residues: 878 sheet: -1.78 (0.32), residues: 263 loop : -1.66 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 507 HIS 0.016 0.001 HIS B 726 PHE 0.013 0.001 PHE D 557 TYR 0.015 0.001 TYR A 658 ARG 0.007 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 621) hydrogen bonds : angle 4.66908 ( 1791) covalent geometry : bond 0.00251 (16971) covalent geometry : angle 0.63603 (23019) *********************** 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 227 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 1.872 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: 0.6573 (mtt) cc_final: 0.5770 (mtt) REVERT: B 472 ASN cc_start: 0.7779 (m-40) cc_final: 0.7135 (t0) REVERT: B 702 MET cc_start: 0.7721 (ptp) cc_final: 0.6637 (ptp) REVERT: C 262 VAL cc_start: 0.5402 (OUTLIER) cc_final: 0.5165 (t) REVERT: C 439 MET cc_start: 0.6752 (mtt) cc_final: 0.6520 (mtt) REVERT: D 258 MET cc_start: 0.2504 (mmt) cc_final: 0.1716 (mmm) REVERT: D 330 LEU cc_start: 0.4740 (OUTLIER) cc_final: 0.4435 (pp) REVERT: D 633 MET cc_start: 0.3237 (mmt) cc_final: 0.2953 (mmt) REVERT: D 666 HIS cc_start: 0.5775 (OUTLIER) cc_final: 0.5185 (m-70) outliers start: 29 outliers final: 17 residues processed: 214 average time/residue: 0.3157 time to fit residues: 99.9674 Evaluate side-chains 205 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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 439 MET 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 468 ILE Chi-restraints excluded: chain C residue 485 MET 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 330 LEU 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 184 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 165 optimal weight: 0.0870 chunk 187 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN A 377 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.163725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.134823 restraints weight = 40173.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.133677 restraints weight = 27895.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.134929 restraints weight = 22287.456| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2098 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= 0.126 Angle : 0.633 11.496 23019 Z= 0.302 Chirality : 0.044 0.146 2616 Planarity : 0.004 0.053 2975 Dihedral : 7.419 158.971 2357 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.37 % Allowed : 15.29 % Favored : 82.34 % 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: -1.11 (0.19), residues: 2120 helix: 0.61 (0.18), residues: 879 sheet: -1.80 (0.32), residues: 266 loop : -1.67 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 602 HIS 0.017 0.001 HIS B 726 PHE 0.011 0.001 PHE D 557 TYR 0.035 0.002 TYR A 768 ARG 0.007 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 621) hydrogen bonds : angle 4.67840 ( 1791) covalent geometry : bond 0.00291 (16971) covalent geometry : angle 0.63296 (23019) *********************** 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 238 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 1.820 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: 0.6644 (mtt) cc_final: 0.5844 (mtt) REVERT: A 698 MET cc_start: 0.7633 (tpp) cc_final: 0.7327 (mmm) REVERT: B 702 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.6621 (ptp) REVERT: C 528 LEU cc_start: 0.8561 (tp) cc_final: 0.8292 (mp) REVERT: D 633 MET cc_start: 0.3398 (mmt) cc_final: 0.3030 (mmt) REVERT: D 666 HIS cc_start: 0.5949 (OUTLIER) cc_final: 0.5329 (m-70) outliers start: 42 outliers final: 23 residues processed: 226 average time/residue: 0.3182 time to fit residues: 107.9505 Evaluate side-chains 208 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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 675 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 391 ARG Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 513 GLU 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 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 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 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 61 optimal weight: 0.8980 chunk 19 optimal weight: 30.0000 chunk 161 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 204 optimal weight: 30.0000 chunk 145 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 GLN B 726 HIS ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.162415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.132584 restraints weight = 39913.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.131296 restraints weight = 27404.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.132712 restraints weight = 21715.416| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16971 Z= 0.147 Angle : 0.669 11.436 23019 Z= 0.318 Chirality : 0.045 0.156 2616 Planarity : 0.004 0.055 2975 Dihedral : 7.371 159.015 2357 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.26 % Allowed : 15.91 % Favored : 81.83 % 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: -1.04 (0.19), residues: 2120 helix: 0.68 (0.18), residues: 872 sheet: -1.79 (0.31), residues: 271 loop : -1.62 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 602 HIS 0.020 0.001 HIS B 726 PHE 0.025 0.002 PHE D 467 TYR 0.014 0.002 TYR C 534 ARG 0.011 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 621) hydrogen bonds : angle 4.70957 ( 1791) covalent geometry : bond 0.00341 (16971) covalent geometry : angle 0.66852 (23019) *********************** 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 234 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6536 (mtt) cc_final: 0.5819 (mtt) REVERT: A 645 ARG cc_start: 0.7127 (mtt90) cc_final: 0.6623 (mtt90) REVERT: B 493 TYR cc_start: 0.6528 (OUTLIER) cc_final: 0.5466 (m-10) REVERT: B 702 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7114 (ptp) REVERT: C 528 LEU cc_start: 0.8631 (tp) cc_final: 0.8353 (mp) REVERT: D 258 MET cc_start: 0.2156 (mmt) cc_final: 0.1527 (mmm) REVERT: D 633 MET cc_start: 0.3313 (mmt) cc_final: 0.2890 (mmt) REVERT: D 666 HIS cc_start: 0.6062 (OUTLIER) cc_final: 0.5403 (m-70) outliers start: 40 outliers final: 30 residues processed: 217 average time/residue: 0.3051 time to fit residues: 98.6204 Evaluate side-chains 217 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 405 LEU 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 352 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 493 TYR Chi-restraints excluded: chain B residue 513 GLU 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 330 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 37 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 170 optimal weight: 0.2980 chunk 138 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 149 optimal weight: 0.0770 chunk 83 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 726 HIS ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.164607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.135512 restraints weight = 39842.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.135484 restraints weight = 27033.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.136856 restraints weight = 21294.190| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16971 Z= 0.113 Angle : 0.655 12.950 23019 Z= 0.310 Chirality : 0.044 0.153 2616 Planarity : 0.004 0.054 2975 Dihedral : 7.299 162.558 2357 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.86 % Allowed : 16.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 2120 helix: 0.76 (0.18), residues: 867 sheet: -1.75 (0.32), residues: 257 loop : -1.67 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 602 HIS 0.016 0.001 HIS B 726 PHE 0.032 0.001 PHE A 657 TYR 0.036 0.001 TYR A 768 ARG 0.008 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 621) hydrogen bonds : angle 4.55383 ( 1791) covalent geometry : bond 0.00256 (16971) covalent geometry : angle 0.65515 (23019) *********************** 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 224 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6806 (mtt) cc_final: 0.6098 (mtt) REVERT: A 645 ARG cc_start: 0.7046 (mtt90) cc_final: 0.6602 (mtt90) REVERT: B 493 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.5035 (m-10) REVERT: B 702 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.6650 (ptp) REVERT: D 258 MET cc_start: 0.2243 (mmt) cc_final: 0.1338 (mmm) REVERT: D 633 MET cc_start: 0.3254 (mmt) cc_final: 0.2895 (mmt) REVERT: D 666 HIS cc_start: 0.5901 (OUTLIER) cc_final: 0.5354 (m-70) outliers start: 33 outliers final: 25 residues processed: 212 average time/residue: 0.3122 time to fit residues: 98.8361 Evaluate side-chains 210 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.924 ------------------------------------------------------------------------------- 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 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 352 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 493 TYR Chi-restraints excluded: chain B residue 513 GLU 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 330 LEU 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 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 535 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 110 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 206 optimal weight: 40.0000 chunk 147 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 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 373 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 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 = 0.4501 r_free = 0.4501 target = 0.162136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.134188 restraints weight = 39737.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.133120 restraints weight = 32514.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.134499 restraints weight = 27872.982| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16971 Z= 0.158 Angle : 0.699 11.379 23019 Z= 0.334 Chirality : 0.045 0.197 2616 Planarity : 0.005 0.055 2975 Dihedral : 7.320 159.665 2357 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.03 % Allowed : 17.16 % Favored : 80.81 % 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: -1.04 (0.19), residues: 2120 helix: 0.69 (0.18), residues: 871 sheet: -1.69 (0.32), residues: 252 loop : -1.67 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 563 HIS 0.013 0.001 HIS D 310 PHE 0.029 0.002 PHE A 657 TYR 0.012 0.002 TYR C 534 ARG 0.008 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.03102 ( 621) hydrogen bonds : angle 4.72644 ( 1791) covalent geometry : bond 0.00366 (16971) covalent geometry : angle 0.69872 (23019) *********************** 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 225 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.823 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: symmetry clash REVERT: A 258 MET cc_start: 0.6679 (mtt) cc_final: 0.5986 (mtt) REVERT: A 427 MET cc_start: 0.2009 (mmt) cc_final: -0.0002 (ptt) REVERT: B 493 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.5549 (m-10) REVERT: B 528 LEU cc_start: 0.7968 (pp) cc_final: 0.7756 (tt) REVERT: B 702 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7085 (ptp) REVERT: C 578 LEU cc_start: 0.6970 (mt) cc_final: 0.6726 (mt) REVERT: D 258 MET cc_start: 0.2228 (mmt) cc_final: 0.1361 (mmm) REVERT: D 372 MET cc_start: 0.7585 (tmm) cc_final: 0.7289 (tmm) REVERT: D 633 MET cc_start: 0.3129 (mmt) cc_final: 0.2745 (mmt) REVERT: D 666 HIS cc_start: 0.5617 (OUTLIER) cc_final: 0.5101 (m-70) REVERT: D 683 MET cc_start: 0.7190 (ptm) cc_final: 0.6805 (ptm) outliers start: 36 outliers final: 26 residues processed: 213 average time/residue: 0.3059 time to fit residues: 97.1749 Evaluate side-chains 215 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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 568 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 493 TYR Chi-restraints excluded: chain B residue 513 GLU 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 330 LEU 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 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 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 129 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 207 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN B 726 HIS C 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.162890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.135430 restraints weight = 40412.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.134015 restraints weight = 34258.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.135376 restraints weight = 29732.409| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16971 Z= 0.137 Angle : 0.679 11.695 23019 Z= 0.323 Chirality : 0.045 0.197 2616 Planarity : 0.005 0.055 2975 Dihedral : 7.310 161.385 2357 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.81 % Allowed : 17.55 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.19), residues: 2120 helix: 0.71 (0.18), residues: 873 sheet: -1.76 (0.32), residues: 252 loop : -1.66 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 563 HIS 0.016 0.001 HIS B 726 PHE 0.029 0.002 PHE A 657 TYR 0.038 0.002 TYR A 768 ARG 0.006 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 621) hydrogen bonds : angle 4.67082 ( 1791) covalent geometry : bond 0.00321 (16971) covalent geometry : angle 0.67925 (23019) ********************** 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 221 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 2.045 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: 0.6751 (mtt) cc_final: 0.6053 (mtt) REVERT: A 427 MET cc_start: 0.1832 (mmt) cc_final: 0.0969 (tmm) REVERT: B 493 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.5438 (m-10) REVERT: B 702 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7184 (ptp) REVERT: C 528 LEU cc_start: 0.8587 (tp) cc_final: 0.8351 (mp) REVERT: C 578 LEU cc_start: 0.6885 (mt) cc_final: 0.6647 (mt) REVERT: D 258 MET cc_start: 0.2177 (mmt) cc_final: 0.1330 (mmm) REVERT: D 633 MET cc_start: 0.3104 (mmt) cc_final: 0.2716 (mmt) REVERT: D 666 HIS cc_start: 0.5632 (OUTLIER) cc_final: 0.5086 (m-70) REVERT: D 683 MET cc_start: 0.7083 (ptm) cc_final: 0.6708 (ptm) outliers start: 32 outliers final: 26 residues processed: 209 average time/residue: 0.2932 time to fit residues: 92.6046 Evaluate side-chains 212 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 2.109 ------------------------------------------------------------------------------- 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 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 319 HIS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 468 ILE 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 330 LEU 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 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 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 4 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 109 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 167 optimal weight: 0.0000 chunk 203 optimal weight: 20.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.162820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.133345 restraints weight = 39960.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.132673 restraints weight = 27837.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.133854 restraints weight = 23043.195| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2594 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= 0.137 Angle : 0.691 13.591 23019 Z= 0.327 Chirality : 0.045 0.210 2616 Planarity : 0.004 0.055 2975 Dihedral : 7.305 161.235 2357 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.75 % Allowed : 17.61 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.19), residues: 2120 helix: 0.74 (0.18), residues: 868 sheet: -1.77 (0.32), residues: 252 loop : -1.64 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 563 HIS 0.005 0.001 HIS B 726 PHE 0.029 0.002 PHE A 657 TYR 0.023 0.002 TYR D 460 ARG 0.007 0.000 ARG C 529 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 621) hydrogen bonds : angle 4.70754 ( 1791) covalent geometry : bond 0.00321 (16971) covalent geometry : angle 0.69087 (23019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5128.42 seconds wall clock time: 89 minutes 52.94 seconds (5392.94 seconds total)