Starting phenix.real_space_refine on Thu Aug 6 15:17:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xj8_38396/08_2026/8xj8_38396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xj8_38396/08_2026/8xj8_38396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xj8_38396/08_2026/8xj8_38396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xj8_38396/08_2026/8xj8_38396.map" model { file = "/net/cci-nas-00/data/ceres_data/8xj8_38396/08_2026/8xj8_38396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xj8_38396/08_2026/8xj8_38396.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.159 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 3 5.21 5 S 78 5.16 5 C 10127 2.51 5 N 2691 2.21 5 O 2990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15904 Number of models: 1 Model: "" Number of chains: 10 Chain: "X" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3427 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 3 Chain: "B" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2990 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 353} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3053 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 360} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2846 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2393 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 297} Chain breaks: 4 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.38, per 1000 atoms: 0.21 Number of scatterers: 15904 At special positions: 0 Unit cell: (116.748, 124.315, 135.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 15 15.00 Mg 3 11.99 O 2990 8.00 N 2691 7.00 C 10127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 525.6 milliseconds 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 25 sheets defined 42.7% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.584A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.544A pdb=" N THR A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.799A pdb=" N LYS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 486 through 491 Processing helix chain 'A' and resid 508 through 521 removed outlier: 3.511A pdb=" N LYS A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.749A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 619 Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.600A pdb=" N HIS A 680 " --> pdb=" O TYR A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 695 removed outlier: 3.707A pdb=" N ILE A 693 " --> pdb=" O PRO A 690 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.563A pdb=" N LYS A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 745 Processing helix chain 'A' and resid 752 through 762 removed outlier: 3.966A pdb=" N ILE A 756 " --> pdb=" O PHE A 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.654A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 400 removed outlier: 3.505A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.529A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 removed outlier: 4.400A pdb=" N GLU B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 removed outlier: 3.990A pdb=" N CYS B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 removed outlier: 3.528A pdb=" N LYS B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.569A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.510A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.588A pdb=" N GLU B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 689 through 693 removed outlier: 3.559A pdb=" N ILE B 693 " --> pdb=" O PRO B 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.782A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 372 through 375 removed outlier: 3.791A pdb=" N LEU C 375 " --> pdb=" O ARG C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 376 through 382 removed outlier: 3.816A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 removed outlier: 3.502A pdb=" N LEU C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.583A pdb=" N GLU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 510 through 521 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 removed outlier: 3.804A pdb=" N ILE C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 619 Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.692A pdb=" N ASN C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 689 through 695 removed outlier: 3.531A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 696 through 702 removed outlier: 3.717A pdb=" N ILE C 702 " --> pdb=" O PHE C 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 362 through 371 removed outlier: 3.689A pdb=" N LYS D 366 " --> pdb=" O PRO D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 375 removed outlier: 3.580A pdb=" N LEU D 375 " --> pdb=" O ARG D 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.900A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 398 Processing helix chain 'D' and resid 432 through 436 removed outlier: 3.611A pdb=" N LYS D 435 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 462 removed outlier: 4.566A pdb=" N MET D 458 " --> pdb=" O ASP D 454 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 577 removed outlier: 3.826A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 619 Processing helix chain 'D' and resid 667 through 679 Processing helix chain 'D' and resid 689 through 695 removed outlier: 3.968A pdb=" N ILE D 693 " --> pdb=" O PRO D 690 " (cutoff:3.500A) Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 696 through 702 removed outlier: 3.909A pdb=" N LYS D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 335 Processing helix chain 'E' and resid 363 through 372 removed outlier: 3.734A pdb=" N ARG E 372 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 384 removed outlier: 4.527A pdb=" N SER E 381 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU E 382 " --> pdb=" O TYR E 379 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 384 " --> pdb=" O SER E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.505A pdb=" N ASP E 398 " --> pdb=" O ALA E 394 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 400 " --> pdb=" O ILE E 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 335 Processing helix chain 'F' and resid 363 through 371 Processing helix chain 'F' and resid 372 through 375 Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.586A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 385 through 400 removed outlier: 3.533A pdb=" N LEU F 400 " --> pdb=" O ILE F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 425 No H-bonds generated for 'chain 'F' and resid 423 through 425' Processing helix chain 'F' and resid 455 through 461 removed outlier: 3.881A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU F 461 " --> pdb=" O GLU F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 468 Processing helix chain 'F' and resid 475 through 486 Processing helix chain 'F' and resid 508 through 521 removed outlier: 3.715A pdb=" N GLY F 521 " --> pdb=" O LYS F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.543A pdb=" N ASP F 534 " --> pdb=" O THR F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 578 Processing helix chain 'F' and resid 665 through 677 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.786A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER A 556 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR A 604 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE A 501 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.258A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 706 through 707 Processing sheet with id=AA7, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA8, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AA9, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.867A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N SER B 556 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB2, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.203A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB4, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AB5, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.952A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N SER C 556 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR C 499 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR C 604 " --> pdb=" O THR C 499 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE C 501 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AB7, first strand: chain 'C' and resid 628 through 631 Processing sheet with id=AB8, first strand: chain 'D' and resid 339 through 341 removed outlier: 4.623A pdb=" N HIS D 347 " --> pdb=" O ASN D 358 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AC1, first strand: chain 'D' and resid 524 through 527 removed outlier: 6.625A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC3, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AC4, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AC5, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AC6, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.633A pdb=" N VAL F 419 " --> pdb=" O TYR F 428 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 524 through 525 removed outlier: 6.315A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2604 1.30 - 1.43: 4061 1.43 - 1.56: 9429 1.56 - 1.69: 26 1.69 - 1.82: 116 Bond restraints: 16236 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" O3A ANP C 801 " pdb=" PB ANP C 801 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C SER B 455 " pdb=" O SER B 455 " ideal model delta sigma weight residual 1.238 1.164 0.074 1.28e-02 6.10e+03 3.34e+01 bond pdb=" C PRO B 456 " pdb=" O PRO B 456 " ideal model delta sigma weight residual 1.238 1.174 0.065 1.22e-02 6.72e+03 2.81e+01 ... (remaining 16231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 21831 3.32 - 6.64: 123 6.64 - 9.96: 18 9.96 - 13.28: 5 13.28 - 16.60: 4 Bond angle restraints: 21981 Sorted by residual: angle pdb=" N PRO B 682 " pdb=" CA PRO B 682 " pdb=" CB PRO B 682 " ideal model delta sigma weight residual 103.25 112.09 -8.84 1.05e+00 9.07e-01 7.09e+01 angle pdb=" N PRO B 682 " pdb=" CA PRO B 682 " pdb=" C PRO B 682 " ideal model delta sigma weight residual 112.47 95.97 16.50 2.06e+00 2.36e-01 6.41e+01 angle pdb=" C ILE B 681 " pdb=" N PRO B 682 " pdb=" CA PRO B 682 " ideal model delta sigma weight residual 119.84 127.73 -7.89 1.25e+00 6.40e-01 3.98e+01 angle pdb=" PB ANP C 801 " pdb=" N3B ANP C 801 " pdb=" PG ANP C 801 " ideal model delta sigma weight residual 126.95 110.35 16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 110.59 16.36 3.00e+00 1.11e-01 2.97e+01 ... (remaining 21976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.60: 8999 23.60 - 47.19: 724 47.19 - 70.79: 148 70.79 - 94.38: 30 94.38 - 117.98: 3 Dihedral angle restraints: 9904 sinusoidal: 4152 harmonic: 5752 Sorted by residual: dihedral pdb=" CA TYR F 428 " pdb=" C TYR F 428 " pdb=" N SER F 429 " pdb=" CA SER F 429 " ideal model delta harmonic sigma weight residual 180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LYS E 416 " pdb=" C LYS E 416 " pdb=" N ASN E 417 " pdb=" CA ASN E 417 " ideal model delta harmonic sigma weight residual 180.00 157.11 22.89 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LYS F 678 " pdb=" C LYS F 678 " pdb=" N TYR F 679 " pdb=" CA TYR F 679 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 9901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2178 0.062 - 0.124: 291 0.124 - 0.186: 8 0.186 - 0.248: 3 0.248 - 0.310: 5 Chirality restraints: 2485 Sorted by residual: chirality pdb=" CA ILE B 681 " pdb=" N ILE B 681 " pdb=" C ILE B 681 " pdb=" CB ILE B 681 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB VAL F 423 " pdb=" CA VAL F 423 " pdb=" CG1 VAL F 423 " pdb=" CG2 VAL F 423 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3' ANP C 801 " pdb=" C2' ANP C 801 " pdb=" C4' ANP C 801 " pdb=" O3' ANP C 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2482 not shown) Planarity restraints: 2761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 450 " -0.022 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C LYS B 450 " 0.074 2.00e-02 2.50e+03 pdb=" O LYS B 450 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE B 451 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 670 " -0.005 2.00e-02 2.50e+03 2.05e-02 8.41e+00 pdb=" CG TYR F 670 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR F 670 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR F 670 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR F 670 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR F 670 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR F 670 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 670 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 421 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" C ASP F 421 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP F 421 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU F 422 " 0.015 2.00e-02 2.50e+03 ... (remaining 2758 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 122 2.59 - 3.17: 12466 3.17 - 3.75: 23477 3.75 - 4.32: 35550 4.32 - 4.90: 56995 Nonbonded interactions: 128610 Sorted by model distance: nonbonded pdb=" O3G ANP C 801 " pdb="MG MG C 802 " model vdw 2.015 2.170 nonbonded pdb=" O2G ANP B 801 " pdb="MG MG B 802 " model vdw 2.061 2.170 nonbonded pdb=" OG SER A 510 " pdb="MG MG A 802 " model vdw 2.099 2.170 nonbonded pdb=" O2B ANP A 801 " pdb="MG MG A 802 " model vdw 2.114 2.170 nonbonded pdb=" OG SER D 359 " pdb=" OE1 GLU D 360 " model vdw 2.175 3.040 ... (remaining 128605 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 324 through 452 or (resid 453 through 455 and (name N or n \ ame CA or name C or name O or name CB )) or resid 456 through 636 or (resid 637 \ through 641 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 2 through 681 or (resid 682 and (name N or name CA or name C or name O or name C \ B )) or resid 683 through 695 or resid 801 through 802)) selection = (chain 'B' and (resid 324 through 484 or resid 486 through 636 or (resid 637 thr \ ough 641 and (name N or name CA or name C or name O or name CB )) or resid 642 t \ hrough 802)) selection = (chain 'C' and (resid 324 through 452 or (resid 453 through 455 and (name N or n \ ame CA or name C or name O or name CB )) or resid 456 through 484 or resid 486 t \ hrough 681 or (resid 682 and (name N or name CA or name C or name O or name CB ) \ ) or resid 683 through 695 or resid 801 through 802)) } ncs_group { reference = (chain 'D' and (resid 324 through 423 or (resid 424 and (name N or name CA or na \ me C or name O or name CB )) or resid 425 or (resid 426 and (name N or name CA o \ r name C or name O or name CB )) or resid 427 through 473 or (resid 474 and (nam \ e N or name CA or name C or name O or name CB )) or resid 475 or (resid 476 thro \ ugh 477 and (name N or name CA or name C or name O or name CB )) or resid 478 th \ rough 503 or (resid 504 and (name N or name CA or name C or name O or name CB )) \ or resid 505 through 528 or (resid 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 533 or (resid 534 and (name N or name CA o \ r name C or name O or name CB )) or resid 543 through 557 or (resid 558 and (nam \ e N or name CA or name C or name O or name CB )) or resid 559 through 561 or (re \ sid 567 through 568 and (name N or name CA or name C or name O or name CB )) or \ resid 569 or (resid 570 and (name N or name CA or name C or name O or name CB )) \ or resid 571 or (resid 572 and (name N or name CA or name C or name O or name C \ B )) or resid 573 through 574 or (resid 575 through 576 and (name N or name CA o \ r name C or name O or name CB )) or resid 577 or (resid 578 through 579 and (nam \ e N or name CA or name C or name O or name CB )) or resid 596 through 611 or (re \ sid 612 and (name N or name CA or name C or name O or name CB )) or resid 613 or \ (resid 614 through 620 and (name N or name CA or name C or name O or name CB )) \ or resid 621 through 624 or (resid 625 and (name N or name CA or name C or name \ O or name CB )) or resid 626 or (resid 627 and (name N or name CA or name C or \ name O or name CB )) or resid 628 or (resid 629 and (name N or name CA or name C \ or name O or name CB )) or resid 655 through 684)) selection = (chain 'F' and (resid 324 through 559 or (resid 560 and (name N or name CA or na \ me C or name O or name CB )) or resid 561 or resid 567 through 684)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.650 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 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:8.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3578 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 : 0.004 0.142 16236 Z= 0.239 Angle : 0.737 16.602 21981 Z= 0.407 Chirality : 0.044 0.310 2485 Planarity : 0.004 0.057 2761 Dihedral : 17.643 117.981 6160 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.00 % Favored : 95.28 % Rotamer: Outliers : 2.00 % Allowed : 16.35 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 1927 helix: -0.02 (0.20), residues: 678 sheet: -0.19 (0.34), residues: 283 loop : -0.69 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 625 TYR 0.045 0.001 TYR F 670 PHE 0.023 0.001 PHE B 451 TRP 0.007 0.001 TRP A 350 HIS 0.006 0.001 HIS B 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.24 (16236) covalent geometry : angle 0.73664 / 0.41 (21981) hydrogen bonds : bond 0.20571 / 15.65 ( 510) hydrogen bonds : angle 6.17539 / 4.81 ( 1452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 274 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 574 ILE cc_start: 0.5818 (mm) cc_final: 0.5515 (mm) REVERT: B 415 PHE cc_start: 0.5596 (m-80) cc_final: 0.5367 (m-80) REVERT: B 432 ASP cc_start: 0.2521 (OUTLIER) cc_final: 0.2215 (t70) REVERT: C 547 MET cc_start: 0.4147 (mtm) cc_final: 0.3850 (pp-130) REVERT: D 447 ASP cc_start: 0.0315 (OUTLIER) cc_final: 0.0023 (p0) REVERT: D 495 LYS cc_start: 0.6093 (mppt) cc_final: 0.5531 (mmtt) REVERT: D 502 PHE cc_start: 0.4751 (t80) cc_final: 0.4544 (t80) REVERT: D 571 SER cc_start: 0.6315 (m) cc_final: 0.5951 (p) REVERT: E 354 SER cc_start: 0.5654 (t) cc_final: 0.5320 (t) REVERT: E 422 LEU cc_start: 0.3097 (OUTLIER) cc_final: 0.2727 (tt) REVERT: E 444 PHE cc_start: 0.5475 (OUTLIER) cc_final: 0.5253 (p90) REVERT: F 354 SER cc_start: 0.4768 (t) cc_final: 0.4468 (t) REVERT: F 366 LYS cc_start: 0.7116 (mttt) cc_final: 0.6515 (mtpp) REVERT: F 413 LEU cc_start: 0.5054 (mt) cc_final: 0.4801 (mt) REVERT: F 423 VAL cc_start: 0.5991 (p) cc_final: 0.5738 (m) REVERT: F 465 ILE cc_start: 0.3814 (pp) cc_final: 0.3371 (mt) outliers start: 35 outliers final: 7 residues processed: 304 average time/residue: 0.5036 time to fit residues: 171.6438 Evaluate side-chains 160 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 444 PHE Chi-restraints excluded: chain F residue 556 SER Chi-restraints excluded: chain F residue 679 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0870 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 GLN A 573 ASN A 593 ASN A 629 HIS A 641 ASN ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 ASN F 680 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.176911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137043 restraints weight = 17120.002| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.01 r_work: 0.3345 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4951 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 16236 Z= 0.170 Angle : 0.676 11.435 21981 Z= 0.354 Chirality : 0.045 0.245 2485 Planarity : 0.005 0.060 2761 Dihedral : 11.343 150.771 2280 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.31 % Favored : 95.12 % Rotamer: Outliers : 4.06 % Allowed : 17.95 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1927 helix: 0.03 (0.19), residues: 724 sheet: -0.17 (0.34), residues: 285 loop : -0.64 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 372 TYR 0.023 0.002 TYR F 670 PHE 0.027 0.002 PHE F 427 TRP 0.013 0.002 TRP F 350 HIS 0.017 0.002 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (16236) covalent geometry : angle 0.67581 / 0.35 (21981) hydrogen bonds : bond 0.03524 / 2.63 ( 510) hydrogen bonds : angle 4.60489 / 3.53 ( 1452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 240 time to evaluate : 0.609 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 474 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6153 (pp20) REVERT: B 350 TRP cc_start: 0.5051 (t-100) cc_final: 0.4815 (t60) REVERT: C 547 MET cc_start: 0.5358 (mtm) cc_final: 0.4600 (pp-130) REVERT: C 656 ASP cc_start: 0.6408 (p0) cc_final: 0.6167 (p0) REVERT: D 399 MET cc_start: 0.6450 (mmm) cc_final: 0.6240 (mpp) REVERT: D 588 PHE cc_start: 0.4143 (m-10) cc_final: 0.3487 (m-80) REVERT: E 444 PHE cc_start: 0.5408 (OUTLIER) cc_final: 0.5045 (p90) REVERT: F 467 ASP cc_start: 0.2932 (OUTLIER) cc_final: 0.2509 (t70) REVERT: F 556 SER cc_start: 0.6305 (p) cc_final: 0.5727 (t) outliers start: 71 outliers final: 9 residues processed: 286 average time/residue: 0.5290 time to fit residues: 169.4865 Evaluate side-chains 180 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 444 PHE Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 679 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 91 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 133 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN A 680 HIS B 548 HIS ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 HIS C 548 HIS C 597 HIS ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN D 593 ASN D 597 HIS F 353 ASN F 478 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.189863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149880 restraints weight = 18094.418| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.04 r_work: 0.3535 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.7765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 16236 Z= 0.227 Angle : 0.865 20.797 21981 Z= 0.437 Chirality : 0.050 0.387 2485 Planarity : 0.006 0.102 2761 Dihedral : 10.372 144.720 2265 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.62 % Allowed : 4.31 % Favored : 95.07 % Rotamer: Outliers : 4.40 % Allowed : 18.98 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.19), residues: 1927 helix: 0.09 (0.19), residues: 726 sheet: -0.60 (0.31), residues: 285 loop : -0.66 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 663 TYR 0.032 0.003 TYR F 664 PHE 0.030 0.003 PHE F 427 TRP 0.027 0.003 TRP C 675 HIS 0.015 0.002 HIS C 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 (16236) covalent geometry : angle 0.86491 / 0.44 (21981) hydrogen bonds : bond 0.05781 / 4.30 ( 510) hydrogen bonds : angle 4.79468 / 3.55 ( 1452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 341 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6708 (tp30) REVERT: B 371 ILE cc_start: 0.7951 (tt) cc_final: 0.7711 (tt) REVERT: B 411 ASP cc_start: 0.8239 (p0) cc_final: 0.8001 (p0) REVERT: B 428 TYR cc_start: 0.6861 (m-80) cc_final: 0.6575 (m-10) REVERT: B 483 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7484 (mt-10) REVERT: B 593 ASN cc_start: 0.8500 (p0) cc_final: 0.8222 (p0) REVERT: C 401 VAL cc_start: 0.6753 (t) cc_final: 0.6524 (m) REVERT: C 475 ASN cc_start: 0.7319 (t0) cc_final: 0.6820 (t160) REVERT: C 593 ASN cc_start: 0.7374 (OUTLIER) cc_final: 0.6685 (p0) REVERT: C 684 MET cc_start: 0.5238 (OUTLIER) cc_final: 0.4930 (ptt) REVERT: D 500 PHE cc_start: 0.6801 (m-80) cc_final: 0.6280 (m-10) REVERT: D 588 PHE cc_start: 0.6742 (m-10) cc_final: 0.6431 (m-80) REVERT: D 677 LYS cc_start: 0.8521 (mtpp) cc_final: 0.7994 (mptm) REVERT: F 420 LEU cc_start: 0.5025 (OUTLIER) cc_final: 0.4405 (tm) REVERT: F 457 GLU cc_start: 0.5859 (mm-30) cc_final: 0.5588 (mp0) REVERT: F 462 MET cc_start: 0.5092 (mmt) cc_final: 0.4830 (mmt) outliers start: 77 outliers final: 17 residues processed: 386 average time/residue: 0.6211 time to fit residues: 263.2446 Evaluate side-chains 226 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 679 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 77 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 164 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 HIS A 475 ASN A 597 HIS B 596 ASN B 597 HIS C 596 ASN D 469 GLN D 548 HIS E 358 ASN F 395 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.179730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137473 restraints weight = 17319.170| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.90 r_work: 0.3326 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.9800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 16236 Z= 0.161 Angle : 0.666 15.306 21981 Z= 0.346 Chirality : 0.045 0.179 2485 Planarity : 0.005 0.074 2761 Dihedral : 9.999 144.691 2261 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.63 % Favored : 95.90 % Rotamer: Outliers : 4.06 % Allowed : 22.41 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1927 helix: 0.50 (0.19), residues: 717 sheet: -0.66 (0.35), residues: 225 loop : -0.73 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 665 TYR 0.021 0.002 TYR C 676 PHE 0.020 0.002 PHE F 427 TRP 0.013 0.002 TRP E 355 HIS 0.006 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (16236) covalent geometry : angle 0.66606 / 0.35 (21981) hydrogen bonds : bond 0.03321 / 2.35 ( 510) hydrogen bonds : angle 4.39382 / 3.28 ( 1452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 266 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7345 (mt0) REVERT: A 405 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: A 484 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7527 (tptm) REVERT: A 677 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7462 (mppt) REVERT: B 397 ARG cc_start: 0.8953 (mtp85) cc_final: 0.8688 (mtt-85) REVERT: B 451 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: B 593 ASN cc_start: 0.8736 (p0) cc_final: 0.8514 (p0) REVERT: B 595 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.8074 (mtt180) REVERT: C 426 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8056 (ttm) REVERT: C 483 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7628 (mt-10) REVERT: C 547 MET cc_start: 0.8156 (mtp) cc_final: 0.7895 (mtm) REVERT: C 593 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7353 (p0) REVERT: C 600 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8166 (mm) REVERT: D 426 MET cc_start: 0.6486 (mpp) cc_final: 0.6286 (mmt) REVERT: D 476 LYS cc_start: 0.7922 (tmtp) cc_final: 0.7387 (ttmt) REVERT: D 677 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8315 (mppt) REVERT: D 684 MET cc_start: 0.6150 (ptm) cc_final: 0.5590 (ptt) REVERT: E 365 THR cc_start: 0.8402 (t) cc_final: 0.8191 (m) REVERT: F 555 CYS cc_start: 0.5547 (OUTLIER) cc_final: 0.2853 (t) REVERT: F 679 TYR cc_start: 0.4623 (OUTLIER) cc_final: 0.3451 (m-80) outliers start: 71 outliers final: 18 residues processed: 315 average time/residue: 0.6691 time to fit residues: 230.6767 Evaluate side-chains 234 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 679 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 0.0040 chunk 168 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 176 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN D 597 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.182447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140584 restraints weight = 18488.272| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.14 r_work: 0.3502 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 1.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16236 Z= 0.119 Angle : 0.578 11.717 21981 Z= 0.303 Chirality : 0.043 0.182 2485 Planarity : 0.004 0.058 2761 Dihedral : 9.625 142.292 2261 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.48 % Favored : 96.00 % Rotamer: Outliers : 3.66 % Allowed : 22.93 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1927 helix: 0.76 (0.20), residues: 724 sheet: -0.69 (0.34), residues: 251 loop : -0.53 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 665 TYR 0.015 0.001 TYR D 670 PHE 0.018 0.001 PHE B 502 TRP 0.012 0.001 TRP E 355 HIS 0.003 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16236) covalent geometry : angle 0.57822 / 0.30 (21981) hydrogen bonds : bond 0.03167 / 2.31 ( 510) hydrogen bonds : angle 4.14467 / 3.11 ( 1452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 234 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7476 (mt0) REVERT: A 387 ARG cc_start: 0.8166 (ptt180) cc_final: 0.7835 (ttp-170) REVERT: A 405 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: A 474 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7319 (pt0) REVERT: A 604 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7709 (p) REVERT: A 685 LYS cc_start: 0.7823 (mtpm) cc_final: 0.6883 (mmmt) REVERT: B 397 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8617 (mtt-85) REVERT: B 419 VAL cc_start: 0.8928 (m) cc_final: 0.8611 (t) REVERT: B 451 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7302 (m-80) REVERT: B 526 GLU cc_start: 0.8242 (pt0) cc_final: 0.7941 (pt0) REVERT: C 387 ARG cc_start: 0.7441 (mtm180) cc_final: 0.7027 (mtp180) REVERT: C 426 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7881 (mtm) REVERT: C 448 ASP cc_start: 0.7124 (p0) cc_final: 0.6753 (p0) REVERT: C 593 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7341 (p0) REVERT: C 618 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7348 (mpp) REVERT: C 677 LYS cc_start: 0.7908 (mppt) cc_final: 0.7622 (mtmm) REVERT: D 476 LYS cc_start: 0.8024 (tmtp) cc_final: 0.7565 (ttmt) REVERT: D 677 LYS cc_start: 0.8591 (mtpp) cc_final: 0.8267 (tppt) REVERT: D 684 MET cc_start: 0.6428 (ptm) cc_final: 0.6030 (ptt) REVERT: E 365 THR cc_start: 0.8378 (t) cc_final: 0.8145 (m) REVERT: E 382 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7859 (mm-30) REVERT: F 382 GLU cc_start: 0.8145 (mp0) cc_final: 0.7917 (mp0) REVERT: F 459 GLU cc_start: 0.6600 (mp0) cc_final: 0.5898 (pm20) REVERT: F 462 MET cc_start: 0.5163 (mpt) cc_final: 0.4167 (mmt) REVERT: F 555 CYS cc_start: 0.5263 (OUTLIER) cc_final: 0.2892 (t) REVERT: F 679 TYR cc_start: 0.4505 (OUTLIER) cc_final: 0.3218 (m-80) outliers start: 64 outliers final: 20 residues processed: 274 average time/residue: 0.6970 time to fit residues: 208.9655 Evaluate side-chains 237 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 679 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 37 optimal weight: 0.3980 chunk 102 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 597 HIS F 374 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.174644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.128826 restraints weight = 18127.462| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.32 r_work: 0.3322 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 1.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 16236 Z= 0.119 Angle : 0.579 11.128 21981 Z= 0.303 Chirality : 0.043 0.154 2485 Planarity : 0.005 0.062 2761 Dihedral : 9.636 142.266 2261 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.32 % Favored : 96.21 % Rotamer: Outliers : 3.60 % Allowed : 23.16 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1927 helix: 0.94 (0.20), residues: 723 sheet: -0.61 (0.35), residues: 238 loop : -0.48 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 665 TYR 0.012 0.001 TYR B 482 PHE 0.015 0.001 PHE B 524 TRP 0.009 0.001 TRP E 355 HIS 0.003 0.001 HIS E 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (16236) covalent geometry : angle 0.57860 / 0.30 (21981) hydrogen bonds : bond 0.02912 / 2.08 ( 510) hydrogen bonds : angle 4.07467 / 3.03 ( 1452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 262 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: A 387 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7853 (ttp-170) REVERT: A 405 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7586 (mm-30) REVERT: A 459 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 513 LYS cc_start: 0.8974 (tttt) cc_final: 0.8720 (tttt) REVERT: A 526 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: A 529 GLN cc_start: 0.7358 (pp30) cc_final: 0.7142 (pp30) REVERT: A 541 ASN cc_start: 0.8162 (p0) cc_final: 0.7909 (p0) REVERT: A 677 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7861 (mttt) REVERT: A 685 LYS cc_start: 0.7794 (mtpm) cc_final: 0.6686 (mmmt) REVERT: B 357 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7710 (t80) REVERT: B 419 VAL cc_start: 0.8827 (m) cc_final: 0.8589 (t) REVERT: B 526 GLU cc_start: 0.8546 (pt0) cc_final: 0.8253 (pt0) REVERT: C 387 ARG cc_start: 0.7429 (mtm180) cc_final: 0.6717 (mtp180) REVERT: C 405 GLU cc_start: 0.7962 (mp0) cc_final: 0.7379 (mp0) REVERT: C 426 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8000 (mtm) REVERT: C 448 ASP cc_start: 0.7416 (p0) cc_final: 0.7057 (p0) REVERT: D 435 LYS cc_start: 0.8337 (pttt) cc_final: 0.8030 (pttm) REVERT: D 476 LYS cc_start: 0.8026 (tmtp) cc_final: 0.7541 (ttmt) REVERT: D 579 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7084 (mm-30) REVERT: D 591 LYS cc_start: 0.8382 (mmtp) cc_final: 0.8037 (mmtm) REVERT: D 677 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7948 (tppt) REVERT: D 684 MET cc_start: 0.6912 (ptm) cc_final: 0.6655 (ptt) REVERT: E 365 THR cc_start: 0.8108 (t) cc_final: 0.7870 (m) REVERT: E 382 GLU cc_start: 0.8520 (mm-30) cc_final: 0.7883 (mm-30) REVERT: F 361 GLU cc_start: 0.7514 (tt0) cc_final: 0.7095 (tt0) REVERT: F 462 MET cc_start: 0.5995 (mpt) cc_final: 0.5124 (mmt) REVERT: F 555 CYS cc_start: 0.5248 (OUTLIER) cc_final: 0.2775 (t) REVERT: F 626 PHE cc_start: 0.3338 (m-80) cc_final: 0.2730 (m-10) outliers start: 63 outliers final: 25 residues processed: 293 average time/residue: 0.6838 time to fit residues: 219.2319 Evaluate side-chains 260 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 94 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 112 optimal weight: 0.0470 chunk 130 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 ASN A 629 HIS D 347 HIS D 478 ASN D 541 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.165965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125074 restraints weight = 17626.573| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.91 r_work: 0.3179 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 1.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16236 Z= 0.199 Angle : 0.712 10.725 21981 Z= 0.375 Chirality : 0.047 0.165 2485 Planarity : 0.005 0.065 2761 Dihedral : 10.198 141.746 2259 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.00 % Favored : 95.59 % Rotamer: Outliers : 3.60 % Allowed : 23.56 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1927 helix: 0.46 (0.19), residues: 728 sheet: -0.60 (0.34), residues: 245 loop : -0.69 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 665 TYR 0.021 0.002 TYR D 670 PHE 0.020 0.002 PHE B 501 TRP 0.019 0.002 TRP F 675 HIS 0.007 0.001 HIS E 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (16236) covalent geometry : angle 0.71187 / 0.38 (21981) hydrogen bonds : bond 0.04650 / 3.42 ( 510) hydrogen bonds : angle 4.53588 / 3.44 ( 1452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 266 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8886 (mtt180) cc_final: 0.8387 (mtp180) REVERT: A 387 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8147 (ttp-170) REVERT: A 529 GLN cc_start: 0.8044 (pp30) cc_final: 0.7822 (pp30) REVERT: A 541 ASN cc_start: 0.8588 (p0) cc_final: 0.8195 (p0) REVERT: A 544 ILE cc_start: 0.8863 (tt) cc_final: 0.8445 (tt) REVERT: A 641 ASN cc_start: 0.8007 (m-40) cc_final: 0.7704 (m-40) REVERT: A 685 LYS cc_start: 0.8263 (mtpm) cc_final: 0.7443 (mmmt) REVERT: B 357 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8082 (t80) REVERT: B 365 THR cc_start: 0.8995 (m) cc_final: 0.8764 (p) REVERT: B 382 GLU cc_start: 0.8139 (tp30) cc_final: 0.7931 (tp30) REVERT: B 526 GLU cc_start: 0.8630 (pt0) cc_final: 0.8314 (pt0) REVERT: C 387 ARG cc_start: 0.7573 (mtm180) cc_final: 0.6970 (mtp180) REVERT: C 405 GLU cc_start: 0.8180 (mp0) cc_final: 0.7837 (mp0) REVERT: C 426 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8125 (mmm) REVERT: C 448 ASP cc_start: 0.7677 (p0) cc_final: 0.7463 (p0) REVERT: C 477 LYS cc_start: 0.8503 (tmtt) cc_final: 0.8257 (ttmt) REVERT: C 618 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.7588 (mpp) REVERT: C 684 MET cc_start: 0.7648 (ttp) cc_final: 0.7377 (ttp) REVERT: D 458 MET cc_start: 0.5460 (tpt) cc_final: 0.4961 (tpt) REVERT: D 476 LYS cc_start: 0.8502 (tmtp) cc_final: 0.8116 (ttmt) REVERT: D 570 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7568 (ttm-80) REVERT: D 579 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7756 (mm-30) REVERT: D 591 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8386 (mmtm) REVERT: D 628 THR cc_start: 0.6542 (OUTLIER) cc_final: 0.6131 (m) REVERT: D 677 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8192 (tppt) REVERT: E 382 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8289 (mm-30) REVERT: F 382 GLU cc_start: 0.8375 (mp0) cc_final: 0.8171 (mp0) REVERT: F 460 GLU cc_start: 0.4640 (pm20) cc_final: 0.4322 (pp20) REVERT: F 462 MET cc_start: 0.5345 (mpt) cc_final: 0.5118 (mmt) outliers start: 63 outliers final: 22 residues processed: 302 average time/residue: 0.6938 time to fit residues: 228.3749 Evaluate side-chains 249 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain D residue 378 GLU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 27 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 352 ASN D 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.164706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122169 restraints weight = 17249.936| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.75 r_work: 0.3092 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 1.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16236 Z= 0.147 Angle : 0.613 10.713 21981 Z= 0.320 Chirality : 0.043 0.152 2485 Planarity : 0.004 0.063 2761 Dihedral : 9.810 137.350 2259 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.43 % Favored : 96.16 % Rotamer: Outliers : 3.09 % Allowed : 23.56 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.19), residues: 1927 helix: 0.65 (0.19), residues: 719 sheet: -0.50 (0.35), residues: 236 loop : -0.64 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 665 TYR 0.017 0.001 TYR B 482 PHE 0.015 0.002 PHE A 524 TRP 0.009 0.001 TRP E 355 HIS 0.003 0.001 HIS E 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (16236) covalent geometry : angle 0.61252 / 0.32 (21981) hydrogen bonds : bond 0.03501 / 2.59 ( 510) hydrogen bonds : angle 4.26455 / 3.23 ( 1452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 225 time to evaluate : 0.636 Fit side-chains REVERT: A 332 ARG cc_start: 0.8975 (mtt180) cc_final: 0.8559 (mtp180) REVERT: A 360 GLU cc_start: 0.7871 (mp0) cc_final: 0.7358 (mp0) REVERT: A 641 ASN cc_start: 0.8117 (m-40) cc_final: 0.7833 (m-40) REVERT: A 685 LYS cc_start: 0.8481 (mtpm) cc_final: 0.7755 (mmmt) REVERT: B 357 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8257 (t80) REVERT: B 365 THR cc_start: 0.9064 (m) cc_final: 0.8846 (p) REVERT: B 526 GLU cc_start: 0.8695 (pt0) cc_final: 0.8459 (pt0) REVERT: C 387 ARG cc_start: 0.7662 (mtm180) cc_final: 0.7107 (mtp180) REVERT: C 405 GLU cc_start: 0.8193 (mp0) cc_final: 0.7930 (mp0) REVERT: D 458 MET cc_start: 0.5456 (tpt) cc_final: 0.5168 (tpt) REVERT: D 476 LYS cc_start: 0.8536 (tmtp) cc_final: 0.8234 (ttmt) REVERT: D 534 ASP cc_start: 0.8190 (m-30) cc_final: 0.7853 (m-30) REVERT: D 570 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7675 (ttm-80) REVERT: D 591 LYS cc_start: 0.8750 (mmtp) cc_final: 0.8494 (mmtm) REVERT: D 628 THR cc_start: 0.6722 (OUTLIER) cc_final: 0.6373 (m) REVERT: E 382 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8388 (mm-30) REVERT: F 346 ASP cc_start: 0.7512 (p0) cc_final: 0.7063 (p0) REVERT: F 374 GLN cc_start: 0.8021 (tt0) cc_final: 0.7654 (mt0) REVERT: F 514 ARG cc_start: 0.5886 (ttm110) cc_final: 0.5676 (mtm-85) outliers start: 54 outliers final: 26 residues processed: 259 average time/residue: 0.6282 time to fit residues: 178.1400 Evaluate side-chains 239 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 680 HIS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 191 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 605 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121621 restraints weight = 17058.804| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.96 r_work: 0.3124 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 1.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16236 Z= 0.121 Angle : 0.580 10.575 21981 Z= 0.304 Chirality : 0.043 0.264 2485 Planarity : 0.004 0.065 2761 Dihedral : 9.599 140.448 2259 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.63 % Favored : 95.95 % Rotamer: Outliers : 2.00 % Allowed : 24.70 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1927 helix: 0.88 (0.20), residues: 719 sheet: -0.43 (0.36), residues: 222 loop : -0.58 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 663 TYR 0.028 0.001 TYR F 670 PHE 0.015 0.001 PHE B 524 TRP 0.010 0.001 TRP E 355 HIS 0.002 0.001 HIS B 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (16236) covalent geometry : angle 0.58046 / 0.30 (21981) hydrogen bonds : bond 0.03171 / 2.32 ( 510) hydrogen bonds : angle 4.17812 / 3.16 ( 1452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.634 Fit side-chains REVERT: A 332 ARG cc_start: 0.8926 (mtt180) cc_final: 0.8497 (mtp180) REVERT: A 360 GLU cc_start: 0.7799 (mp0) cc_final: 0.7285 (mp0) REVERT: A 447 ASP cc_start: 0.8510 (m-30) cc_final: 0.8240 (t0) REVERT: A 451 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.5692 (m-80) REVERT: A 641 ASN cc_start: 0.8101 (m-40) cc_final: 0.7804 (m-40) REVERT: A 685 LYS cc_start: 0.8351 (mtpm) cc_final: 0.7651 (mmmt) REVERT: B 357 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8243 (t80) REVERT: B 365 THR cc_start: 0.9029 (m) cc_final: 0.8812 (p) REVERT: B 377 LYS cc_start: 0.8589 (ttpt) cc_final: 0.8363 (ttpm) REVERT: B 526 GLU cc_start: 0.8645 (pt0) cc_final: 0.8391 (pt0) REVERT: C 387 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7024 (mtp180) REVERT: C 405 GLU cc_start: 0.8082 (mp0) cc_final: 0.7819 (mp0) REVERT: C 603 ASP cc_start: 0.8542 (p0) cc_final: 0.8242 (p0) REVERT: C 660 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: D 458 MET cc_start: 0.5385 (tpt) cc_final: 0.5065 (tpt) REVERT: D 476 LYS cc_start: 0.8478 (tmtp) cc_final: 0.8178 (ttmt) REVERT: D 516 LEU cc_start: 0.8871 (tp) cc_final: 0.8671 (tm) REVERT: D 517 LYS cc_start: 0.8606 (tptm) cc_final: 0.8099 (tppt) REVERT: D 591 LYS cc_start: 0.8715 (mmtp) cc_final: 0.8437 (mmtm) REVERT: D 628 THR cc_start: 0.6778 (OUTLIER) cc_final: 0.6453 (m) REVERT: E 382 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8360 (mm-30) REVERT: F 374 GLN cc_start: 0.7837 (tt0) cc_final: 0.7621 (mt0) REVERT: F 514 ARG cc_start: 0.5923 (ttm110) cc_final: 0.5694 (mtm-85) outliers start: 35 outliers final: 20 residues processed: 245 average time/residue: 0.6460 time to fit residues: 172.3957 Evaluate side-chains 238 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 680 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 138 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 10 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 178 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 596 ASN D 597 HIS D 605 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.167212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124637 restraints weight = 17164.890| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.82 r_work: 0.3145 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 1.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16236 Z= 0.102 Angle : 0.557 10.798 21981 Z= 0.292 Chirality : 0.041 0.230 2485 Planarity : 0.004 0.064 2761 Dihedral : 9.451 139.696 2259 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.22 % Favored : 96.32 % Rotamer: Outliers : 1.54 % Allowed : 25.67 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1927 helix: 1.09 (0.20), residues: 716 sheet: -0.27 (0.36), residues: 238 loop : -0.47 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 663 TYR 0.032 0.001 TYR F 670 PHE 0.015 0.001 PHE B 427 TRP 0.009 0.001 TRP E 355 HIS 0.002 0.000 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (16236) covalent geometry : angle 0.55670 / 0.29 (21981) hydrogen bonds : bond 0.02688 / 1.95 ( 510) hydrogen bonds : angle 4.08540 / 3.08 ( 1452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 0.618 Fit side-chains REVERT: A 332 ARG cc_start: 0.8932 (mtt180) cc_final: 0.8528 (mtp180) REVERT: A 360 GLU cc_start: 0.7865 (mp0) cc_final: 0.7309 (mp0) REVERT: A 447 ASP cc_start: 0.8497 (m-30) cc_final: 0.8243 (t0) REVERT: A 451 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.5659 (m-80) REVERT: A 513 LYS cc_start: 0.9111 (tttt) cc_final: 0.8902 (tttt) REVERT: A 641 ASN cc_start: 0.8015 (m-40) cc_final: 0.7739 (m-40) REVERT: A 685 LYS cc_start: 0.8204 (mtpm) cc_final: 0.7626 (mmmt) REVERT: B 365 THR cc_start: 0.9007 (m) cc_final: 0.8782 (p) REVERT: B 377 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8331 (ttpm) REVERT: B 399 MET cc_start: 0.8429 (mtt) cc_final: 0.8194 (mtt) REVERT: B 526 GLU cc_start: 0.8642 (pt0) cc_final: 0.8387 (pt0) REVERT: B 643 ASP cc_start: 0.7998 (p0) cc_final: 0.7709 (p0) REVERT: C 387 ARG cc_start: 0.7684 (mtm180) cc_final: 0.7146 (mtp180) REVERT: C 405 GLU cc_start: 0.8089 (mp0) cc_final: 0.7845 (mp0) REVERT: C 593 ASN cc_start: 0.8273 (p0) cc_final: 0.8011 (m-40) REVERT: C 603 ASP cc_start: 0.8528 (p0) cc_final: 0.8211 (p0) REVERT: C 660 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: D 458 MET cc_start: 0.5322 (tpt) cc_final: 0.5023 (tpt) REVERT: D 476 LYS cc_start: 0.8479 (tmtp) cc_final: 0.8250 (ttmt) REVERT: D 517 LYS cc_start: 0.8604 (tptm) cc_final: 0.8102 (tppt) REVERT: D 546 ASN cc_start: 0.8360 (t0) cc_final: 0.8158 (t0) REVERT: D 591 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8464 (mmtm) REVERT: D 595 ARG cc_start: 0.8469 (ptm160) cc_final: 0.8178 (mtp180) REVERT: D 628 THR cc_start: 0.6777 (OUTLIER) cc_final: 0.6457 (m) REVERT: E 382 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8399 (mm-30) REVERT: F 462 MET cc_start: 0.5250 (mpt) cc_final: 0.4685 (mmt) REVERT: F 514 ARG cc_start: 0.5899 (ttm110) cc_final: 0.5666 (mtm-85) outliers start: 27 outliers final: 16 residues processed: 245 average time/residue: 0.6643 time to fit residues: 177.4534 Evaluate side-chains 234 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 680 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 54 optimal weight: 0.0020 chunk 143 optimal weight: 0.0470 chunk 144 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 182 optimal weight: 0.5980 overall best weight: 0.3886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 662 ASN D 680 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.167273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125196 restraints weight = 17060.228| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.11 r_work: 0.3148 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 1.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16236 Z= 0.101 Angle : 0.551 10.700 21981 Z= 0.288 Chirality : 0.041 0.222 2485 Planarity : 0.004 0.064 2761 Dihedral : 9.372 139.145 2259 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.43 % Favored : 96.11 % Rotamer: Outliers : 1.43 % Allowed : 26.42 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1927 helix: 1.24 (0.20), residues: 712 sheet: -0.19 (0.37), residues: 223 loop : -0.45 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 663 TYR 0.018 0.001 TYR F 670 PHE 0.014 0.001 PHE B 524 TRP 0.009 0.001 TRP E 355 HIS 0.002 0.000 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (16236) covalent geometry : angle 0.55101 / 0.29 (21981) hydrogen bonds : bond 0.02650 / 1.92 ( 510) hydrogen bonds : angle 4.07180 / 3.06 ( 1452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6503.04 seconds wall clock time: 111 minutes 9.97 seconds (6669.97 seconds total)