Starting phenix.real_space_refine on Fri Jul 3 19:52:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xj8_38396/07_2026/8xj8_38396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xj8_38396/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xj8_38396/07_2026/8xj8_38396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xj8_38396/07_2026/8xj8_38396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xj8_38396/07_2026/8xj8_38396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xj8_38396/07_2026/8xj8_38396.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 3.55, per 1000 atoms: 0.22 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 735.0 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: 0.60 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: 2.48 Time building geometry restraints manager: 1.72 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: 1.610 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.600 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- 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 0.73655 / 0.41 (21981) hydrogen bonds : bond 0.20571 / 15.58 ( 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 : 0.514 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: 0.5108 time to fit residues: 174.6331 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 : 0.581 ------------------------------------------------------------------------------- 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 629 HIS A 641 ASN B 596 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 = 0.4000 r_free = 0.4000 target = 0.178099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137897 restraints weight = 17191.922| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.14 r_work: 0.3372 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5134 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16236 Z= 0.210 Angle : 0.727 12.102 21981 Z= 0.390 Chirality : 0.047 0.294 2485 Planarity : 0.006 0.071 2761 Dihedral : 11.222 152.288 2280 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.36 % Favored : 95.12 % Rotamer: Outliers : 4.35 % Allowed : 17.78 % Favored : 77.87 % 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: -0.70 (0.19), residues: 1927 helix: -0.11 (0.19), residues: 725 sheet: -0.24 (0.33), residues: 289 loop : -0.71 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG F 663 TYR 0.033 0.002 TYR A 776 PHE 0.031 0.002 PHE F 427 TRP 0.035 0.002 TRP E 355 HIS 0.011 0.002 HIS B 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (16236) covalent geometry : angle 0.72680 / 0.39 (21981) hydrogen bonds : bond 0.03775 / 2.82 ( 510) hydrogen bonds : angle 4.66745 / 3.57 ( 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 321 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 245 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6196 (pp20) REVERT: B 350 TRP cc_start: 0.5149 (t-100) cc_final: 0.4891 (t60) REVERT: B 547 MET cc_start: 0.5802 (OUTLIER) cc_final: 0.5537 (ptm) REVERT: C 347 HIS cc_start: 0.4028 (m-70) cc_final: 0.3453 (m90) REVERT: C 547 MET cc_start: 0.5527 (OUTLIER) cc_final: 0.4650 (pp-130) REVERT: C 656 ASP cc_start: 0.6458 (p0) cc_final: 0.6213 (p0) REVERT: D 504 GLU cc_start: 0.6584 (tp30) cc_final: 0.6300 (pm20) REVERT: D 588 PHE cc_start: 0.4367 (m-10) cc_final: 0.3832 (m-80) REVERT: D 660 GLN cc_start: 0.6575 (tm-30) cc_final: 0.6350 (mt0) REVERT: F 467 ASP cc_start: 0.2880 (OUTLIER) cc_final: 0.2441 (t70) REVERT: F 556 SER cc_start: 0.5945 (p) cc_final: 0.5379 (t) outliers start: 76 outliers final: 9 residues processed: 292 average time/residue: 0.5587 time to fit residues: 182.1573 Evaluate side-chains 188 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 547 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain E residue 365 THR 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: 1.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 83 optimal weight: 0.0050 chunk 133 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN A 680 HIS B 548 HIS B 629 HIS C 548 HIS C 597 HIS ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN D 597 HIS E 358 ASN 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 = 0.4088 r_free = 0.4088 target = 0.187277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146491 restraints weight = 18005.482| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.23 r_work: 0.3490 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.7786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 16236 Z= 0.227 Angle : 0.818 18.903 21981 Z= 0.414 Chirality : 0.050 0.404 2485 Planarity : 0.006 0.082 2761 Dihedral : 10.205 148.652 2261 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.62 % Allowed : 4.15 % Favored : 95.23 % Rotamer: Outliers : 4.23 % Allowed : 20.64 % Favored : 75.13 % 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: 0.07 (0.19), residues: 722 sheet: -0.61 (0.32), residues: 272 loop : -0.65 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 397 TYR 0.028 0.002 TYR F 670 PHE 0.025 0.003 PHE B 451 TRP 0.028 0.003 TRP E 355 HIS 0.015 0.002 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (16236) covalent geometry : angle 0.81815 / 0.41 (21981) hydrogen bonds : bond 0.05942 / 4.44 ( 510) hydrogen bonds : angle 4.83534 / 3.53 ( 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 399 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 325 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 428 TYR cc_start: 0.7064 (m-80) cc_final: 0.6719 (m-10) REVERT: B 451 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.5515 (m-80) REVERT: B 547 MET cc_start: 0.7718 (ppp) cc_final: 0.7513 (ptm) REVERT: B 593 ASN cc_start: 0.8624 (p0) cc_final: 0.8330 (p0) REVERT: B 595 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7533 (mtm180) REVERT: C 377 LYS cc_start: 0.7398 (ttpp) cc_final: 0.6848 (mmtm) REVERT: C 401 VAL cc_start: 0.6852 (t) cc_final: 0.6587 (m) REVERT: C 593 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.6724 (p0) REVERT: C 628 THR cc_start: 0.7392 (p) cc_final: 0.7149 (m) REVERT: D 356 LYS cc_start: 0.6660 (mttm) cc_final: 0.6444 (mtmm) REVERT: D 500 PHE cc_start: 0.7017 (m-80) cc_final: 0.6496 (m-10) REVERT: D 504 GLU cc_start: 0.7250 (tp30) cc_final: 0.7004 (tp30) REVERT: D 541 ASN cc_start: 0.7041 (t0) cc_final: 0.6837 (t160) REVERT: D 588 PHE cc_start: 0.6832 (m-10) cc_final: 0.6560 (m-80) REVERT: D 677 LYS cc_start: 0.8446 (mtpp) cc_final: 0.7938 (mtmm) REVERT: F 555 CYS cc_start: 0.5420 (OUTLIER) cc_final: 0.2865 (t) outliers start: 74 outliers final: 22 residues processed: 370 average time/residue: 0.6287 time to fit residues: 256.3136 Evaluate side-chains 243 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 525 VAL 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 D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 527 THR 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 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: 0.9990 chunk 78 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 164 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 HIS A 475 ASN A 597 HIS B 597 HIS C 352 ASN C 475 ASN D 352 ASN D 475 ASN E 347 HIS E 395 ASN F 395 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.141791 restraints weight = 17193.319| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.58 r_work: 0.3343 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.9628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16236 Z= 0.155 Angle : 0.641 11.117 21981 Z= 0.337 Chirality : 0.046 0.374 2485 Planarity : 0.005 0.069 2761 Dihedral : 9.948 144.598 2261 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.62 % Allowed : 3.84 % Favored : 95.54 % Rotamer: Outliers : 4.17 % Allowed : 22.70 % Favored : 73.13 % 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: 0.45 (0.19), residues: 724 sheet: -0.73 (0.33), residues: 246 loop : -0.66 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 663 TYR 0.016 0.002 TYR F 670 PHE 0.021 0.002 PHE A 752 TRP 0.013 0.002 TRP C 675 HIS 0.004 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (16236) covalent geometry : angle 0.64128 / 0.34 (21981) hydrogen bonds : bond 0.03565 / 3.00 ( 510) hydrogen bonds : angle 4.48828 / 3.41 ( 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 347 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 274 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.8300 (mtt) cc_final: 0.8037 (mtt) REVERT: A 522 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6596 (t0) REVERT: A 526 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: A 677 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7307 (mppt) REVERT: B 593 ASN cc_start: 0.8581 (p0) cc_final: 0.8366 (p0) REVERT: C 375 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7528 (tp) REVERT: C 405 GLU cc_start: 0.7525 (mp0) cc_final: 0.7284 (mt-10) REVERT: C 483 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7734 (mt-10) REVERT: C 547 MET cc_start: 0.7998 (mtp) cc_final: 0.7746 (mtm) REVERT: C 593 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.7149 (p0) REVERT: C 619 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8323 (ttt90) REVERT: D 504 GLU cc_start: 0.7484 (tp30) cc_final: 0.7174 (tp30) REVERT: D 541 ASN cc_start: 0.7387 (t0) cc_final: 0.7174 (t160) REVERT: D 546 ASN cc_start: 0.7153 (t0) cc_final: 0.6927 (t0) REVERT: D 677 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8316 (mppt) REVERT: D 684 MET cc_start: 0.6087 (ptm) cc_final: 0.5627 (ptt) REVERT: E 387 ARG cc_start: 0.7151 (ptt-90) cc_final: 0.6873 (ptm-80) REVERT: F 462 MET cc_start: 0.4920 (mpt) cc_final: 0.3813 (mmt) REVERT: F 555 CYS cc_start: 0.5536 (OUTLIER) cc_final: 0.3070 (t) REVERT: F 556 SER cc_start: 0.5729 (p) cc_final: 0.5278 (m) REVERT: F 665 ARG cc_start: 0.5841 (tpp-160) cc_final: 0.5580 (ttm170) outliers start: 73 outliers final: 18 residues processed: 320 average time/residue: 0.6835 time to fit residues: 239.5914 Evaluate side-chains 234 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 522 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 505 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 F residue 356 LYS Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 3.9990 chunk 162 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 190 optimal weight: 0.0070 chunk 168 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 615 ASN C 573 ASN D 352 ASN D 469 GLN D 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.176750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133115 restraints weight = 18119.412| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.17 r_work: 0.3376 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 1.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 16236 Z= 0.142 Angle : 0.632 13.155 21981 Z= 0.329 Chirality : 0.045 0.214 2485 Planarity : 0.005 0.062 2761 Dihedral : 9.767 143.488 2259 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.84 % Favored : 95.69 % Rotamer: Outliers : 4.12 % Allowed : 22.98 % Favored : 72.90 % 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: -0.27 (0.19), residues: 1927 helix: 0.68 (0.19), residues: 733 sheet: -0.73 (0.33), residues: 253 loop : -0.64 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 750 TYR 0.017 0.001 TYR C 676 PHE 0.016 0.002 PHE B 524 TRP 0.016 0.002 TRP F 675 HIS 0.005 0.001 HIS D 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (16236) covalent geometry : angle 0.63207 / 0.33 (21981) hydrogen bonds : bond 0.03748 / 2.79 ( 510) hydrogen bonds : angle 4.29596 / 3.21 ( 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 341 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 269 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8123 (tp40) REVERT: A 372 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7781 (ttp80) REVERT: A 374 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: A 387 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7982 (ttp-170) REVERT: A 405 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7705 (mm-30) REVERT: A 474 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7266 (pt0) REVERT: A 685 LYS cc_start: 0.7661 (ptmt) cc_final: 0.6705 (mmmt) REVERT: B 357 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7622 (t80) REVERT: B 547 MET cc_start: 0.8260 (ptm) cc_final: 0.7958 (ptp) REVERT: C 387 ARG cc_start: 0.7544 (mtm180) cc_final: 0.6984 (mtp180) REVERT: C 426 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7888 (mtm) REVERT: C 448 ASP cc_start: 0.7309 (p0) cc_final: 0.6939 (p0) REVERT: C 483 GLU cc_start: 0.8734 (mt-10) cc_final: 0.7942 (mt-10) REVERT: C 593 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7677 (p0) REVERT: C 618 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7628 (mpp) REVERT: C 677 LYS cc_start: 0.7916 (mmpt) cc_final: 0.7440 (mtmm) REVERT: D 435 LYS cc_start: 0.7976 (pttm) cc_final: 0.7776 (pttt) REVERT: D 504 GLU cc_start: 0.7806 (tp30) cc_final: 0.7301 (tp30) REVERT: D 541 ASN cc_start: 0.7824 (t0) cc_final: 0.7482 (t160) REVERT: D 579 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7059 (mt-10) REVERT: D 625 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6593 (ppt170) REVERT: D 677 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7950 (tppt) REVERT: D 684 MET cc_start: 0.6891 (ptm) cc_final: 0.6611 (ptt) REVERT: E 333 ILE cc_start: 0.7703 (mm) cc_final: 0.7502 (mt) REVERT: E 382 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8048 (mm-30) REVERT: F 416 LYS cc_start: 0.6945 (tmmm) cc_final: 0.6639 (tmmm) REVERT: F 462 MET cc_start: 0.5355 (OUTLIER) cc_final: 0.4316 (mmt) REVERT: F 555 CYS cc_start: 0.5218 (OUTLIER) cc_final: 0.2815 (t) REVERT: F 626 PHE cc_start: 0.3181 (m-80) cc_final: 0.2714 (m-10) outliers start: 72 outliers final: 21 residues processed: 313 average time/residue: 0.6988 time to fit residues: 239.1495 Evaluate side-chains 266 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 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 372 ARG 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 431 ASP Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 625 ARG 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 440 VAL Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 507 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 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 37 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 156 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 661 ASN D 347 HIS D 352 ASN D 463 ASN ** D 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.166366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124747 restraints weight = 17760.680| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.88 r_work: 0.3193 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 1.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16236 Z= 0.212 Angle : 0.710 10.879 21981 Z= 0.375 Chirality : 0.047 0.254 2485 Planarity : 0.005 0.056 2761 Dihedral : 10.263 140.790 2259 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.26 % Favored : 95.17 % Rotamer: Outliers : 4.06 % Allowed : 22.87 % Favored : 73.07 % 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: -0.51 (0.19), residues: 1927 helix: 0.43 (0.19), residues: 719 sheet: -0.79 (0.33), residues: 249 loop : -0.72 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 570 TYR 0.024 0.002 TYR D 670 PHE 0.023 0.002 PHE A 524 TRP 0.017 0.002 TRP F 675 HIS 0.005 0.001 HIS E 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (16236) covalent geometry : angle 0.70975 / 0.38 (21981) hydrogen bonds : bond 0.04490 / 3.43 ( 510) hydrogen bonds : angle 4.53405 / 3.48 ( 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 335 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 264 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8766 (mtt180) cc_final: 0.8185 (mtp180) REVERT: A 372 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8128 (ttp80) REVERT: A 374 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: A 405 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: A 451 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.5608 (m-80) REVERT: A 476 LYS cc_start: 0.8303 (tmmt) cc_final: 0.7583 (ttmt) REVERT: A 641 ASN cc_start: 0.7865 (m-40) cc_final: 0.7601 (m-40) REVERT: A 684 MET cc_start: 0.8191 (ptp) cc_final: 0.7723 (ttp) REVERT: B 357 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8052 (t80) REVERT: B 547 MET cc_start: 0.8376 (ptm) cc_final: 0.7969 (ptm) REVERT: B 624 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8738 (t) REVERT: C 387 ARG cc_start: 0.7450 (mtm180) cc_final: 0.6783 (mtp180) REVERT: C 405 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: C 426 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8031 (mmm) REVERT: C 448 ASP cc_start: 0.7684 (p0) cc_final: 0.7472 (p0) REVERT: C 477 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8155 (ttmt) REVERT: C 568 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7798 (mmmm) REVERT: C 618 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.7677 (mpp) REVERT: C 677 LYS cc_start: 0.8394 (mmpt) cc_final: 0.7995 (mtmm) REVERT: C 684 MET cc_start: 0.7629 (ttp) cc_final: 0.6835 (ttm) REVERT: D 424 ASP cc_start: 0.7627 (t0) cc_final: 0.7321 (t0) REVERT: D 543 PHE cc_start: 0.7074 (m-10) cc_final: 0.6867 (m-80) REVERT: D 570 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.6963 (ttm-80) REVERT: D 591 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8319 (mmtm) REVERT: D 595 ARG cc_start: 0.8714 (mtp180) cc_final: 0.8466 (mtm-85) REVERT: D 628 THR cc_start: 0.5997 (OUTLIER) cc_final: 0.5435 (m) REVERT: E 341 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7385 (tp) REVERT: E 382 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8362 (mm-30) REVERT: E 412 LYS cc_start: 0.5304 (OUTLIER) cc_final: 0.5029 (tppp) REVERT: F 413 LEU cc_start: 0.7445 (mt) cc_final: 0.7239 (mt) REVERT: F 416 LYS cc_start: 0.7398 (tmmm) cc_final: 0.6918 (tmmm) REVERT: F 462 MET cc_start: 0.5531 (OUTLIER) cc_final: 0.5167 (mmt) REVERT: F 483 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6018 (tp30) REVERT: F 626 PHE cc_start: 0.3562 (m-80) cc_final: 0.3001 (m-10) outliers start: 71 outliers final: 23 residues processed: 302 average time/residue: 0.7298 time to fit residues: 239.8779 Evaluate side-chains 259 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 372 ARG Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 405 GLU 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 592 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 412 LYS Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 436 TYR Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 483 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 604 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 352 ASN D 478 ASN ** D 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.166088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124352 restraints weight = 17000.330| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.65 r_work: 0.3104 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 1.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16236 Z= 0.132 Angle : 0.590 10.722 21981 Z= 0.311 Chirality : 0.043 0.225 2485 Planarity : 0.004 0.064 2761 Dihedral : 9.784 139.156 2259 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.43 % Favored : 96.11 % Rotamer: Outliers : 2.92 % Allowed : 23.79 % 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: -0.19 (0.19), residues: 1927 helix: 0.73 (0.20), residues: 721 sheet: -0.66 (0.33), residues: 266 loop : -0.56 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 663 TYR 0.015 0.001 TYR B 482 PHE 0.016 0.001 PHE B 524 TRP 0.008 0.001 TRP A 350 HIS 0.003 0.001 HIS E 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (16236) covalent geometry : angle 0.59000 / 0.31 (21981) hydrogen bonds : bond 0.03379 / 2.54 ( 510) hydrogen bonds : angle 4.26507 / 3.25 ( 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 288 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8942 (mtt180) cc_final: 0.8557 (mtp180) REVERT: A 372 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8298 (ttp80) REVERT: A 374 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7725 (mt0) REVERT: A 476 LYS cc_start: 0.8415 (tmmt) cc_final: 0.8046 (ttmt) REVERT: A 641 ASN cc_start: 0.8098 (m-40) cc_final: 0.7812 (m-40) REVERT: A 684 MET cc_start: 0.8312 (ptp) cc_final: 0.7949 (ttp) REVERT: B 357 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8191 (t80) REVERT: B 365 THR cc_start: 0.9034 (m) cc_final: 0.8815 (p) REVERT: B 547 MET cc_start: 0.8375 (ptm) cc_final: 0.8169 (ptm) REVERT: C 387 ARG cc_start: 0.7625 (mtm180) cc_final: 0.7122 (mtp180) REVERT: C 405 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: C 568 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8166 (mmmm) REVERT: C 618 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8625 (mtm) REVERT: D 424 ASP cc_start: 0.7786 (t0) cc_final: 0.7563 (t0) REVERT: D 570 ARG cc_start: 0.7816 (ttm-80) cc_final: 0.7589 (ttm-80) REVERT: D 591 LYS cc_start: 0.8814 (mmtp) cc_final: 0.8588 (mmtm) REVERT: D 628 THR cc_start: 0.6236 (OUTLIER) cc_final: 0.5724 (m) REVERT: E 341 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7658 (tp) REVERT: E 382 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8438 (mm-30) REVERT: E 401 VAL cc_start: 0.7778 (m) cc_final: 0.7411 (t) REVERT: F 413 LEU cc_start: 0.7512 (mt) cc_final: 0.7288 (mt) REVERT: F 416 LYS cc_start: 0.7404 (tmmm) cc_final: 0.6982 (tmmm) outliers start: 51 outliers final: 22 residues processed: 269 average time/residue: 0.6801 time to fit residues: 200.8832 Evaluate side-chains 240 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 372 ARG Chi-restraints excluded: chain A residue 374 GLN 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 B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain C residue 405 GLU 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 472 THR Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 436 TYR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 165 optimal weight: 0.0020 chunk 148 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 HIS D 548 HIS F 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119472 restraints weight = 17128.882| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.75 r_work: 0.3032 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 1.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16236 Z= 0.187 Angle : 0.664 10.320 21981 Z= 0.349 Chirality : 0.047 0.255 2485 Planarity : 0.005 0.065 2761 Dihedral : 9.948 137.527 2259 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.00 % Favored : 95.49 % Rotamer: Outliers : 3.14 % Allowed : 23.67 % Favored : 73.18 % 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: -0.30 (0.19), residues: 1927 helix: 0.58 (0.19), residues: 721 sheet: -0.52 (0.35), residues: 245 loop : -0.64 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 663 TYR 0.020 0.002 TYR B 482 PHE 0.018 0.002 PHE A 666 TRP 0.020 0.002 TRP F 675 HIS 0.004 0.001 HIS F 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (16236) covalent geometry : angle 0.66404 / 0.35 (21981) hydrogen bonds : bond 0.04333 / 3.26 ( 510) hydrogen bonds : angle 4.47315 / 3.43 ( 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 277 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8968 (mtt180) cc_final: 0.8576 (mtp180) REVERT: A 343 GLU cc_start: 0.8215 (mp0) cc_final: 0.7912 (mp0) REVERT: A 360 GLU cc_start: 0.7937 (mp0) cc_final: 0.7465 (mp0) REVERT: A 372 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8493 (ttp-170) REVERT: A 374 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: A 405 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: A 451 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.5780 (m-80) REVERT: A 476 LYS cc_start: 0.8405 (tmmt) cc_final: 0.8044 (ttmt) REVERT: A 641 ASN cc_start: 0.8392 (m-40) cc_final: 0.8010 (m-40) REVERT: A 684 MET cc_start: 0.8472 (ptp) cc_final: 0.8139 (ttp) REVERT: B 357 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8353 (t80) REVERT: B 643 ASP cc_start: 0.8190 (p0) cc_final: 0.7970 (p0) REVERT: C 387 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7138 (mtp180) REVERT: C 405 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: C 568 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8253 (mmtp) REVERT: C 618 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8691 (mtm) REVERT: D 458 MET cc_start: 0.5824 (tpt) cc_final: 0.5422 (tpt) REVERT: D 570 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7698 (ttm-80) REVERT: D 591 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8593 (mmtm) REVERT: D 618 MET cc_start: 0.8377 (mpp) cc_final: 0.8025 (mmm) REVERT: D 628 THR cc_start: 0.7019 (OUTLIER) cc_final: 0.6662 (m) REVERT: E 341 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7816 (tp) REVERT: E 382 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8520 (mm-30) REVERT: F 413 LEU cc_start: 0.7594 (mt) cc_final: 0.7387 (mt) REVERT: F 416 LYS cc_start: 0.7811 (tmmm) cc_final: 0.7461 (tmmm) REVERT: F 480 GLU cc_start: 0.4828 (OUTLIER) cc_final: 0.4611 (tp30) outliers start: 55 outliers final: 24 residues processed: 257 average time/residue: 0.7022 time to fit residues: 197.2322 Evaluate side-chains 248 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 372 ARG Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 405 GLU 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 582 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 505 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 E residue 341 LEU Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 480 GLU Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 554 PHE 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: 0.8980 chunk 47 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 593 ASN D 548 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.162246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120779 restraints weight = 17083.421| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.71 r_work: 0.3062 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 1.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16236 Z= 0.123 Angle : 0.581 10.370 21981 Z= 0.307 Chirality : 0.043 0.211 2485 Planarity : 0.004 0.065 2761 Dihedral : 9.679 139.012 2259 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.48 % Favored : 96.00 % Rotamer: Outliers : 2.34 % Allowed : 24.99 % Favored : 72.67 % 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: -0.09 (0.19), residues: 1927 helix: 0.78 (0.20), residues: 720 sheet: -0.38 (0.32), residues: 292 loop : -0.55 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 663 TYR 0.031 0.001 TYR F 670 PHE 0.015 0.001 PHE B 524 TRP 0.013 0.002 TRP F 675 HIS 0.003 0.001 HIS B 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (16236) covalent geometry : angle 0.58076 / 0.31 (21981) hydrogen bonds : bond 0.03221 / 2.40 ( 510) hydrogen bonds : angle 4.24841 / 3.23 ( 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 271 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.673 Fit side-chains REVERT: A 332 ARG cc_start: 0.8942 (mtt180) cc_final: 0.8590 (mtp180) REVERT: A 360 GLU cc_start: 0.7924 (mp0) cc_final: 0.7498 (mp0) REVERT: A 372 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8441 (ttp-170) REVERT: A 447 ASP cc_start: 0.8606 (m-30) cc_final: 0.8376 (t0) REVERT: A 451 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.5685 (m-80) REVERT: A 476 LYS cc_start: 0.8393 (tmmt) cc_final: 0.8091 (ttmt) REVERT: A 641 ASN cc_start: 0.8407 (m-40) cc_final: 0.8008 (m-40) REVERT: A 684 MET cc_start: 0.8419 (ptp) cc_final: 0.8166 (ttp) REVERT: B 357 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8306 (t80) REVERT: B 372 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8038 (ttp-170) REVERT: B 643 ASP cc_start: 0.8238 (p0) cc_final: 0.8024 (p0) REVERT: C 387 ARG cc_start: 0.7680 (mtm180) cc_final: 0.7166 (mtp180) REVERT: C 405 GLU cc_start: 0.8319 (mp0) cc_final: 0.8054 (mp0) REVERT: C 568 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8289 (mmtp) REVERT: C 660 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: D 458 MET cc_start: 0.5738 (tpt) cc_final: 0.5342 (tpt) REVERT: D 517 LYS cc_start: 0.8736 (tptm) cc_final: 0.8240 (tppt) REVERT: D 570 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7805 (ttm-80) REVERT: D 591 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8636 (mmtm) REVERT: D 628 THR cc_start: 0.7066 (OUTLIER) cc_final: 0.6755 (m) REVERT: E 382 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8527 (mm-30) REVERT: E 426 MET cc_start: 0.4033 (ppp) cc_final: 0.3603 (ppp) REVERT: E 428 TYR cc_start: 0.5813 (OUTLIER) cc_final: 0.4937 (m-10) REVERT: F 416 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7309 (tmmm) REVERT: F 462 MET cc_start: 0.5735 (mmt) cc_final: 0.4924 (mmt) REVERT: F 517 LYS cc_start: 0.6909 (tptt) cc_final: 0.6684 (tptt) outliers start: 41 outliers final: 16 residues processed: 258 average time/residue: 0.7240 time to fit residues: 203.7422 Evaluate side-chains 239 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 372 ARG 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 582 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 571 SER 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: 7.9990 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 548 HIS D 605 ASN D 662 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.161390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119534 restraints weight = 17031.021| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.72 r_work: 0.3065 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 1.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16236 Z= 0.141 Angle : 0.612 9.773 21981 Z= 0.321 Chirality : 0.044 0.212 2485 Planarity : 0.005 0.065 2761 Dihedral : 9.683 137.133 2259 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.68 % Favored : 95.80 % Rotamer: Outliers : 1.94 % Allowed : 25.56 % Favored : 72.50 % 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: -0.08 (0.19), residues: 1927 helix: 0.79 (0.20), residues: 716 sheet: -0.37 (0.33), residues: 283 loop : -0.54 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 663 TYR 0.018 0.001 TYR B 482 PHE 0.015 0.002 PHE B 524 TRP 0.010 0.001 TRP E 355 HIS 0.005 0.001 HIS E 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (16236) covalent geometry : angle 0.61222 / 0.32 (21981) hydrogen bonds : bond 0.03562 / 2.67 ( 510) hydrogen bonds : angle 4.27761 / 3.27 ( 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 268 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8924 (mtt180) cc_final: 0.8555 (mtp180) REVERT: A 360 GLU cc_start: 0.7858 (mp0) cc_final: 0.7401 (mp0) REVERT: A 372 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8435 (ttp-170) REVERT: A 447 ASP cc_start: 0.8507 (m-30) cc_final: 0.8254 (t0) REVERT: A 451 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.5780 (m-80) REVERT: A 476 LYS cc_start: 0.8370 (tmmt) cc_final: 0.8058 (ttmt) REVERT: A 641 ASN cc_start: 0.8346 (m-40) cc_final: 0.7949 (m-40) REVERT: A 684 MET cc_start: 0.8462 (ptp) cc_final: 0.8180 (ttp) REVERT: B 356 LYS cc_start: 0.8937 (ptpp) cc_final: 0.8671 (ptmt) REVERT: C 387 ARG cc_start: 0.7624 (mtm180) cc_final: 0.7119 (mtp180) REVERT: C 405 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: C 529 GLN cc_start: 0.8186 (pt0) cc_final: 0.7793 (pp30) REVERT: C 568 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8232 (mmtp) REVERT: C 660 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: D 458 MET cc_start: 0.5625 (tpt) cc_final: 0.5260 (tpt) REVERT: D 517 LYS cc_start: 0.8683 (tptm) cc_final: 0.8147 (tppt) REVERT: D 579 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8109 (tm-30) REVERT: D 591 LYS cc_start: 0.8802 (mmtp) cc_final: 0.8583 (mmtm) REVERT: D 618 MET cc_start: 0.8360 (mpp) cc_final: 0.7959 (mmm) REVERT: D 628 THR cc_start: 0.7052 (OUTLIER) cc_final: 0.6821 (m) REVERT: E 382 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8489 (mm-30) REVERT: E 426 MET cc_start: 0.4208 (ppp) cc_final: 0.3959 (ppp) REVERT: F 416 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7442 (tmmm) REVERT: F 502 PHE cc_start: 0.5980 (OUTLIER) cc_final: 0.5363 (m-80) REVERT: F 514 ARG cc_start: 0.5738 (mtm-85) cc_final: 0.5442 (mtm-85) REVERT: F 517 LYS cc_start: 0.6949 (tptt) cc_final: 0.6720 (tptt) outliers start: 34 outliers final: 19 residues processed: 257 average time/residue: 0.6926 time to fit residues: 194.6663 Evaluate side-chains 248 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 372 ARG 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 582 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 502 PHE Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 571 SER 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: 0.9980 chunk 143 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 191 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 629 HIS D 548 HIS D 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119204 restraints weight = 16898.559| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.70 r_work: 0.3061 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 1.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16236 Z= 0.141 Angle : 0.604 9.300 21981 Z= 0.318 Chirality : 0.044 0.251 2485 Planarity : 0.005 0.066 2761 Dihedral : 9.682 138.275 2259 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.32 % Favored : 96.11 % Rotamer: Outliers : 2.46 % Allowed : 24.93 % Favored : 72.61 % 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: -0.08 (0.19), residues: 1927 helix: 0.79 (0.20), residues: 714 sheet: -0.42 (0.33), residues: 270 loop : -0.52 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 619 TYR 0.017 0.001 TYR B 482 PHE 0.015 0.002 PHE B 524 TRP 0.011 0.001 TRP F 675 HIS 0.004 0.001 HIS B 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (16236) covalent geometry : angle 0.60446 / 0.32 (21981) hydrogen bonds : bond 0.03467 / 2.60 ( 510) hydrogen bonds : angle 4.26003 / 3.24 ( 1452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6883.45 seconds wall clock time: 117 minutes 59.46 seconds (7079.46 seconds total)