Starting phenix.real_space_refine on Sat Jun 14 07:47:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xj8_38396/06_2025/8xj8_38396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xj8_38396/06_2025/8xj8_38396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xj8_38396/06_2025/8xj8_38396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xj8_38396/06_2025/8xj8_38396.map" model { file = "/net/cci-nas-00/data/ceres_data/8xj8_38396/06_2025/8xj8_38396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xj8_38396/06_2025/8xj8_38396.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.159 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP: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: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} 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: 10.02, per 1000 atoms: 0.63 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: 4.08 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.97 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: 5.33 Time building geometry restraints manager: 4.84 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: 2183 0.062 - 0.124: 286 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 695 or resid 801 through 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.820 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3505 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= 0.232 Angle : 0.732 16.602 21981 Z= 0.394 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 : 5.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP A 350 HIS 0.006 0.001 HIS B 680 PHE 0.023 0.001 PHE B 451 TYR 0.045 0.001 TYR F 670 ARG 0.016 0.000 ARG D 625 Details of bonding type rmsd hydrogen bonds : bond 0.20571 ( 510) hydrogen bonds : angle 6.17539 ( 1452) covalent geometry : bond 0.00429 (16236) covalent geometry : angle 0.73231 (21981) *********************** 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 : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 574 ILE cc_start: 0.5818 (mm) cc_final: 0.5519 (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: 0.2199 (t70) REVERT: C 547 MET cc_start: 0.4147 (mtm) cc_final: 0.3850 (pp-130) 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: 0.4543 (t80) REVERT: D 571 SER cc_start: 0.6315 (m) cc_final: 0.5952 (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: 0.2726 (tt) REVERT: E 444 PHE cc_start: 0.5475 (OUTLIER) cc_final: 0.5252 (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: 0.5737 (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: 1.1116 time to fit residues: 378.6135 Evaluate side-chains 158 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 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 163 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 573 ASN A 594 ASN A 629 HIS A 641 ASN A 680 HIS B 596 ASN B 629 HIS C 548 HIS C 615 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN D 548 HIS D 661 ASN F 347 HIS F 478 ASN F 546 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.195020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151717 restraints weight = 18093.406| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.26 r_work: 0.3556 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 1.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 16236 Z= 0.310 Angle : 0.967 11.228 21981 Z= 0.513 Chirality : 0.054 0.288 2485 Planarity : 0.008 0.104 2761 Dihedral : 12.003 162.543 2278 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.93 % Favored : 94.50 % Rotamer: Outliers : 5.95 % Allowed : 16.75 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.18), residues: 1927 helix: -0.81 (0.18), residues: 705 sheet: -1.00 (0.31), residues: 271 loop : -1.04 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 355 HIS 0.019 0.003 HIS C 680 PHE 0.031 0.003 PHE F 427 TYR 0.037 0.003 TYR A 670 ARG 0.016 0.001 ARG D 625 Details of bonding type rmsd hydrogen bonds : bond 0.05193 ( 510) hydrogen bonds : angle 5.46262 ( 1452) covalent geometry : bond 0.00637 (16236) covalent geometry : angle 0.96705 (21981) *********************** 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 437 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 333 time to evaluate : 1.799 Fit side-chains revert: symmetry clash REVERT: A 344 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7861 (mtp85) REVERT: A 374 GLN cc_start: 0.8119 (tt0) cc_final: 0.7655 (mt0) REVERT: A 462 MET cc_start: 0.8651 (mmm) cc_final: 0.8296 (mmt) REVERT: A 526 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: A 557 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6280 (mp0) REVERT: A 685 LYS cc_start: 0.7333 (ptmt) cc_final: 0.7004 (mmmt) REVERT: B 357 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7773 (t80) REVERT: B 547 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8013 (ptm) REVERT: B 572 ASP cc_start: 0.8406 (p0) cc_final: 0.8150 (p0) REVERT: B 683 ILE cc_start: 0.7338 (mm) cc_final: 0.7110 (mt) REVERT: C 387 ARG cc_start: 0.7054 (mtm180) cc_final: 0.6709 (mtm110) REVERT: C 458 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7421 (mmt) REVERT: C 467 ASP cc_start: 0.8461 (m-30) cc_final: 0.8210 (m-30) REVERT: C 483 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8251 (mt-10) REVERT: C 656 ASP cc_start: 0.7828 (p0) cc_final: 0.7621 (p0) REVERT: D 377 LYS cc_start: 0.7908 (tptp) cc_final: 0.7574 (ttmt) REVERT: D 378 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: D 390 LYS cc_start: 0.9018 (mttt) cc_final: 0.8745 (mmpt) REVERT: D 401 VAL cc_start: 0.7430 (OUTLIER) cc_final: 0.7148 (t) REVERT: D 426 MET cc_start: 0.6621 (tpp) cc_final: 0.6355 (mmt) REVERT: D 534 ASP cc_start: 0.7058 (m-30) cc_final: 0.6810 (m-30) REVERT: D 570 ARG cc_start: 0.7195 (ttm-80) cc_final: 0.6844 (ttm-80) REVERT: D 578 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.8090 (p) REVERT: D 604 THR cc_start: 0.5511 (t) cc_final: 0.5243 (t) REVERT: D 684 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.5822 (ptt) REVERT: E 341 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6438 (tp) REVERT: E 378 GLU cc_start: 0.7474 (mp0) cc_final: 0.7265 (pm20) REVERT: F 403 SER cc_start: 0.6995 (m) cc_final: 0.6416 (t) REVERT: F 440 VAL cc_start: 0.6517 (OUTLIER) cc_final: 0.6293 (t) REVERT: F 457 GLU cc_start: 0.5178 (mm-30) cc_final: 0.4950 (mm-30) REVERT: F 465 ILE cc_start: 0.5165 (pp) cc_final: 0.4957 (pt) REVERT: F 467 ASP cc_start: 0.3406 (OUTLIER) cc_final: 0.2604 (t70) REVERT: F 483 GLU cc_start: 0.5280 (pp20) cc_final: 0.4864 (pm20) REVERT: F 665 ARG cc_start: 0.5171 (OUTLIER) cc_final: 0.4460 (ttm170) outliers start: 104 outliers final: 15 residues processed: 393 average time/residue: 1.4770 time to fit residues: 632.7652 Evaluate side-chains 237 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain D residue 378 GLU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 665 ARG 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 2 optimal weight: 5.9990 chunk 148 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 142 optimal weight: 0.0770 chunk 157 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 ASN B 596 ASN C 475 ASN C 573 ASN C 593 ASN C 661 ASN D 347 HIS D 469 GLN D 478 ASN D 593 ASN F 680 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.171721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125600 restraints weight = 17817.539| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.48 r_work: 0.3278 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 1.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16236 Z= 0.143 Angle : 0.620 10.772 21981 Z= 0.328 Chirality : 0.043 0.149 2485 Planarity : 0.005 0.058 2761 Dihedral : 9.971 143.698 2263 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.58 % Favored : 95.95 % Rotamer: Outliers : 4.17 % Allowed : 19.73 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 1927 helix: 0.15 (0.19), residues: 717 sheet: -0.50 (0.34), residues: 256 loop : -0.91 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 355 HIS 0.008 0.001 HIS B 597 PHE 0.020 0.002 PHE F 427 TYR 0.020 0.002 TYR B 482 ARG 0.009 0.001 ARG F 663 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 510) hydrogen bonds : angle 4.50006 ( 1452) covalent geometry : bond 0.00333 (16236) covalent geometry : angle 0.61957 (21981) *********************** 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 339 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 266 time to evaluate : 2.015 Fit side-chains revert: symmetry clash REVERT: A 343 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: A 374 GLN cc_start: 0.7756 (tt0) cc_final: 0.7435 (mt0) REVERT: A 405 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: A 459 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7664 (mm-30) REVERT: A 462 MET cc_start: 0.9011 (mmm) cc_final: 0.8698 (mmm) REVERT: A 612 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7232 (ptp90) REVERT: A 660 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: A 674 LYS cc_start: 0.8558 (tttt) cc_final: 0.8304 (ttmt) REVERT: A 692 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7383 (mm-30) REVERT: B 356 LYS cc_start: 0.8577 (ptpp) cc_final: 0.8204 (mttm) REVERT: B 526 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: B 547 MET cc_start: 0.8019 (ppp) cc_final: 0.7788 (ptm) REVERT: C 387 ARG cc_start: 0.7469 (mtm180) cc_final: 0.6809 (mtp180) REVERT: C 426 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7760 (mtm) REVERT: D 346 ASP cc_start: 0.7026 (m-30) cc_final: 0.6673 (t0) REVERT: D 377 LYS cc_start: 0.7890 (tptp) cc_final: 0.7548 (tppp) REVERT: D 390 LYS cc_start: 0.8994 (mttt) cc_final: 0.8506 (mmpt) REVERT: D 426 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6454 (mmt) REVERT: D 517 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7695 (tptm) REVERT: D 543 PHE cc_start: 0.6650 (m-10) cc_final: 0.6379 (m-80) REVERT: D 570 ARG cc_start: 0.7107 (ttm-80) cc_final: 0.6885 (ttm-80) REVERT: D 576 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7461 (mttp) REVERT: D 618 MET cc_start: 0.7106 (mmm) cc_final: 0.6846 (mmp) REVERT: E 378 GLU cc_start: 0.7409 (mp0) cc_final: 0.7128 (pm20) REVERT: E 426 MET cc_start: 0.4329 (OUTLIER) cc_final: 0.3872 (ppp) REVERT: E 428 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.5098 (m-10) REVERT: F 462 MET cc_start: 0.5188 (mmm) cc_final: 0.4833 (mmt) REVERT: F 467 ASP cc_start: 0.4346 (OUTLIER) cc_final: 0.3444 (t70) REVERT: F 555 CYS cc_start: 0.5445 (OUTLIER) cc_final: 0.3123 (t) REVERT: F 626 PHE cc_start: 0.3263 (m-80) cc_final: 0.2912 (m-10) outliers start: 73 outliers final: 12 residues processed: 307 average time/residue: 1.4822 time to fit residues: 497.2668 Evaluate side-chains 239 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 576 LYS Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 374 GLN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 555 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 124 optimal weight: 0.9980 chunk 92 optimal weight: 0.0270 chunk 173 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 chunk 37 optimal weight: 0.0170 chunk 130 optimal weight: 5.9990 chunk 157 optimal weight: 0.0870 chunk 140 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 680 HIS D 661 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127452 restraints weight = 17927.244| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.17 r_work: 0.3317 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 1.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16236 Z= 0.096 Angle : 0.522 11.762 21981 Z= 0.276 Chirality : 0.040 0.132 2485 Planarity : 0.004 0.056 2761 Dihedral : 9.396 142.212 2261 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.05 % Favored : 95.54 % Rotamer: Outliers : 2.92 % Allowed : 20.75 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1927 helix: 0.66 (0.20), residues: 716 sheet: -0.31 (0.34), residues: 269 loop : -0.60 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 355 HIS 0.002 0.000 HIS B 597 PHE 0.012 0.001 PHE F 427 TYR 0.015 0.001 TYR F 670 ARG 0.007 0.000 ARG D 663 Details of bonding type rmsd hydrogen bonds : bond 0.02540 ( 510) hydrogen bonds : angle 4.12705 ( 1452) covalent geometry : bond 0.00217 (16236) covalent geometry : angle 0.52158 (21981) *********************** 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 294 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7864 (tt0) cc_final: 0.7630 (mt0) REVERT: A 459 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7442 (mm-30) REVERT: A 462 MET cc_start: 0.8989 (mmm) cc_final: 0.8669 (mmm) REVERT: A 612 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7051 (ptp90) REVERT: A 614 ASP cc_start: 0.7816 (p0) cc_final: 0.7600 (p0) REVERT: A 674 LYS cc_start: 0.8459 (tttt) cc_final: 0.8241 (ttmt) REVERT: A 692 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7496 (mm-30) REVERT: B 356 LYS cc_start: 0.8536 (ptpp) cc_final: 0.8244 (mttm) REVERT: B 426 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7970 (ttm) REVERT: B 529 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7447 (pp30) REVERT: B 547 MET cc_start: 0.8135 (ppp) cc_final: 0.7876 (ptm) REVERT: B 572 ASP cc_start: 0.8128 (p0) cc_final: 0.7927 (p0) REVERT: B 655 LEU cc_start: 0.8490 (tt) cc_final: 0.8221 (tm) REVERT: B 692 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6419 (mt-10) REVERT: C 387 ARG cc_start: 0.7327 (mtm180) cc_final: 0.6750 (mtp180) REVERT: C 426 MET cc_start: 0.8210 (ttm) cc_final: 0.7884 (mmm) REVERT: C 604 THR cc_start: 0.8728 (p) cc_final: 0.8467 (p) REVERT: C 677 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7858 (tppp) REVERT: D 346 ASP cc_start: 0.7001 (m-30) cc_final: 0.6629 (t0) REVERT: D 377 LYS cc_start: 0.7906 (tptp) cc_final: 0.7588 (tppp) REVERT: D 424 ASP cc_start: 0.7665 (t0) cc_final: 0.7162 (t0) REVERT: D 517 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7689 (tptm) REVERT: D 543 PHE cc_start: 0.6795 (m-10) cc_final: 0.6507 (m-80) REVERT: D 570 ARG cc_start: 0.7126 (ttm-80) cc_final: 0.6825 (ttm-80) REVERT: D 677 LYS cc_start: 0.8160 (tppt) cc_final: 0.7914 (tppp) REVERT: E 378 GLU cc_start: 0.7431 (mp0) cc_final: 0.7172 (pm20) REVERT: E 426 MET cc_start: 0.3920 (OUTLIER) cc_final: 0.3430 (ppp) REVERT: E 428 TYR cc_start: 0.5586 (OUTLIER) cc_final: 0.4857 (m-10) REVERT: F 377 LYS cc_start: 0.7742 (mptt) cc_final: 0.7419 (ttpt) REVERT: F 462 MET cc_start: 0.5594 (mmm) cc_final: 0.5265 (mmt) REVERT: F 467 ASP cc_start: 0.4275 (OUTLIER) cc_final: 0.3328 (t70) REVERT: F 555 CYS cc_start: 0.5144 (OUTLIER) cc_final: 0.3721 (p) REVERT: F 626 PHE cc_start: 0.3325 (m-80) cc_final: 0.2992 (m-10) REVERT: F 684 MET cc_start: 0.4980 (tpt) cc_final: 0.4294 (tpp) outliers start: 51 outliers final: 12 residues processed: 274 average time/residue: 1.5129 time to fit residues: 452.3669 Evaluate side-chains 251 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F 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 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 0.0470 chunk 61 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 chunk 125 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 597 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.172332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126328 restraints weight = 18114.754| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.18 r_work: 0.3289 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 1.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16236 Z= 0.092 Angle : 0.498 10.630 21981 Z= 0.265 Chirality : 0.040 0.138 2485 Planarity : 0.004 0.058 2761 Dihedral : 9.267 143.628 2259 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.00 % Favored : 95.59 % Rotamer: Outliers : 3.03 % Allowed : 20.53 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1927 helix: 0.86 (0.20), residues: 732 sheet: -0.21 (0.33), residues: 281 loop : -0.44 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 355 HIS 0.003 0.001 HIS A 597 PHE 0.011 0.001 PHE F 427 TYR 0.015 0.001 TYR B 482 ARG 0.008 0.000 ARG F 665 Details of bonding type rmsd hydrogen bonds : bond 0.02510 ( 510) hydrogen bonds : angle 3.96477 ( 1452) covalent geometry : bond 0.00207 (16236) covalent geometry : angle 0.49837 (21981) *********************** 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 297 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7746 (tt0) cc_final: 0.7530 (mt0) REVERT: A 459 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7434 (mm-30) REVERT: A 462 MET cc_start: 0.8972 (mmm) cc_final: 0.8600 (mmm) REVERT: A 612 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6981 (ptp90) REVERT: A 674 LYS cc_start: 0.8469 (tttt) cc_final: 0.8227 (ttmt) REVERT: A 692 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 356 LYS cc_start: 0.8617 (ptpp) cc_final: 0.8295 (mttm) REVERT: B 477 LYS cc_start: 0.8755 (mtpp) cc_final: 0.8541 (mtmt) REVERT: B 529 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7452 (pp30) REVERT: B 547 MET cc_start: 0.8169 (ppp) cc_final: 0.7881 (ptm) REVERT: B 655 LEU cc_start: 0.8638 (tt) cc_final: 0.8402 (tm) REVERT: B 692 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6549 (mt-10) REVERT: C 387 ARG cc_start: 0.7343 (mtm180) cc_final: 0.6692 (mtp180) REVERT: C 426 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7893 (mmm) REVERT: C 604 THR cc_start: 0.8722 (p) cc_final: 0.8487 (p) REVERT: C 618 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7478 (mtp) REVERT: C 677 LYS cc_start: 0.8144 (mtmm) cc_final: 0.7929 (tppp) REVERT: C 680 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.6401 (t-90) REVERT: D 346 ASP cc_start: 0.7038 (m-30) cc_final: 0.6682 (t70) REVERT: D 377 LYS cc_start: 0.7952 (tptp) cc_final: 0.7676 (tppp) REVERT: D 424 ASP cc_start: 0.7582 (t0) cc_final: 0.7303 (t0) REVERT: D 517 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7300 (tppt) REVERT: D 534 ASP cc_start: 0.7593 (m-30) cc_final: 0.7145 (m-30) REVERT: D 543 PHE cc_start: 0.6933 (m-10) cc_final: 0.6643 (m-80) REVERT: D 570 ARG cc_start: 0.7166 (ttm-80) cc_final: 0.6821 (ttm-80) REVERT: D 628 THR cc_start: 0.5667 (OUTLIER) cc_final: 0.5071 (m) REVERT: D 677 LYS cc_start: 0.8114 (tppt) cc_final: 0.7840 (tppp) REVERT: E 378 GLU cc_start: 0.7448 (mp0) cc_final: 0.7213 (pm20) REVERT: E 426 MET cc_start: 0.3777 (ppp) cc_final: 0.3143 (ppp) REVERT: E 428 TYR cc_start: 0.5338 (OUTLIER) cc_final: 0.4613 (m-10) REVERT: F 377 LYS cc_start: 0.7806 (mptt) cc_final: 0.7457 (ttpt) REVERT: F 416 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6562 (tmmm) REVERT: F 467 ASP cc_start: 0.4134 (OUTLIER) cc_final: 0.3060 (t70) REVERT: F 555 CYS cc_start: 0.4660 (OUTLIER) cc_final: 0.3550 (p) REVERT: F 626 PHE cc_start: 0.3366 (m-80) cc_final: 0.2963 (m-10) outliers start: 53 outliers final: 21 residues processed: 274 average time/residue: 1.4379 time to fit residues: 431.9017 Evaluate side-chains 263 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 467 ASP 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 47 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 41 optimal weight: 0.0270 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.165195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124455 restraints weight = 17154.127| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.84 r_work: 0.3087 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 1.3245 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= 0.110 Angle : 0.532 10.397 21981 Z= 0.282 Chirality : 0.041 0.151 2485 Planarity : 0.004 0.062 2761 Dihedral : 9.435 140.157 2259 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.00 % Favored : 95.59 % Rotamer: Outliers : 3.37 % Allowed : 21.21 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1927 helix: 0.96 (0.20), residues: 727 sheet: -0.12 (0.34), residues: 278 loop : -0.44 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 675 HIS 0.005 0.001 HIS B 597 PHE 0.014 0.001 PHE F 427 TYR 0.017 0.001 TYR B 482 ARG 0.008 0.000 ARG D 663 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 510) hydrogen bonds : angle 4.01699 ( 1452) covalent geometry : bond 0.00253 (16236) covalent geometry : angle 0.53202 (21981) *********************** 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 294 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 2.213 Fit side-chains revert: symmetry clash REVERT: A 343 GLU cc_start: 0.8228 (mp0) cc_final: 0.7965 (mp0) REVERT: A 405 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: A 462 MET cc_start: 0.9069 (mmm) cc_final: 0.8790 (mmm) REVERT: B 426 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7843 (ttm) REVERT: B 526 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: B 529 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7992 (pp30) REVERT: B 692 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6858 (mt-10) REVERT: C 387 ARG cc_start: 0.7951 (mtm180) cc_final: 0.7437 (mtp180) REVERT: C 680 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.6565 (t-90) REVERT: D 458 MET cc_start: 0.5442 (tpt) cc_final: 0.4999 (tpt) REVERT: D 517 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8055 (tppt) REVERT: D 534 ASP cc_start: 0.7949 (m-30) cc_final: 0.7657 (m-30) REVERT: D 570 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7689 (ttm-80) REVERT: D 628 THR cc_start: 0.6436 (OUTLIER) cc_final: 0.5966 (m) REVERT: E 426 MET cc_start: 0.3384 (ppp) cc_final: 0.3071 (ppp) REVERT: E 428 TYR cc_start: 0.5386 (OUTLIER) cc_final: 0.4763 (m-10) REVERT: F 674 LYS cc_start: 0.7596 (mmpt) cc_final: 0.7257 (mtpt) outliers start: 59 outliers final: 18 residues processed: 270 average time/residue: 1.5697 time to fit residues: 464.9517 Evaluate side-chains 235 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 461 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 0.0000 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 179 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS D 596 ASN F 353 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 = 0.161132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120779 restraints weight = 17196.400| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.92 r_work: 0.3029 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 1.3764 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= 0.134 Angle : 0.573 12.779 21981 Z= 0.301 Chirality : 0.043 0.159 2485 Planarity : 0.005 0.076 2761 Dihedral : 9.727 141.664 2259 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.84 % Favored : 95.74 % Rotamer: Outliers : 3.09 % Allowed : 21.44 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 1927 helix: 0.87 (0.19), residues: 720 sheet: 0.03 (0.36), residues: 237 loop : -0.49 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 675 HIS 0.007 0.001 HIS B 597 PHE 0.016 0.002 PHE F 357 TYR 0.018 0.001 TYR B 482 ARG 0.013 0.001 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 510) hydrogen bonds : angle 4.12204 ( 1452) covalent geometry : bond 0.00320 (16236) covalent geometry : angle 0.57279 (21981) *********************** 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 289 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 235 time to evaluate : 2.120 Fit side-chains revert: symmetry clash REVERT: A 360 GLU cc_start: 0.8016 (mp0) cc_final: 0.7653 (pm20) REVERT: A 462 MET cc_start: 0.9150 (mmm) cc_final: 0.8900 (mmm) REVERT: A 509 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8221 (ttpp) REVERT: A 684 MET cc_start: 0.8337 (ttm) cc_final: 0.8130 (ttp) REVERT: B 356 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8557 (mttm) REVERT: B 357 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8352 (t80) REVERT: B 526 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: B 529 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7956 (pp30) REVERT: B 568 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8528 (mmmm) REVERT: B 643 ASP cc_start: 0.8391 (p0) cc_final: 0.8160 (p0) REVERT: B 692 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: C 387 ARG cc_start: 0.7982 (mtm180) cc_final: 0.7379 (mtp180) REVERT: C 535 VAL cc_start: 0.9260 (t) cc_final: 0.9044 (p) REVERT: C 660 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: C 680 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.6563 (t-90) REVERT: D 458 MET cc_start: 0.5747 (tpt) cc_final: 0.5464 (tpt) REVERT: D 462 MET cc_start: 0.7900 (mmm) cc_final: 0.7294 (mmt) REVERT: D 472 THR cc_start: 0.7869 (p) cc_final: 0.7574 (p) REVERT: D 517 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8054 (tptm) REVERT: D 628 THR cc_start: 0.6971 (OUTLIER) cc_final: 0.6635 (m) REVERT: E 426 MET cc_start: 0.3774 (ppp) cc_final: 0.3480 (ppp) REVERT: E 428 TYR cc_start: 0.5609 (OUTLIER) cc_final: 0.5151 (m-10) REVERT: F 375 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8250 (mt) outliers start: 54 outliers final: 21 residues processed: 272 average time/residue: 1.4533 time to fit residues: 432.0571 Evaluate side-chains 252 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 680 HIS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 681 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 79 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 193 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 108 optimal weight: 0.5980 chunk 44 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN F 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.162631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121360 restraints weight = 17025.257| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.68 r_work: 0.3077 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 1.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16236 Z= 0.103 Angle : 0.538 12.145 21981 Z= 0.283 Chirality : 0.041 0.147 2485 Planarity : 0.004 0.062 2761 Dihedral : 9.494 141.051 2259 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.74 % Favored : 95.85 % Rotamer: Outliers : 2.40 % Allowed : 22.41 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1927 helix: 1.03 (0.20), residues: 729 sheet: -0.02 (0.34), residues: 255 loop : -0.46 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 675 HIS 0.004 0.001 HIS B 597 PHE 0.023 0.001 PHE A 752 TYR 0.016 0.001 TYR B 482 ARG 0.009 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.02798 ( 510) hydrogen bonds : angle 3.95432 ( 1452) covalent geometry : bond 0.00240 (16236) covalent geometry : angle 0.53823 (21981) *********************** 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 271 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 1.812 Fit side-chains REVERT: A 360 GLU cc_start: 0.7914 (mp0) cc_final: 0.7565 (pm20) REVERT: A 372 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8109 (ttp80) REVERT: A 462 MET cc_start: 0.9088 (mmm) cc_final: 0.8835 (tpp) REVERT: A 509 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8100 (mtmm) REVERT: A 614 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7905 (p0) REVERT: A 684 MET cc_start: 0.8430 (ttm) cc_final: 0.8087 (ttp) REVERT: B 356 LYS cc_start: 0.8823 (ptpp) cc_final: 0.8563 (mttm) REVERT: B 526 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: B 529 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7910 (pp30) REVERT: B 568 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8499 (mmmm) REVERT: B 643 ASP cc_start: 0.8380 (p0) cc_final: 0.8129 (p0) REVERT: B 692 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: C 387 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7428 (mtp180) REVERT: C 535 VAL cc_start: 0.9279 (t) cc_final: 0.9075 (p) REVERT: C 660 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: C 680 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.6509 (t-90) REVERT: D 453 GLU cc_start: 0.5992 (tp30) cc_final: 0.5758 (mm-30) REVERT: D 458 MET cc_start: 0.5959 (tpt) cc_final: 0.5553 (tpt) REVERT: D 472 THR cc_start: 0.7929 (p) cc_final: 0.7639 (p) REVERT: D 517 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8038 (tppt) REVERT: D 628 THR cc_start: 0.6973 (OUTLIER) cc_final: 0.6713 (m) REVERT: E 428 TYR cc_start: 0.5607 (OUTLIER) cc_final: 0.5367 (m-10) REVERT: F 553 VAL cc_start: 0.6228 (t) cc_final: 0.5920 (m) outliers start: 42 outliers final: 18 residues processed: 255 average time/residue: 1.4736 time to fit residues: 410.3811 Evaluate side-chains 252 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 64 optimal weight: 0.6980 chunk 193 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 188 optimal weight: 0.0030 chunk 116 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122845 restraints weight = 17174.271| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.67 r_work: 0.3092 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 1.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16236 Z= 0.099 Angle : 0.539 11.698 21981 Z= 0.282 Chirality : 0.041 0.178 2485 Planarity : 0.004 0.065 2761 Dihedral : 9.282 140.999 2259 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.53 % Favored : 96.06 % Rotamer: Outliers : 2.06 % Allowed : 23.44 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1927 helix: 1.15 (0.20), residues: 730 sheet: 0.03 (0.38), residues: 220 loop : -0.44 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 355 HIS 0.004 0.001 HIS B 597 PHE 0.015 0.001 PHE A 752 TYR 0.019 0.001 TYR F 670 ARG 0.007 0.000 ARG D 663 Details of bonding type rmsd hydrogen bonds : bond 0.02651 ( 510) hydrogen bonds : angle 3.89194 ( 1452) covalent geometry : bond 0.00230 (16236) covalent geometry : angle 0.53914 (21981) *********************** 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 262 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 1.865 Fit side-chains revert: symmetry clash REVERT: A 360 GLU cc_start: 0.7870 (mp0) cc_final: 0.7519 (pm20) REVERT: A 462 MET cc_start: 0.9002 (mmm) cc_final: 0.8785 (tpp) REVERT: A 614 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7817 (p0) REVERT: A 684 MET cc_start: 0.8466 (ttm) cc_final: 0.8133 (ttp) REVERT: B 356 LYS cc_start: 0.8795 (ptpp) cc_final: 0.8519 (mttm) REVERT: B 529 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7929 (pp30) REVERT: B 568 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8469 (mmmm) REVERT: B 643 ASP cc_start: 0.8279 (p0) cc_final: 0.8055 (p0) REVERT: B 692 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: C 387 ARG cc_start: 0.7908 (mtm180) cc_final: 0.7390 (mtp180) REVERT: C 535 VAL cc_start: 0.9287 (t) cc_final: 0.9070 (p) REVERT: C 558 LEU cc_start: 0.8044 (mt) cc_final: 0.7601 (pp) REVERT: C 612 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7553 (ttt90) REVERT: C 660 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8453 (tt0) REVERT: C 680 HIS cc_start: 0.8783 (OUTLIER) cc_final: 0.6496 (t-90) REVERT: D 458 MET cc_start: 0.5663 (tpt) cc_final: 0.5316 (tpt) REVERT: D 517 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7927 (tppt) REVERT: D 628 THR cc_start: 0.7025 (OUTLIER) cc_final: 0.6791 (m) REVERT: F 360 GLU cc_start: 0.7406 (tp30) cc_final: 0.7190 (tp30) REVERT: F 361 GLU cc_start: 0.7506 (pt0) cc_final: 0.6970 (mt-10) REVERT: F 553 VAL cc_start: 0.6331 (t) cc_final: 0.6038 (m) REVERT: F 555 CYS cc_start: 0.5435 (OUTLIER) cc_final: 0.4464 (p) outliers start: 36 outliers final: 15 residues processed: 251 average time/residue: 1.7271 time to fit residues: 472.6350 Evaluate side-chains 242 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 152 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 109 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 605 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.162679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121221 restraints weight = 17169.693| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.75 r_work: 0.3081 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 1.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16236 Z= 0.104 Angle : 0.554 11.535 21981 Z= 0.289 Chirality : 0.041 0.156 2485 Planarity : 0.004 0.064 2761 Dihedral : 9.266 139.965 2259 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.74 % Favored : 95.90 % Rotamer: Outliers : 1.89 % Allowed : 23.44 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1927 helix: 1.14 (0.20), residues: 730 sheet: 0.08 (0.38), residues: 220 loop : -0.46 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 355 HIS 0.005 0.001 HIS A 597 PHE 0.017 0.001 PHE A 752 TYR 0.016 0.001 TYR B 482 ARG 0.007 0.000 ARG D 663 Details of bonding type rmsd hydrogen bonds : bond 0.02720 ( 510) hydrogen bonds : angle 3.90684 ( 1452) covalent geometry : bond 0.00244 (16236) covalent geometry : angle 0.55433 (21981) ********************** 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 259 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: A 360 GLU cc_start: 0.7874 (mp0) cc_final: 0.7521 (pm20) REVERT: A 462 MET cc_start: 0.9076 (mmm) cc_final: 0.8818 (tpp) REVERT: A 684 MET cc_start: 0.8518 (ttm) cc_final: 0.8065 (ttp) REVERT: B 356 LYS cc_start: 0.8818 (ptpp) cc_final: 0.8519 (mttm) REVERT: B 526 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: B 529 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7951 (pp30) REVERT: B 568 LYS cc_start: 0.8676 (mmtt) cc_final: 0.8464 (mmmm) REVERT: B 692 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: C 387 ARG cc_start: 0.7915 (mtm180) cc_final: 0.7397 (mtp180) REVERT: C 535 VAL cc_start: 0.9288 (t) cc_final: 0.9068 (p) REVERT: C 558 LEU cc_start: 0.8032 (mt) cc_final: 0.7612 (pp) REVERT: C 612 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7527 (ttt90) REVERT: C 660 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: C 680 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.6495 (t-90) REVERT: D 399 MET cc_start: 0.8231 (mtt) cc_final: 0.7961 (mtt) REVERT: D 458 MET cc_start: 0.5499 (tpt) cc_final: 0.5161 (tpt) REVERT: D 517 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7931 (tppt) REVERT: D 628 THR cc_start: 0.7033 (OUTLIER) cc_final: 0.6817 (m) REVERT: F 360 GLU cc_start: 0.7332 (tp30) cc_final: 0.7061 (tp30) REVERT: F 361 GLU cc_start: 0.7474 (pt0) cc_final: 0.6915 (mt-10) REVERT: F 552 SER cc_start: 0.6950 (t) cc_final: 0.6649 (p) REVERT: F 553 VAL cc_start: 0.6413 (t) cc_final: 0.6096 (m) REVERT: F 555 CYS cc_start: 0.5426 (OUTLIER) cc_final: 0.4521 (p) REVERT: F 604 THR cc_start: 0.5921 (OUTLIER) cc_final: 0.5464 (t) REVERT: F 665 ARG cc_start: 0.6665 (tpp80) cc_final: 0.6312 (tpp-160) outliers start: 33 outliers final: 20 residues processed: 247 average time/residue: 1.7102 time to fit residues: 461.5155 Evaluate side-chains 246 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 111 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 150 optimal weight: 0.1980 chunk 156 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN B 629 HIS E 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.157010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116357 restraints weight = 16982.638| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.64 r_work: 0.3002 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 1.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16236 Z= 0.193 Angle : 0.662 11.458 21981 Z= 0.345 Chirality : 0.046 0.196 2485 Planarity : 0.005 0.064 2761 Dihedral : 10.005 136.700 2259 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.36 % Favored : 95.23 % Rotamer: Outliers : 2.23 % Allowed : 23.21 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1927 helix: 0.72 (0.19), residues: 713 sheet: 0.06 (0.38), residues: 212 loop : -0.55 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 355 HIS 0.011 0.002 HIS A 597 PHE 0.017 0.002 PHE A 752 TYR 0.022 0.002 TYR B 482 ARG 0.007 0.001 ARG F 665 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 510) hydrogen bonds : angle 4.36220 ( 1452) covalent geometry : bond 0.00476 (16236) covalent geometry : angle 0.66206 (21981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15870.19 seconds wall clock time: 277 minutes 47.63 seconds (16667.63 seconds total)