Starting phenix.real_space_refine on Thu Sep 18 10:06:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xj8_38396/09_2025/8xj8_38396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xj8_38396/09_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_38396/09_2025/8xj8_38396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xj8_38396/09_2025/8xj8_38396.map" model { file = "/net/cci-nas-00/data/ceres_data/8xj8_38396/09_2025/8xj8_38396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xj8_38396/09_2025/8xj8_38396.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.159 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 3 5.21 5 S 78 5.16 5 C 10127 2.51 5 N 2691 2.21 5 O 2990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15904 Number of models: 1 Model: "" Number of chains: 10 Chain: "X" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3427 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 3 Chain: "B" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2990 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 353} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3053 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 360} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2846 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2393 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 297} Chain breaks: 4 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.38, per 1000 atoms: 0.21 Number of scatterers: 15904 At special positions: 0 Unit cell: (116.748, 124.315, 135.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 15 15.00 Mg 3 11.99 O 2990 8.00 N 2691 7.00 C 10127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 609.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 25 sheets defined 42.7% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.584A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.544A pdb=" N THR A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.799A pdb=" N LYS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 486 through 491 Processing helix chain 'A' and resid 508 through 521 removed outlier: 3.511A pdb=" N LYS A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.749A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 619 Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.600A pdb=" N HIS A 680 " --> pdb=" O TYR A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 695 removed outlier: 3.707A pdb=" N ILE A 693 " --> pdb=" O PRO A 690 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.563A pdb=" N LYS A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 745 Processing helix chain 'A' and resid 752 through 762 removed outlier: 3.966A pdb=" N ILE A 756 " --> pdb=" O PHE A 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.654A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 400 removed outlier: 3.505A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.529A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 removed outlier: 4.400A pdb=" N GLU B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 removed outlier: 3.990A pdb=" N CYS B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 removed outlier: 3.528A pdb=" N LYS B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.569A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.510A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.588A pdb=" N GLU B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 689 through 693 removed outlier: 3.559A pdb=" N ILE B 693 " --> pdb=" O PRO B 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.782A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 372 through 375 removed outlier: 3.791A pdb=" N LEU C 375 " --> pdb=" O ARG C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 376 through 382 removed outlier: 3.816A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 removed outlier: 3.502A pdb=" N LEU C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.583A pdb=" N GLU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 510 through 521 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 removed outlier: 3.804A pdb=" N ILE C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 619 Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.692A pdb=" N ASN C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 689 through 695 removed outlier: 3.531A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 696 through 702 removed outlier: 3.717A pdb=" N ILE C 702 " --> pdb=" O PHE C 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 362 through 371 removed outlier: 3.689A pdb=" N LYS D 366 " --> pdb=" O PRO D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 375 removed outlier: 3.580A pdb=" N LEU D 375 " --> pdb=" O ARG D 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.900A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 398 Processing helix chain 'D' and resid 432 through 436 removed outlier: 3.611A pdb=" N LYS D 435 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 462 removed outlier: 4.566A pdb=" N MET D 458 " --> pdb=" O ASP D 454 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 577 removed outlier: 3.826A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 619 Processing helix chain 'D' and resid 667 through 679 Processing helix chain 'D' and resid 689 through 695 removed outlier: 3.968A pdb=" N ILE D 693 " --> pdb=" O PRO D 690 " (cutoff:3.500A) Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 696 through 702 removed outlier: 3.909A pdb=" N LYS D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 335 Processing helix chain 'E' and resid 363 through 372 removed outlier: 3.734A pdb=" N ARG E 372 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 384 removed outlier: 4.527A pdb=" N SER E 381 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU E 382 " --> pdb=" O TYR E 379 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 384 " --> pdb=" O SER E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.505A pdb=" N ASP E 398 " --> pdb=" O ALA E 394 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 400 " --> pdb=" O ILE E 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 335 Processing helix chain 'F' and resid 363 through 371 Processing helix chain 'F' and resid 372 through 375 Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.586A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 385 through 400 removed outlier: 3.533A pdb=" N LEU F 400 " --> pdb=" O ILE F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 425 No H-bonds generated for 'chain 'F' and resid 423 through 425' Processing helix chain 'F' and resid 455 through 461 removed outlier: 3.881A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU F 461 " --> pdb=" O GLU F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 468 Processing helix chain 'F' and resid 475 through 486 Processing helix chain 'F' and resid 508 through 521 removed outlier: 3.715A pdb=" N GLY F 521 " --> pdb=" O LYS F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.543A pdb=" N ASP F 534 " --> pdb=" O THR F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 578 Processing helix chain 'F' and resid 665 through 677 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.786A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER A 556 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR A 604 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE A 501 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.258A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 706 through 707 Processing sheet with id=AA7, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA8, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AA9, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.867A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N SER B 556 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB2, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.203A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB4, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AB5, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.952A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N SER C 556 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR C 499 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR C 604 " --> pdb=" O THR C 499 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE C 501 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AB7, first strand: chain 'C' and resid 628 through 631 Processing sheet with id=AB8, first strand: chain 'D' and resid 339 through 341 removed outlier: 4.623A pdb=" N HIS D 347 " --> pdb=" O ASN D 358 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AC1, first strand: chain 'D' and resid 524 through 527 removed outlier: 6.625A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC3, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AC4, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AC5, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AC6, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.633A pdb=" N VAL F 419 " --> pdb=" O TYR F 428 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 524 through 525 removed outlier: 6.315A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.30 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 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.510 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.290 ------------------------------------------------------------------------------- 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 : 5.58 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.00 % Favored : 95.28 % Rotamer: Outliers : 2.00 % Allowed : 16.35 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.19), residues: 1927 helix: -0.02 (0.20), residues: 678 sheet: -0.19 (0.34), residues: 283 loop : -0.69 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 625 TYR 0.045 0.001 TYR F 670 PHE 0.023 0.001 PHE B 451 TRP 0.007 0.001 TRP A 350 HIS 0.006 0.001 HIS B 680 Details of bonding type rmsd covalent geometry : bond 0.00429 (16236) covalent geometry : angle 0.73231 (21981) hydrogen bonds : bond 0.20571 ( 510) hydrogen bonds : angle 6.17539 ( 1452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 274 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 574 ILE cc_start: 0.5818 (mm) cc_final: 0.5515 (mm) REVERT: B 415 PHE cc_start: 0.5596 (m-80) cc_final: 0.5367 (m-80) REVERT: B 432 ASP cc_start: 0.2521 (OUTLIER) cc_final: 0.2215 (t70) REVERT: C 547 MET cc_start: 0.4147 (mtm) cc_final: 0.3850 (pp-130) REVERT: D 447 ASP cc_start: 0.0315 (OUTLIER) cc_final: 0.0023 (p0) REVERT: D 495 LYS cc_start: 0.6093 (mppt) cc_final: 0.5531 (mmtt) REVERT: D 502 PHE cc_start: 0.4751 (t80) cc_final: 0.4543 (t80) REVERT: D 571 SER cc_start: 0.6315 (m) cc_final: 0.5951 (p) REVERT: E 354 SER cc_start: 0.5654 (t) cc_final: 0.5320 (t) REVERT: E 422 LEU cc_start: 0.3097 (OUTLIER) cc_final: 0.2727 (tt) REVERT: E 444 PHE cc_start: 0.5475 (OUTLIER) cc_final: 0.5253 (p90) REVERT: F 354 SER cc_start: 0.4768 (t) cc_final: 0.4468 (t) REVERT: F 366 LYS cc_start: 0.7116 (mttt) cc_final: 0.6515 (mtpp) REVERT: F 413 LEU cc_start: 0.5054 (mt) cc_final: 0.4801 (mt) REVERT: F 423 VAL cc_start: 0.5991 (p) cc_final: 0.5738 (m) REVERT: F 465 ILE cc_start: 0.3814 (pp) cc_final: 0.3371 (mt) outliers start: 35 outliers final: 7 residues processed: 304 average time/residue: 0.5288 time to fit residues: 179.6267 Evaluate side-chains 160 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 444 PHE Chi-restraints excluded: chain F residue 556 SER Chi-restraints excluded: chain F residue 679 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0870 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS A 374 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 629 HIS A 641 ASN A 680 HIS B 596 ASN ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS C 548 HIS ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 ASN F 546 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.185782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.143530 restraints weight = 17730.550| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.61 r_work: 0.3490 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 16236 Z= 0.203 Angle : 0.780 14.001 21981 Z= 0.404 Chirality : 0.047 0.239 2485 Planarity : 0.006 0.079 2761 Dihedral : 10.660 148.940 2280 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.31 % Favored : 95.17 % Rotamer: Outliers : 4.69 % Allowed : 18.24 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.19), residues: 1927 helix: -0.29 (0.19), residues: 719 sheet: -0.55 (0.32), residues: 275 loop : -0.61 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 625 TYR 0.017 0.002 TYR F 670 PHE 0.031 0.002 PHE F 427 TRP 0.012 0.002 TRP F 350 HIS 0.012 0.002 HIS F 680 Details of bonding type rmsd covalent geometry : bond 0.00460 (16236) covalent geometry : angle 0.77973 (21981) hydrogen bonds : bond 0.03783 ( 510) hydrogen bonds : angle 4.82399 ( 1452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 322 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6523 (pp20) REVERT: A 526 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5866 (tp30) REVERT: C 377 LYS cc_start: 0.7263 (ttpp) cc_final: 0.6743 (mmtm) REVERT: C 597 HIS cc_start: 0.6470 (m170) cc_final: 0.6129 (m170) REVERT: C 656 ASP cc_start: 0.6939 (p0) cc_final: 0.6714 (p0) REVERT: D 435 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7076 (pttm) REVERT: D 442 THR cc_start: 0.6503 (p) cc_final: 0.5976 (t) REVERT: D 588 PHE cc_start: 0.6089 (m-10) cc_final: 0.5829 (m-80) REVERT: F 420 LEU cc_start: 0.6412 (tp) cc_final: 0.6045 (tm) REVERT: F 458 MET cc_start: 0.4577 (OUTLIER) cc_final: 0.4368 (tpt) REVERT: F 465 ILE cc_start: 0.4769 (OUTLIER) cc_final: 0.4074 (mt) REVERT: F 467 ASP cc_start: 0.2354 (OUTLIER) cc_final: 0.2001 (t70) REVERT: F 556 SER cc_start: 0.5381 (p) cc_final: 0.4761 (t) REVERT: F 665 ARG cc_start: 0.4760 (OUTLIER) cc_final: 0.4453 (ttm170) outliers start: 82 outliers final: 15 residues processed: 371 average time/residue: 0.6088 time to fit residues: 249.2063 Evaluate side-chains 227 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 465 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 91 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 164 optimal weight: 0.0870 chunk 141 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS D 352 ASN D 463 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 HIS D 597 HIS E 358 ASN E 395 ASN F 347 HIS F 353 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 = 0.4028 r_free = 0.4028 target = 0.181500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141341 restraints weight = 17561.814| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.65 r_work: 0.3307 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 1.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16236 Z= 0.188 Angle : 0.768 8.542 21981 Z= 0.404 Chirality : 0.048 0.271 2485 Planarity : 0.005 0.060 2761 Dihedral : 10.604 164.810 2261 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.79 % Favored : 95.80 % Rotamer: Outliers : 4.57 % Allowed : 20.35 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.19), residues: 1927 helix: -0.08 (0.19), residues: 711 sheet: -0.68 (0.32), residues: 263 loop : -0.75 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 570 TYR 0.026 0.002 TYR C 676 PHE 0.021 0.002 PHE B 524 TRP 0.012 0.002 TRP D 355 HIS 0.007 0.002 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00421 (16236) covalent geometry : angle 0.76769 (21981) hydrogen bonds : bond 0.06050 ( 510) hydrogen bonds : angle 4.97426 ( 1452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 325 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: A 379 TYR cc_start: 0.8340 (m-10) cc_final: 0.8118 (m-10) REVERT: A 451 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.5735 (m-80) REVERT: A 483 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8340 (mt-10) REVERT: A 612 ARG cc_start: 0.7466 (ttm110) cc_final: 0.7259 (ptm-80) REVERT: A 685 LYS cc_start: 0.7687 (ptmt) cc_final: 0.7364 (mmmt) REVERT: B 334 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8633 (mp) REVERT: B 357 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7714 (t80) REVERT: B 382 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8015 (tp30) REVERT: B 547 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7912 (ptm) REVERT: B 603 ASP cc_start: 0.8530 (p0) cc_final: 0.8242 (p0) REVERT: B 664 TYR cc_start: 0.8271 (m-80) cc_final: 0.7907 (m-80) REVERT: B 684 MET cc_start: 0.6221 (ptt) cc_final: 0.6014 (ptt) REVERT: C 387 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7434 (mtp180) REVERT: C 405 GLU cc_start: 0.8507 (mp0) cc_final: 0.8165 (mm-30) REVERT: D 377 LYS cc_start: 0.7923 (tptp) cc_final: 0.7658 (tppp) REVERT: D 504 GLU cc_start: 0.7761 (tp30) cc_final: 0.7558 (tp30) REVERT: D 625 ARG cc_start: 0.7157 (ptp-110) cc_final: 0.6627 (ptt90) REVERT: E 354 SER cc_start: 0.6584 (t) cc_final: 0.6266 (t) REVERT: F 462 MET cc_start: 0.5237 (mmt) cc_final: 0.4839 (mmt) REVERT: F 465 ILE cc_start: 0.3865 (OUTLIER) cc_final: 0.3523 (mt) REVERT: F 510 SER cc_start: 0.7241 (m) cc_final: 0.6748 (t) REVERT: F 555 CYS cc_start: 0.5477 (OUTLIER) cc_final: 0.3803 (p) REVERT: F 672 LEU cc_start: 0.6891 (tp) cc_final: 0.6519 (tt) REVERT: F 679 TYR cc_start: 0.4859 (OUTLIER) cc_final: 0.3426 (m-80) outliers start: 80 outliers final: 11 residues processed: 367 average time/residue: 0.7102 time to fit residues: 283.0426 Evaluate side-chains 238 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 679 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 629 HIS C 573 ASN C 661 ASN D 347 HIS ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 HIS D 593 ASN D 680 HIS F 478 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.168579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126877 restraints weight = 17691.741| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.91 r_work: 0.3213 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 1.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16236 Z= 0.161 Angle : 0.648 10.971 21981 Z= 0.338 Chirality : 0.045 0.245 2485 Planarity : 0.005 0.062 2761 Dihedral : 9.878 137.669 2259 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.94 % Favored : 95.64 % Rotamer: Outliers : 4.17 % Allowed : 21.50 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.19), residues: 1927 helix: 0.29 (0.19), residues: 719 sheet: -0.52 (0.33), residues: 270 loop : -0.80 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 570 TYR 0.016 0.002 TYR F 679 PHE 0.017 0.002 PHE F 427 TRP 0.010 0.002 TRP A 355 HIS 0.009 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00380 (16236) covalent geometry : angle 0.64808 (21981) hydrogen bonds : bond 0.03407 ( 510) hydrogen bonds : angle 4.35671 ( 1452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 264 time to evaluate : 0.645 Fit side-chains REVERT: A 374 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: A 387 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7828 (ttp-170) REVERT: A 619 ARG cc_start: 0.7874 (ptp90) cc_final: 0.7661 (ptp90) REVERT: B 382 GLU cc_start: 0.8270 (tp30) cc_final: 0.8020 (tp30) REVERT: B 477 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8616 (mtmm) REVERT: B 529 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7896 (pt0) REVERT: B 547 MET cc_start: 0.8422 (ptm) cc_final: 0.8064 (ptm) REVERT: B 612 ARG cc_start: 0.8126 (tmt170) cc_final: 0.7749 (tpt90) REVERT: C 387 ARG cc_start: 0.7643 (mtm180) cc_final: 0.7120 (mtt180) REVERT: C 405 GLU cc_start: 0.8287 (mp0) cc_final: 0.8065 (mm-30) REVERT: C 476 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8547 (tttp) REVERT: C 526 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8331 (mt-10) REVERT: C 568 LYS cc_start: 0.7833 (mtmt) cc_final: 0.7630 (mttp) REVERT: C 593 ASN cc_start: 0.8252 (p0) cc_final: 0.7974 (m-40) REVERT: C 677 LYS cc_start: 0.8369 (mmpt) cc_final: 0.7891 (mtmm) REVERT: C 684 MET cc_start: 0.7582 (ttp) cc_final: 0.6862 (ttm) REVERT: D 390 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8828 (mttt) REVERT: D 401 VAL cc_start: 0.7923 (m) cc_final: 0.7663 (t) REVERT: D 625 ARG cc_start: 0.7437 (ptp-110) cc_final: 0.6681 (ptt90) REVERT: D 663 ARG cc_start: 0.6643 (ttt90) cc_final: 0.6386 (ttt90) REVERT: F 413 LEU cc_start: 0.7379 (mt) cc_final: 0.7171 (mt) REVERT: F 465 ILE cc_start: 0.4819 (OUTLIER) cc_final: 0.4495 (mt) REVERT: F 467 ASP cc_start: 0.3344 (OUTLIER) cc_final: 0.2374 (t70) REVERT: F 483 GLU cc_start: 0.5851 (pp20) cc_final: 0.5485 (pm20) REVERT: F 502 PHE cc_start: 0.5944 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: F 626 PHE cc_start: 0.3624 (m-80) cc_final: 0.3167 (m-10) outliers start: 73 outliers final: 19 residues processed: 305 average time/residue: 0.7255 time to fit residues: 241.2551 Evaluate side-chains 245 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 436 TYR Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 502 PHE Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 40.0000 chunk 168 optimal weight: 0.5980 chunk 144 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 50 optimal weight: 0.0570 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 352 ASN D 417 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.167130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123371 restraints weight = 17258.390| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.84 r_work: 0.3125 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 1.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16236 Z= 0.116 Angle : 0.560 11.184 21981 Z= 0.296 Chirality : 0.042 0.139 2485 Planarity : 0.004 0.064 2761 Dihedral : 9.503 144.983 2259 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.68 % Favored : 95.90 % Rotamer: Outliers : 3.37 % Allowed : 22.58 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.19), residues: 1927 helix: 0.64 (0.19), residues: 720 sheet: -0.39 (0.34), residues: 262 loop : -0.59 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 585 TYR 0.015 0.001 TYR B 482 PHE 0.015 0.001 PHE F 427 TRP 0.010 0.001 TRP E 355 HIS 0.005 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00271 (16236) covalent geometry : angle 0.56025 (21981) hydrogen bonds : bond 0.03093 ( 510) hydrogen bonds : angle 4.14794 ( 1452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 0.700 Fit side-chains REVERT: A 332 ARG cc_start: 0.8948 (mmt180) cc_final: 0.8544 (mtp180) REVERT: A 374 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: A 451 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.4989 (m-80) REVERT: A 684 MET cc_start: 0.8395 (ttm) cc_final: 0.8005 (ttp) REVERT: B 357 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8154 (t80) REVERT: B 529 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7790 (pp30) REVERT: B 547 MET cc_start: 0.8388 (ptm) cc_final: 0.8099 (ptm) REVERT: B 612 ARG cc_start: 0.8407 (tmt170) cc_final: 0.8156 (tpt90) REVERT: C 387 ARG cc_start: 0.7896 (mtm180) cc_final: 0.7314 (mtp180) REVERT: C 476 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8499 (tttp) REVERT: C 618 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8228 (mtp) REVERT: C 677 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8105 (mtmm) REVERT: D 390 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8901 (mttt) REVERT: D 625 ARG cc_start: 0.7705 (ptp-110) cc_final: 0.7007 (ptt90) REVERT: D 628 THR cc_start: 0.6179 (OUTLIER) cc_final: 0.5659 (m) REVERT: D 663 ARG cc_start: 0.6712 (ttt90) cc_final: 0.6471 (ttt90) REVERT: E 426 MET cc_start: 0.3920 (pp-130) cc_final: 0.2715 (ppp) REVERT: F 361 GLU cc_start: 0.7572 (tt0) cc_final: 0.7250 (mt-10) REVERT: F 413 LEU cc_start: 0.7521 (mt) cc_final: 0.7312 (mt) REVERT: F 415 PHE cc_start: 0.7027 (m-80) cc_final: 0.6816 (m-80) REVERT: F 467 ASP cc_start: 0.3869 (OUTLIER) cc_final: 0.2731 (t70) REVERT: F 502 PHE cc_start: 0.5772 (OUTLIER) cc_final: 0.5139 (m-80) outliers start: 59 outliers final: 19 residues processed: 279 average time/residue: 0.7530 time to fit residues: 227.8329 Evaluate side-chains 248 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 677 LYS Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 436 TYR Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 502 PHE Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS D 417 ASN D 469 GLN D 478 ASN D 548 HIS F 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.161578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118655 restraints weight = 17121.261| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.96 r_work: 0.3050 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 1.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16236 Z= 0.168 Angle : 0.627 10.180 21981 Z= 0.329 Chirality : 0.044 0.166 2485 Planarity : 0.005 0.064 2761 Dihedral : 9.816 133.847 2259 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.51 % Favored : 95.07 % Rotamer: Outliers : 4.35 % Allowed : 21.44 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.19), residues: 1927 helix: 0.48 (0.19), residues: 727 sheet: -0.18 (0.37), residues: 225 loop : -0.64 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 514 TYR 0.022 0.002 TYR E 428 PHE 0.022 0.002 PHE F 357 TRP 0.011 0.001 TRP E 355 HIS 0.008 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00404 (16236) covalent geometry : angle 0.62715 (21981) hydrogen bonds : bond 0.03899 ( 510) hydrogen bonds : angle 4.35428 ( 1452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 251 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8948 (mmt180) cc_final: 0.8566 (mtp180) REVERT: A 343 GLU cc_start: 0.8179 (mp0) cc_final: 0.7889 (mp0) REVERT: A 372 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8369 (ttp-170) REVERT: A 405 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: A 451 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.6222 (m-80) REVERT: A 658 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8635 (mttp) REVERT: A 684 MET cc_start: 0.8566 (ttm) cc_final: 0.8082 (ttp) REVERT: B 356 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8532 (mttm) REVERT: B 357 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8357 (t80) REVERT: B 529 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8202 (pt0) REVERT: B 547 MET cc_start: 0.8501 (ptm) cc_final: 0.8247 (ptm) REVERT: B 612 ARG cc_start: 0.8526 (tmt170) cc_final: 0.8312 (tpt90) REVERT: B 643 ASP cc_start: 0.8374 (p0) cc_final: 0.8156 (p0) REVERT: C 387 ARG cc_start: 0.7722 (mtm180) cc_final: 0.7085 (mtp180) REVERT: C 405 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7815 (mm-30) REVERT: C 476 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8585 (tttp) REVERT: C 660 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8462 (tt0) REVERT: D 458 MET cc_start: 0.5620 (tpt) cc_final: 0.5229 (tpt) REVERT: D 543 PHE cc_start: 0.7331 (m-10) cc_final: 0.7079 (m-80) REVERT: D 570 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.8036 (ttm-80) REVERT: D 619 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7483 (mtp180) REVERT: D 628 THR cc_start: 0.6873 (OUTLIER) cc_final: 0.6553 (m) REVERT: D 663 ARG cc_start: 0.6767 (ttt90) cc_final: 0.6511 (ttt90) REVERT: F 403 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.8032 (m) REVERT: F 413 LEU cc_start: 0.7708 (mt) cc_final: 0.7470 (mt) REVERT: F 461 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6907 (mt) REVERT: F 465 ILE cc_start: 0.5221 (OUTLIER) cc_final: 0.4888 (pt) REVERT: F 483 GLU cc_start: 0.6817 (pp20) cc_final: 0.5913 (pm20) REVERT: F 502 PHE cc_start: 0.5761 (OUTLIER) cc_final: 0.4970 (m-80) REVERT: F 517 LYS cc_start: 0.6912 (tptt) cc_final: 0.6703 (tptt) REVERT: F 663 ARG cc_start: 0.5939 (ptm160) cc_final: 0.5687 (ttp80) outliers start: 76 outliers final: 23 residues processed: 292 average time/residue: 0.7880 time to fit residues: 249.3633 Evaluate side-chains 263 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 405 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 502 PHE Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 106 optimal weight: 0.0370 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 417 ASN ** D 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.162841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119816 restraints weight = 16898.820| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.95 r_work: 0.3081 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 1.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16236 Z= 0.111 Angle : 0.561 12.285 21981 Z= 0.295 Chirality : 0.042 0.147 2485 Planarity : 0.004 0.065 2761 Dihedral : 9.418 137.266 2259 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.63 % Favored : 95.95 % Rotamer: Outliers : 2.46 % Allowed : 24.19 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.20), residues: 1927 helix: 0.81 (0.19), residues: 716 sheet: -0.24 (0.36), residues: 240 loop : -0.52 (0.21), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 514 TYR 0.019 0.001 TYR E 428 PHE 0.012 0.001 PHE A 446 TRP 0.010 0.001 TRP E 355 HIS 0.005 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00261 (16236) covalent geometry : angle 0.56121 (21981) hydrogen bonds : bond 0.02889 ( 510) hydrogen bonds : angle 4.09156 ( 1452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8893 (mmt180) cc_final: 0.8540 (mtp180) REVERT: A 360 GLU cc_start: 0.8053 (mp0) cc_final: 0.7544 (pm20) REVERT: A 451 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.5774 (m-80) REVERT: A 684 MET cc_start: 0.8549 (ttm) cc_final: 0.8317 (ttm) REVERT: B 356 LYS cc_start: 0.8844 (ptpp) cc_final: 0.8472 (mttm) REVERT: B 529 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7814 (pp30) REVERT: B 547 MET cc_start: 0.8431 (ptm) cc_final: 0.8147 (ptm) REVERT: C 387 ARG cc_start: 0.7869 (mtm180) cc_final: 0.7282 (mtp180) REVERT: C 558 LEU cc_start: 0.7953 (mt) cc_final: 0.7611 (pp) REVERT: C 660 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: D 390 LYS cc_start: 0.9168 (mmpt) cc_final: 0.8880 (mttt) REVERT: D 458 MET cc_start: 0.5695 (tpt) cc_final: 0.5352 (tpt) REVERT: D 570 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7848 (ttm-80) REVERT: D 578 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7934 (p) REVERT: D 628 THR cc_start: 0.6942 (OUTLIER) cc_final: 0.6675 (m) REVERT: D 663 ARG cc_start: 0.6711 (ttt90) cc_final: 0.6468 (ttt90) REVERT: D 677 LYS cc_start: 0.8587 (tppt) cc_final: 0.8224 (tptm) REVERT: F 403 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.7979 (m) REVERT: F 413 LEU cc_start: 0.7716 (mt) cc_final: 0.7462 (mt) REVERT: F 461 LEU cc_start: 0.7195 (pt) cc_final: 0.6766 (mt) REVERT: F 483 GLU cc_start: 0.6719 (pp20) cc_final: 0.5712 (pm20) REVERT: F 502 PHE cc_start: 0.5860 (OUTLIER) cc_final: 0.5257 (m-80) REVERT: F 517 LYS cc_start: 0.6929 (tptt) cc_final: 0.6684 (tptt) REVERT: F 553 VAL cc_start: 0.5975 (t) cc_final: 0.5705 (m) REVERT: F 604 THR cc_start: 0.5825 (OUTLIER) cc_final: 0.5318 (t) outliers start: 43 outliers final: 17 residues processed: 275 average time/residue: 0.6812 time to fit residues: 203.6755 Evaluate side-chains 250 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 502 PHE Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 162 optimal weight: 0.2980 chunk 165 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 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 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.162826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121050 restraints weight = 17107.600| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.69 r_work: 0.3101 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 1.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16236 Z= 0.109 Angle : 0.562 11.080 21981 Z= 0.296 Chirality : 0.042 0.155 2485 Planarity : 0.004 0.062 2761 Dihedral : 9.310 138.859 2259 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.74 % Favored : 95.85 % Rotamer: Outliers : 2.57 % Allowed : 24.47 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.20), residues: 1927 helix: 0.92 (0.20), residues: 717 sheet: -0.26 (0.37), residues: 223 loop : -0.46 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 514 TYR 0.025 0.001 TYR F 664 PHE 0.012 0.001 PHE A 446 TRP 0.008 0.001 TRP E 355 HIS 0.004 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00253 (16236) covalent geometry : angle 0.56250 (21981) hydrogen bonds : bond 0.02797 ( 510) hydrogen bonds : angle 4.02233 ( 1452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8886 (mmt180) cc_final: 0.8550 (mtp180) REVERT: A 360 GLU cc_start: 0.8148 (mp0) cc_final: 0.7652 (pm20) REVERT: A 372 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8346 (ttp-170) REVERT: A 614 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7832 (p0) REVERT: A 684 MET cc_start: 0.8592 (ttm) cc_final: 0.8323 (ttm) REVERT: B 356 LYS cc_start: 0.8816 (ptpp) cc_final: 0.8481 (mttm) REVERT: B 529 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7873 (pp30) REVERT: B 547 MET cc_start: 0.8398 (ptm) cc_final: 0.8132 (ptm) REVERT: C 387 ARG cc_start: 0.7781 (mtm180) cc_final: 0.7268 (mtp180) REVERT: C 476 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8470 (tttp) REVERT: D 374 GLN cc_start: 0.7358 (mt0) cc_final: 0.7018 (mt0) REVERT: D 458 MET cc_start: 0.5757 (tpt) cc_final: 0.5375 (tpt) REVERT: D 570 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7837 (ttm-80) REVERT: D 578 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8018 (p) REVERT: D 628 THR cc_start: 0.7039 (OUTLIER) cc_final: 0.6797 (m) REVERT: D 663 ARG cc_start: 0.6716 (ttt90) cc_final: 0.6488 (ttt90) REVERT: E 388 LYS cc_start: 0.8785 (mttt) cc_final: 0.8549 (mttt) REVERT: F 361 GLU cc_start: 0.7385 (tt0) cc_final: 0.6695 (mt-10) REVERT: F 403 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7897 (m) REVERT: F 413 LEU cc_start: 0.7767 (mt) cc_final: 0.7496 (mt) REVERT: F 481 LEU cc_start: 0.6227 (mm) cc_final: 0.5702 (tp) REVERT: F 502 PHE cc_start: 0.6080 (OUTLIER) cc_final: 0.5461 (m-80) REVERT: F 514 ARG cc_start: 0.5817 (mtm-85) cc_final: 0.4730 (mpp80) REVERT: F 552 SER cc_start: 0.6936 (t) cc_final: 0.6688 (p) REVERT: F 553 VAL cc_start: 0.6224 (t) cc_final: 0.5967 (m) REVERT: F 555 CYS cc_start: 0.5471 (OUTLIER) cc_final: 0.4484 (p) REVERT: F 604 THR cc_start: 0.5999 (OUTLIER) cc_final: 0.5502 (t) outliers start: 45 outliers final: 18 residues processed: 254 average time/residue: 0.6605 time to fit residues: 183.0023 Evaluate side-chains 250 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 497 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 502 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 548 HIS D 596 ASN D 605 ASN D 662 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119115 restraints weight = 17127.969| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.68 r_work: 0.3056 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 1.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16236 Z= 0.123 Angle : 0.580 10.730 21981 Z= 0.304 Chirality : 0.042 0.167 2485 Planarity : 0.004 0.062 2761 Dihedral : 9.425 136.817 2259 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.79 % Favored : 95.80 % Rotamer: Outliers : 2.40 % Allowed : 24.76 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.19), residues: 1927 helix: 0.82 (0.19), residues: 724 sheet: -0.20 (0.38), residues: 219 loop : -0.50 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 514 TYR 0.017 0.001 TYR E 428 PHE 0.013 0.001 PHE B 502 TRP 0.009 0.001 TRP E 355 HIS 0.006 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00294 (16236) covalent geometry : angle 0.57961 (21981) hydrogen bonds : bond 0.03115 ( 510) hydrogen bonds : angle 4.10971 ( 1452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 0.584 Fit side-chains REVERT: A 332 ARG cc_start: 0.8935 (mmt180) cc_final: 0.8607 (mtp180) REVERT: A 360 GLU cc_start: 0.8137 (mp0) cc_final: 0.7648 (pm20) REVERT: A 372 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8422 (ttp-170) REVERT: A 451 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: A 637 GLU cc_start: 0.6595 (mm-30) cc_final: 0.6348 (mp0) REVERT: A 684 MET cc_start: 0.8654 (ttm) cc_final: 0.8266 (ttp) REVERT: B 356 LYS cc_start: 0.8875 (ptpp) cc_final: 0.8501 (mttm) REVERT: B 529 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7925 (pp30) REVERT: B 547 MET cc_start: 0.8423 (ptm) cc_final: 0.8199 (ptm) REVERT: C 387 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7341 (mtp180) REVERT: C 529 GLN cc_start: 0.8214 (pt0) cc_final: 0.7839 (pp30) REVERT: C 558 LEU cc_start: 0.8153 (mt) cc_final: 0.7704 (pp) REVERT: C 680 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.6661 (t70) REVERT: D 374 GLN cc_start: 0.7655 (mt0) cc_final: 0.7346 (mt0) REVERT: D 570 ARG cc_start: 0.8098 (ttm-80) cc_final: 0.7774 (ttm-80) REVERT: D 578 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7994 (p) REVERT: D 625 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.7694 (mtm180) REVERT: D 663 ARG cc_start: 0.6805 (ttt90) cc_final: 0.6580 (ttt90) REVERT: F 361 GLU cc_start: 0.7441 (tt0) cc_final: 0.6962 (mt-10) REVERT: F 403 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7878 (m) REVERT: F 413 LEU cc_start: 0.7845 (mt) cc_final: 0.7552 (mt) REVERT: F 481 LEU cc_start: 0.6351 (mm) cc_final: 0.5853 (tp) REVERT: F 502 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5503 (m-80) REVERT: F 514 ARG cc_start: 0.5874 (mtm-85) cc_final: 0.5367 (mpp80) REVERT: F 552 SER cc_start: 0.7044 (t) cc_final: 0.6782 (p) REVERT: F 555 CYS cc_start: 0.5610 (OUTLIER) cc_final: 0.4654 (p) REVERT: F 604 THR cc_start: 0.5890 (OUTLIER) cc_final: 0.5466 (t) outliers start: 42 outliers final: 21 residues processed: 255 average time/residue: 0.6449 time to fit residues: 179.9913 Evaluate side-chains 247 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 451 PHE Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 685 LYS Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 502 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 138 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 106 optimal weight: 0.0970 chunk 71 optimal weight: 0.5980 chunk 178 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 597 HIS ** D 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.162753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120138 restraints weight = 17098.794| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.79 r_work: 0.3093 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 1.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16236 Z= 0.106 Angle : 0.570 10.705 21981 Z= 0.297 Chirality : 0.041 0.157 2485 Planarity : 0.004 0.061 2761 Dihedral : 9.252 138.284 2259 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.43 % Favored : 96.11 % Rotamer: Outliers : 1.77 % Allowed : 25.10 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.20), residues: 1927 helix: 0.95 (0.19), residues: 724 sheet: -0.21 (0.38), residues: 223 loop : -0.43 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 514 TYR 0.015 0.001 TYR B 482 PHE 0.013 0.001 PHE F 554 TRP 0.009 0.001 TRP E 355 HIS 0.004 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00247 (16236) covalent geometry : angle 0.57024 (21981) hydrogen bonds : bond 0.02652 ( 510) hydrogen bonds : angle 3.99001 ( 1452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 0.719 Fit side-chains REVERT: A 332 ARG cc_start: 0.8895 (mmt180) cc_final: 0.8553 (mtp180) REVERT: A 360 GLU cc_start: 0.8098 (mp0) cc_final: 0.7620 (pm20) REVERT: A 372 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8384 (ttp-170) REVERT: A 451 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.5360 (m-80) REVERT: A 684 MET cc_start: 0.8596 (ttm) cc_final: 0.8310 (ttp) REVERT: B 356 LYS cc_start: 0.8852 (ptpp) cc_final: 0.8536 (mttm) REVERT: B 529 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7909 (pp30) REVERT: B 547 MET cc_start: 0.8414 (ptm) cc_final: 0.8138 (ptm) REVERT: C 387 ARG cc_start: 0.7803 (mtm180) cc_final: 0.7265 (mtp180) REVERT: C 529 GLN cc_start: 0.8136 (pt0) cc_final: 0.7749 (pp30) REVERT: C 558 LEU cc_start: 0.8003 (mt) cc_final: 0.7671 (pp) REVERT: C 612 ARG cc_start: 0.8071 (mtp180) cc_final: 0.7655 (ttt90) REVERT: C 680 HIS cc_start: 0.8461 (OUTLIER) cc_final: 0.6628 (t70) REVERT: D 570 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7609 (ttm-80) REVERT: D 578 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8002 (p) REVERT: D 603 ASP cc_start: 0.7970 (m-30) cc_final: 0.7713 (m-30) REVERT: D 625 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7652 (mtm180) REVERT: D 663 ARG cc_start: 0.6693 (ttt90) cc_final: 0.6491 (ttt90) REVERT: F 361 GLU cc_start: 0.7402 (tt0) cc_final: 0.6737 (mt-10) REVERT: F 403 SER cc_start: 0.8213 (OUTLIER) cc_final: 0.7778 (m) REVERT: F 413 LEU cc_start: 0.7813 (mt) cc_final: 0.7586 (mt) REVERT: F 481 LEU cc_start: 0.6365 (mm) cc_final: 0.5859 (tp) REVERT: F 502 PHE cc_start: 0.6112 (OUTLIER) cc_final: 0.5483 (m-80) REVERT: F 552 SER cc_start: 0.6938 (t) cc_final: 0.6665 (p) REVERT: F 555 CYS cc_start: 0.5565 (OUTLIER) cc_final: 0.4682 (p) REVERT: F 604 THR cc_start: 0.5918 (OUTLIER) cc_final: 0.5491 (t) REVERT: F 665 ARG cc_start: 0.6607 (tpp80) cc_final: 0.6192 (tpp-160) outliers start: 31 outliers final: 17 residues processed: 248 average time/residue: 0.7285 time to fit residues: 196.3229 Evaluate side-chains 246 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 451 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 502 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 54 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 113 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 191 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 629 HIS D 548 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.157333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115400 restraints weight = 16922.226| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.84 r_work: 0.3011 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 1.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16236 Z= 0.210 Angle : 0.698 10.224 21981 Z= 0.362 Chirality : 0.047 0.229 2485 Planarity : 0.005 0.062 2761 Dihedral : 10.092 134.771 2259 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.46 % Favored : 95.07 % Rotamer: Outliers : 1.94 % Allowed : 25.27 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.19), residues: 1927 helix: 0.53 (0.19), residues: 707 sheet: -0.29 (0.35), residues: 240 loop : -0.59 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 514 TYR 0.028 0.002 TYR F 670 PHE 0.018 0.002 PHE B 502 TRP 0.010 0.002 TRP E 355 HIS 0.012 0.002 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00519 (16236) covalent geometry : angle 0.69835 (21981) hydrogen bonds : bond 0.04390 ( 510) hydrogen bonds : angle 4.46945 ( 1452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6894.66 seconds wall clock time: 117 minutes 50.61 seconds (7070.61 seconds total)