Starting phenix.real_space_refine on Fri Aug 7 01:31:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hwf_35056/08_2026/8hwf_35056.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwf_35056/08_2026/8hwf_35056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwf_35056/08_2026/8hwf_35056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwf_35056/08_2026/8hwf_35056.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwf_35056/08_2026/8hwf_35056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwf_35056/08_2026/8hwf_35056.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hwf_35056/08_2026/8hwf_35056.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hwf_35056/08_2026/8hwf_35056.cif" } resolution = 3.3 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= 0.000 sd= 0.004 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 18 5.49 5 Mg 3 5.21 5 S 96 5.16 5 C 11684 2.51 5 N 3133 2.21 5 O 3507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18441 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3051 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3051 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain: "F" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2989 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 17, 'TRANS': 353} Chain: "E" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2963 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3051 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3051 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.59, per 1000 atoms: 0.19 Number of scatterers: 18441 At special positions: 0 Unit cell: (115.776, 122.208, 129.712, 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 96 16.00 P 18 15.00 Mg 3 11.99 O 3507 8.00 N 3133 7.00 C 11684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 570.3 milliseconds 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4286 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 27 sheets defined 42.6% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.653A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 removed outlier: 3.567A pdb=" N ARG C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 385 through 400 removed outlier: 3.543A pdb=" N THR C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 434 Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.795A pdb=" N GLU C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 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 508 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 Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 635 through 641 removed outlier: 3.566A pdb=" N ALA C 639 " --> pdb=" O GLY C 635 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 640 " --> pdb=" O ARG C 636 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 635 through 641' Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.553A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN C 661 " --> pdb=" O GLY C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 661' Processing helix chain 'C' and resid 665 through 680 Processing helix chain 'C' and resid 693 through 700 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.647A 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: 4.089A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.712A pdb=" N ILE B 531 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.680A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.940A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 removed outlier: 3.804A pdb=" N ASN B 641 " --> pdb=" O ALA B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 removed outlier: 3.578A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN B 661 " --> pdb=" O GLY B 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 656 through 661' Processing helix chain 'B' and resid 665 through 680 removed outlier: 3.662A pdb=" N LYS B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 692 Processing helix chain 'B' and resid 693 through 700 Processing helix chain 'F' and resid 324 through 335 Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 429 through 434 removed outlier: 3.568A pdb=" N LYS F 434 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'F' and resid 455 through 469 removed outlier: 3.596A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 488 Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 508 through 520 Processing helix chain 'F' and resid 528 through 533 removed outlier: 3.559A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 546 removed outlier: 3.847A pdb=" N ALA F 545 " --> pdb=" O ASN F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 578 removed outlier: 3.578A pdb=" N THR F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 632 through 634 No H-bonds generated for 'chain 'F' and resid 632 through 634' Processing helix chain 'F' and resid 635 through 640 Processing helix chain 'F' and resid 652 through 661 removed outlier: 4.104A pdb=" N ASP F 656 " --> pdb=" O ASP F 652 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS F 658 " --> pdb=" O GLY F 654 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE F 659 " --> pdb=" O LEU F 655 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN F 660 " --> pdb=" O ASP F 656 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN F 661 " --> pdb=" O GLY F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 680 Processing helix chain 'E' and resid 324 through 335 Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 429 through 434 Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 476 through 488 Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 528 through 533 removed outlier: 3.784A pdb=" N ILE E 531 " --> pdb=" O GLY E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 547 removed outlier: 4.415A pdb=" N ASN E 546 " --> pdb=" O PRO E 542 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET E 547 " --> pdb=" O PHE E 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 542 through 547' Processing helix chain 'E' and resid 570 through 577 removed outlier: 3.569A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 619 removed outlier: 3.618A pdb=" N MET E 618 " --> pdb=" O ASP E 614 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 619 " --> pdb=" O ASN E 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 614 through 619' Processing helix chain 'E' and resid 635 through 641 removed outlier: 3.847A pdb=" N ASN E 641 " --> pdb=" O GLU E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 661 removed outlier: 4.121A pdb=" N GLN E 660 " --> pdb=" O ASP E 656 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN E 661 " --> pdb=" O GLY E 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 656 through 661' Processing helix chain 'E' and resid 665 through 680 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.585A pdb=" N ILE D 329 " --> pdb=" O LYS D 325 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.776A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 398 removed outlier: 3.651A pdb=" N THR D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.681A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 472 through 475 Processing helix chain 'D' and resid 476 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: 3.618A pdb=" N LEU D 577 " --> pdb=" O ASN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 621 removed outlier: 4.254A pdb=" N ILE D 621 " --> pdb=" O MET D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 656 through 661 removed outlier: 3.645A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 removed outlier: 3.551A pdb=" N PHE D 668 " --> pdb=" O TYR D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 700 Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.879A pdb=" N ILE A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.831A pdb=" N LEU A 375 " --> pdb=" O ARG A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.597A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 478 through 488 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 508 through 521 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: 3.662A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 570 through 577' Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.884A pdb=" N ASN A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 660 removed outlier: 4.246A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.758A pdb=" N LYS A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 692 removed outlier: 3.733A pdb=" N GLU A 692 " --> pdb=" O THR A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 693 through 700 Processing sheet with id=AA1, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AA2, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.974A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 525 through 526 removed outlier: 6.874A pdb=" N THR C 499 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AA5, first strand: chain 'C' and resid 628 through 631 Processing sheet with id=AA6, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AA7, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.961A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 525 through 526 removed outlier: 6.871A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR B 499 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB1, first strand: chain 'B' and resid 628 through 631 Processing sheet with id=AB2, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AB3, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AB4, first strand: chain 'F' and resid 525 through 527 removed outlier: 3.590A pdb=" N PHE F 554 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR F 527 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR F 499 " --> pdb=" O ILE F 602 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR F 604 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE F 501 " --> pdb=" O THR F 604 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 581 through 583 Processing sheet with id=AB6, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AB7, first strand: chain 'E' and resid 412 through 415 removed outlier: 3.712A pdb=" N GLY E 418 " --> pdb=" O PHE E 415 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 525 through 527 removed outlier: 6.722A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR E 604 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AC1, first strand: chain 'E' and resid 628 through 631 Processing sheet with id=AC2, first strand: chain 'D' and resid 340 through 341 Processing sheet with id=AC3, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.818A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 524 through 525 removed outlier: 6.518A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC6, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AC7, first strand: chain 'A' and resid 412 through 415 Processing sheet with id=AC8, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.976A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 582 through 583 579 hydrogen bonds defined for protein. 1626 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: 2.94 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4941 1.33 - 1.45: 3305 1.45 - 1.58: 10424 1.58 - 1.70: 29 1.70 - 1.82: 138 Bond restraints: 18837 Sorted by residual: bond pdb=" C1' DT S 3 " pdb=" N1 DT S 3 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.81e+00 bond pdb=" C1' DT S 4 " pdb=" N1 DT S 4 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 6.86e+00 bond pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " ideal model delta sigma weight residual 1.435 1.467 -0.032 1.30e-02 5.92e+03 6.07e+00 bond pdb=" C3' DT S 2 " pdb=" C2' DT S 2 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.91e+00 bond pdb=" C SER F 455 " pdb=" N PRO F 456 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.20e-02 6.94e+03 5.08e+00 ... (remaining 18832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 24971 2.03 - 4.05: 438 4.05 - 6.08: 73 6.08 - 8.10: 10 8.10 - 10.13: 3 Bond angle restraints: 25495 Sorted by residual: angle pdb=" N LEU D 532 " pdb=" CA LEU D 532 " pdb=" C LEU D 532 " ideal model delta sigma weight residual 114.75 108.27 6.48 1.26e+00 6.30e-01 2.65e+01 angle pdb=" N LYS E 434 " pdb=" CA LYS E 434 " pdb=" C LYS E 434 " ideal model delta sigma weight residual 114.62 108.76 5.86 1.14e+00 7.69e-01 2.64e+01 angle pdb=" N3 DT S 3 " pdb=" C4 DT S 3 " pdb=" O4 DT S 3 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N ILE B 371 " pdb=" CA ILE B 371 " pdb=" C ILE B 371 " ideal model delta sigma weight residual 112.98 107.84 5.14 1.25e+00 6.40e-01 1.69e+01 angle pdb=" N3 DT S 1 " pdb=" C4 DT S 1 " pdb=" O4 DT S 1 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 25490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.63: 10898 31.63 - 63.26: 545 63.26 - 94.89: 20 94.89 - 126.52: 0 126.52 - 158.15: 3 Dihedral angle restraints: 11466 sinusoidal: 4859 harmonic: 6607 Sorted by residual: dihedral pdb=" C2' ADP C1001 " pdb=" C1' ADP C1001 " pdb=" N9 ADP C1001 " pdb=" C4 ADP C1001 " ideal model delta sinusoidal sigma weight residual 91.55 -39.79 131.34 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" CA ILE D 531 " pdb=" C ILE D 531 " pdb=" N LEU D 532 " pdb=" CA LEU D 532 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DT S 3 " pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " pdb=" P DT S 4 " ideal model delta sinusoidal sigma weight residual 220.00 61.85 158.15 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 11463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2239 0.049 - 0.098: 499 0.098 - 0.147: 94 0.147 - 0.196: 3 0.196 - 0.245: 1 Chirality restraints: 2836 Sorted by residual: chirality pdb=" CG LEU F 671 " pdb=" CB LEU F 671 " pdb=" CD1 LEU F 671 " pdb=" CD2 LEU F 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU E 577 " pdb=" CB LEU E 577 " pdb=" CD1 LEU E 577 " pdb=" CD2 LEU E 577 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" C3' DT S 3 " pdb=" C4' DT S 3 " pdb=" O3' DT S 3 " pdb=" C2' DT S 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 2833 not shown) Planarity restraints: 3229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 361 " 0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO D 362 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO D 362 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 362 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 361 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO C 362 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 362 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 362 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 522 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C ASP A 522 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP A 522 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 523 " 0.009 2.00e-02 2.50e+03 ... (remaining 3226 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 217 2.61 - 3.18: 15507 3.18 - 3.76: 27502 3.76 - 4.33: 39448 4.33 - 4.90: 65588 Nonbonded interactions: 148262 Sorted by model distance: nonbonded pdb=" O3B ADP B1001 " pdb="MG MG B1002 " model vdw 2.039 2.170 nonbonded pdb=" OG SER B 510 " pdb="MG MG B1002 " model vdw 2.056 2.170 nonbonded pdb=" OG SER A 510 " pdb="MG MG A1002 " model vdw 2.069 2.170 nonbonded pdb=" OG SER C 510 " pdb="MG MG C1002 " model vdw 2.108 2.170 nonbonded pdb=" O2B ADP C1001 " pdb="MG MG C1002 " model vdw 2.183 2.170 ... (remaining 148257 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 323 through 690) selection = (chain 'B' and resid 323 through 690) selection = (chain 'C' and resid 323 through 690) selection = (chain 'D' and resid 323 through 690) selection = (chain 'E' and resid 323 through 690) selection = (chain 'F' and resid 323 through 690) } 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: 0.990 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 14.990 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18837 Z= 0.144 Angle : 0.660 10.128 25495 Z= 0.362 Chirality : 0.041 0.245 2836 Planarity : 0.003 0.085 3229 Dihedral : 17.293 158.154 7180 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.15 % Allowed : 25.77 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.18), residues: 2239 helix: 0.56 (0.21), residues: 697 sheet: -1.65 (0.30), residues: 319 loop : -1.42 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 612 TYR 0.018 0.001 TYR E 482 PHE 0.016 0.001 PHE C 588 TRP 0.009 0.001 TRP B 350 HIS 0.004 0.000 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (18837) covalent geometry : angle 0.66014 / 0.36 (25495) hydrogen bonds : bond 0.18829 / 12.05 ( 579) hydrogen bonds : angle 6.22316 / 4.40 ( 1626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 236 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 387 ARG cc_start: 0.8387 (ptt90) cc_final: 0.8148 (ptt-90) REVERT: C 618 MET cc_start: 0.8642 (mtm) cc_final: 0.8249 (mmm) REVERT: F 618 MET cc_start: 0.8414 (mtm) cc_final: 0.8172 (mmp) REVERT: F 684 MET cc_start: 0.6667 (tmm) cc_final: 0.6462 (tmm) REVERT: E 578 THR cc_start: 0.8001 (m) cc_final: 0.7710 (p) REVERT: D 361 GLU cc_start: 0.8478 (pm20) cc_final: 0.8268 (pm20) REVERT: D 374 GLN cc_start: 0.8829 (mt0) cc_final: 0.8571 (mt0) REVERT: A 612 ARG cc_start: 0.8598 (mtm110) cc_final: 0.7474 (ptp90) outliers start: 3 outliers final: 1 residues processed: 237 average time/residue: 0.1258 time to fit residues: 45.5608 Evaluate side-chains 209 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 571 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.4980 chunk 212 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 353 ASN B 374 GLN F 475 ASN F 478 ASN E 352 ASN E 590 ASN ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.091631 restraints weight = 28720.876| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.55 r_work: 0.2883 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18837 Z= 0.129 Angle : 0.590 7.029 25495 Z= 0.288 Chirality : 0.043 0.318 2836 Planarity : 0.004 0.065 3229 Dihedral : 9.217 156.528 2565 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.54 % Allowed : 24.01 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.18), residues: 2239 helix: 0.73 (0.20), residues: 732 sheet: -1.67 (0.29), residues: 331 loop : -1.35 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.017 0.001 TYR E 482 PHE 0.009 0.001 PHE F 630 TRP 0.008 0.001 TRP B 350 HIS 0.002 0.001 HIS E 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (18837) covalent geometry : angle 0.58954 / 0.29 (25495) hydrogen bonds : bond 0.03801 / 2.46 ( 579) hydrogen bonds : angle 4.72780 / 3.37 ( 1626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8613 (tp40) cc_final: 0.8171 (tp-100) REVERT: C 335 ASP cc_start: 0.8329 (m-30) cc_final: 0.7969 (m-30) REVERT: C 460 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8534 (mt-10) REVERT: F 618 MET cc_start: 0.8545 (mtm) cc_final: 0.8158 (mmp) REVERT: E 426 MET cc_start: 0.7155 (ptt) cc_final: 0.6143 (ptp) REVERT: E 578 THR cc_start: 0.8137 (m) cc_final: 0.7932 (p) REVERT: E 579 GLU cc_start: 0.8111 (mp0) cc_final: 0.7827 (mp0) REVERT: D 361 GLU cc_start: 0.8554 (pm20) cc_final: 0.8028 (pm20) REVERT: D 614 ASP cc_start: 0.8659 (p0) cc_final: 0.8391 (p0) REVERT: A 334 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8715 (mt) REVERT: A 344 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.7262 (ttp-170) REVERT: A 399 MET cc_start: 0.8499 (mtt) cc_final: 0.8278 (mtt) REVERT: A 579 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8032 (tm-30) outliers start: 52 outliers final: 25 residues processed: 261 average time/residue: 0.1343 time to fit residues: 53.1456 Evaluate side-chains 241 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 536 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 594 ASN B 374 GLN F 615 ASN ** F 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN D 541 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.087517 restraints weight = 29115.666| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.58 r_work: 0.2830 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18837 Z= 0.222 Angle : 0.638 11.081 25495 Z= 0.309 Chirality : 0.045 0.314 2836 Planarity : 0.004 0.056 3229 Dihedral : 9.303 156.982 2564 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.70 % Favored : 93.26 % Rotamer: Outliers : 3.71 % Allowed : 23.43 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.18), residues: 2239 helix: 0.55 (0.20), residues: 752 sheet: -1.68 (0.28), residues: 353 loop : -1.38 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 387 TYR 0.021 0.001 TYR B 482 PHE 0.014 0.001 PHE C 444 TRP 0.010 0.001 TRP C 350 HIS 0.005 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (18837) covalent geometry : angle 0.63820 / 0.31 (25495) hydrogen bonds : bond 0.04090 / 2.64 ( 579) hydrogen bonds : angle 4.73275 / 3.38 ( 1626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 225 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8801 (tp40) cc_final: 0.8275 (tp40) REVERT: C 335 ASP cc_start: 0.8347 (m-30) cc_final: 0.8007 (m-30) REVERT: C 460 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8701 (mt-10) REVERT: F 612 ARG cc_start: 0.7944 (ptm160) cc_final: 0.7629 (ptm160) REVERT: F 618 MET cc_start: 0.8485 (mtm) cc_final: 0.8177 (mmp) REVERT: E 331 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8671 (mm-40) REVERT: E 344 ARG cc_start: 0.7910 (tpp80) cc_final: 0.7669 (tpp80) REVERT: E 653 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: D 361 GLU cc_start: 0.8648 (pm20) cc_final: 0.8390 (pm20) REVERT: D 579 GLU cc_start: 0.9009 (mp0) cc_final: 0.8459 (mp0) REVERT: D 614 ASP cc_start: 0.8716 (p0) cc_final: 0.8445 (p0) REVERT: D 649 LYS cc_start: 0.9055 (mmtp) cc_final: 0.8818 (mmmm) REVERT: A 344 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.7379 (ttp-170) REVERT: A 416 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8822 (tttt) REVERT: A 579 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7982 (tm-30) REVERT: A 681 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8167 (mm) outliers start: 76 outliers final: 45 residues processed: 281 average time/residue: 0.1351 time to fit residues: 57.4121 Evaluate side-chains 251 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 653 GLU Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 681 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 184 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 118 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 594 ASN B 374 GLN F 615 ASN ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.090892 restraints weight = 29064.922| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.62 r_work: 0.2887 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18837 Z= 0.100 Angle : 0.563 9.024 25495 Z= 0.272 Chirality : 0.042 0.311 2836 Planarity : 0.003 0.050 3229 Dihedral : 9.134 156.645 2564 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.93 % Allowed : 23.96 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.18), residues: 2239 helix: 0.76 (0.20), residues: 766 sheet: -1.49 (0.28), residues: 370 loop : -1.23 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 387 TYR 0.015 0.001 TYR E 482 PHE 0.029 0.001 PHE F 630 TRP 0.008 0.001 TRP D 350 HIS 0.005 0.001 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (18837) covalent geometry : angle 0.56310 / 0.27 (25495) hydrogen bonds : bond 0.02848 / 1.86 ( 579) hydrogen bonds : angle 4.31716 / 3.08 ( 1626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 228 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8610 (tp40) cc_final: 0.8074 (tp40) REVERT: C 335 ASP cc_start: 0.8085 (m-30) cc_final: 0.7717 (m-30) REVERT: F 387 ARG cc_start: 0.7635 (ptt-90) cc_final: 0.7431 (mtm180) REVERT: F 612 ARG cc_start: 0.7939 (ptm160) cc_final: 0.7602 (ptm160) REVERT: F 618 MET cc_start: 0.8550 (mtm) cc_final: 0.8202 (mmp) REVERT: E 578 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7772 (p) REVERT: E 579 GLU cc_start: 0.8203 (mp0) cc_final: 0.7921 (mp0) REVERT: E 653 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: D 361 GLU cc_start: 0.8611 (pm20) cc_final: 0.8372 (pm20) REVERT: D 538 LYS cc_start: 0.8322 (pttp) cc_final: 0.8110 (pptt) REVERT: D 614 ASP cc_start: 0.8546 (p0) cc_final: 0.8240 (p0) REVERT: A 334 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8798 (mt) REVERT: A 416 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8658 (tttt) REVERT: A 522 ASP cc_start: 0.8072 (t0) cc_final: 0.7785 (t0) REVERT: A 579 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7873 (tm-30) REVERT: A 660 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7725 (mp10) outliers start: 60 outliers final: 33 residues processed: 274 average time/residue: 0.1204 time to fit residues: 50.1592 Evaluate side-chains 242 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 653 GLU Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 660 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 0.0770 chunk 53 optimal weight: 0.4980 chunk 145 optimal weight: 8.9990 chunk 190 optimal weight: 0.0970 chunk 153 optimal weight: 0.5980 chunk 139 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 573 ASN ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** 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 = 0.3554 r_free = 0.3554 target = 0.126378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.092757 restraints weight = 28640.296| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.59 r_work: 0.2918 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18837 Z= 0.090 Angle : 0.558 9.445 25495 Z= 0.266 Chirality : 0.041 0.310 2836 Planarity : 0.003 0.045 3229 Dihedral : 8.981 157.468 2564 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.22 % Allowed : 23.87 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.18), residues: 2239 helix: 0.97 (0.20), residues: 771 sheet: -1.50 (0.29), residues: 350 loop : -1.15 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 387 TYR 0.015 0.001 TYR E 482 PHE 0.010 0.001 PHE F 630 TRP 0.007 0.001 TRP D 350 HIS 0.003 0.000 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (18837) covalent geometry : angle 0.55765 / 0.27 (25495) hydrogen bonds : bond 0.02513 / 1.64 ( 579) hydrogen bonds : angle 4.07292 / 2.90 ( 1626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 226 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8743 (tp40) cc_final: 0.8009 (tp40) REVERT: C 335 ASP cc_start: 0.8382 (m-30) cc_final: 0.7999 (m-30) REVERT: C 399 MET cc_start: 0.9221 (mtm) cc_final: 0.9012 (mtp) REVERT: C 460 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8487 (mt-10) REVERT: C 529 GLN cc_start: 0.8496 (pm20) cc_final: 0.8267 (pm20) REVERT: C 618 MET cc_start: 0.8926 (mtm) cc_final: 0.8686 (mtm) REVERT: F 387 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7512 (mpp-170) REVERT: F 399 MET cc_start: 0.8937 (mtm) cc_final: 0.8719 (mtp) REVERT: F 612 ARG cc_start: 0.7637 (ptm160) cc_final: 0.7336 (ptm160) REVERT: F 618 MET cc_start: 0.8604 (mtm) cc_final: 0.8209 (mmp) REVERT: E 576 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8128 (mtpt) REVERT: E 578 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7575 (p) REVERT: E 579 GLU cc_start: 0.8220 (mp0) cc_final: 0.7871 (mp0) REVERT: E 653 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: D 361 GLU cc_start: 0.8741 (pm20) cc_final: 0.8514 (pm20) REVERT: D 572 ASP cc_start: 0.8772 (p0) cc_final: 0.8397 (t0) REVERT: D 611 ASP cc_start: 0.8374 (m-30) cc_final: 0.7990 (m-30) REVERT: D 614 ASP cc_start: 0.8587 (p0) cc_final: 0.8264 (p0) REVERT: A 334 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8798 (mt) REVERT: A 522 ASP cc_start: 0.8460 (t0) cc_final: 0.8160 (t0) REVERT: A 579 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7857 (tm-30) REVERT: A 660 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: A 684 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8378 (ttp) outliers start: 66 outliers final: 38 residues processed: 275 average time/residue: 0.1242 time to fit residues: 51.8882 Evaluate side-chains 252 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 640 GLU Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 653 GLU Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 684 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 210 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 4 optimal weight: 0.5980 chunk 123 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 1 optimal weight: 0.0570 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 324 ASN E 353 ASN ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.093565 restraints weight = 28706.563| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.62 r_work: 0.2932 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18837 Z= 0.087 Angle : 0.547 7.717 25495 Z= 0.261 Chirality : 0.041 0.312 2836 Planarity : 0.003 0.041 3229 Dihedral : 8.888 157.613 2564 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.44 % Allowed : 24.74 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.18), residues: 2239 helix: 1.13 (0.20), residues: 773 sheet: -1.43 (0.29), residues: 353 loop : -1.05 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 612 TYR 0.014 0.001 TYR E 482 PHE 0.008 0.001 PHE F 630 TRP 0.015 0.001 TRP F 675 HIS 0.004 0.000 HIS E 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (18837) covalent geometry : angle 0.54733 / 0.26 (25495) hydrogen bonds : bond 0.02331 / 1.52 ( 579) hydrogen bonds : angle 3.96154 / 2.82 ( 1626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8558 (tp40) cc_final: 0.7719 (tp40) REVERT: C 335 ASP cc_start: 0.8145 (m-30) cc_final: 0.7738 (m-30) REVERT: C 460 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8341 (mt-10) REVERT: C 529 GLN cc_start: 0.8386 (pm20) cc_final: 0.8138 (pm20) REVERT: F 387 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7184 (mpp-170) REVERT: F 399 MET cc_start: 0.8804 (mtm) cc_final: 0.8600 (mtp) REVERT: F 428 TYR cc_start: 0.8449 (m-80) cc_final: 0.8038 (m-10) REVERT: F 618 MET cc_start: 0.8579 (mtm) cc_final: 0.8190 (mmp) REVERT: E 497 CYS cc_start: 0.8672 (t) cc_final: 0.7945 (m) REVERT: E 576 LYS cc_start: 0.8299 (mtpt) cc_final: 0.8085 (mtpt) REVERT: E 578 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7464 (p) REVERT: E 579 GLU cc_start: 0.8193 (mp0) cc_final: 0.7839 (mp0) REVERT: D 572 ASP cc_start: 0.8587 (p0) cc_final: 0.8339 (t0) REVERT: D 579 GLU cc_start: 0.8747 (mp0) cc_final: 0.8100 (mp0) REVERT: D 607 LYS cc_start: 0.8223 (tppt) cc_final: 0.7616 (ttpp) REVERT: D 611 ASP cc_start: 0.8433 (m-30) cc_final: 0.8094 (m-30) REVERT: D 614 ASP cc_start: 0.8480 (p0) cc_final: 0.8122 (p0) REVERT: A 334 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8766 (mt) REVERT: A 497 CYS cc_start: 0.8844 (m) cc_final: 0.8635 (t) REVERT: A 522 ASP cc_start: 0.8351 (t0) cc_final: 0.8031 (t0) REVERT: A 660 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7696 (mp10) outliers start: 50 outliers final: 36 residues processed: 266 average time/residue: 0.1279 time to fit residues: 51.7442 Evaluate side-chains 252 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 660 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 20 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 169 optimal weight: 0.0040 chunk 117 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 324 ASN ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** 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 = 0.3565 r_free = 0.3565 target = 0.127025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093321 restraints weight = 28920.790| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.60 r_work: 0.2926 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18837 Z= 0.095 Angle : 0.559 8.708 25495 Z= 0.266 Chirality : 0.042 0.313 2836 Planarity : 0.003 0.038 3229 Dihedral : 8.868 157.706 2564 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.47 % Allowed : 24.21 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.18), residues: 2239 helix: 1.15 (0.20), residues: 778 sheet: -1.30 (0.30), residues: 343 loop : -1.04 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 612 TYR 0.014 0.001 TYR E 482 PHE 0.006 0.001 PHE E 327 TRP 0.009 0.001 TRP F 675 HIS 0.004 0.000 HIS E 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (18837) covalent geometry : angle 0.55896 / 0.27 (25495) hydrogen bonds : bond 0.02398 / 1.56 ( 579) hydrogen bonds : angle 3.95379 / 2.81 ( 1626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 224 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8898 (tp40) cc_final: 0.8589 (tp-100) REVERT: C 335 ASP cc_start: 0.8078 (m-30) cc_final: 0.7836 (m-30) REVERT: C 460 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8311 (mt-10) REVERT: C 529 GLN cc_start: 0.8411 (pm20) cc_final: 0.8202 (mp10) REVERT: F 387 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7241 (mpp-170) REVERT: F 428 TYR cc_start: 0.8546 (m-80) cc_final: 0.8147 (m-10) REVERT: F 462 MET cc_start: 0.8513 (tpt) cc_final: 0.8079 (tpp) REVERT: F 618 MET cc_start: 0.8565 (mtm) cc_final: 0.8204 (mmp) REVERT: E 497 CYS cc_start: 0.8695 (t) cc_final: 0.7970 (m) REVERT: E 576 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8139 (mtpt) REVERT: D 538 LYS cc_start: 0.8363 (pptt) cc_final: 0.7921 (pttm) REVERT: D 572 ASP cc_start: 0.8647 (p0) cc_final: 0.8435 (t0) REVERT: D 579 GLU cc_start: 0.8778 (mp0) cc_final: 0.8158 (mp0) REVERT: D 607 LYS cc_start: 0.8227 (tppt) cc_final: 0.7610 (ttpp) REVERT: D 611 ASP cc_start: 0.8454 (m-30) cc_final: 0.8037 (m-30) REVERT: D 614 ASP cc_start: 0.8476 (p0) cc_final: 0.8103 (p0) REVERT: A 334 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8779 (mt) REVERT: A 344 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.7407 (ttp-170) REVERT: A 522 ASP cc_start: 0.8341 (t0) cc_final: 0.7984 (t0) REVERT: A 611 ASP cc_start: 0.9002 (t0) cc_final: 0.8548 (p0) REVERT: A 660 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7708 (mp10) REVERT: A 684 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8260 (ttp) outliers start: 71 outliers final: 47 residues processed: 279 average time/residue: 0.1216 time to fit residues: 51.5185 Evaluate side-chains 261 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 556 SER Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 684 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 146 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 324 ASN ** F 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** 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 = 0.3544 r_free = 0.3544 target = 0.125513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091714 restraints weight = 28757.775| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.58 r_work: 0.2903 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18837 Z= 0.126 Angle : 0.578 7.168 25495 Z= 0.277 Chirality : 0.042 0.315 2836 Planarity : 0.003 0.037 3229 Dihedral : 8.900 157.712 2564 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.32 % Allowed : 24.11 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.18), residues: 2239 helix: 1.18 (0.20), residues: 772 sheet: -1.31 (0.30), residues: 343 loop : -1.02 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 612 TYR 0.015 0.001 TYR B 482 PHE 0.009 0.001 PHE C 444 TRP 0.019 0.001 TRP F 675 HIS 0.003 0.001 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (18837) covalent geometry : angle 0.57793 / 0.28 (25495) hydrogen bonds : bond 0.02760 / 1.80 ( 579) hydrogen bonds : angle 4.05170 / 2.87 ( 1626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 214 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.9060 (tp40) cc_final: 0.8809 (tp-100) REVERT: C 335 ASP cc_start: 0.8357 (m-30) cc_final: 0.8127 (m-30) REVERT: C 460 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8442 (mt-10) REVERT: C 529 GLN cc_start: 0.8596 (pm20) cc_final: 0.8337 (pm20) REVERT: C 534 ASP cc_start: 0.8146 (m-30) cc_final: 0.7884 (m-30) REVERT: F 387 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7579 (mpp-170) REVERT: F 428 TYR cc_start: 0.8542 (m-80) cc_final: 0.8153 (m-10) REVERT: F 461 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7603 (tt) REVERT: F 462 MET cc_start: 0.8502 (tpt) cc_final: 0.8042 (tpp) REVERT: F 618 MET cc_start: 0.8624 (mtm) cc_final: 0.8193 (mmp) REVERT: E 497 CYS cc_start: 0.8873 (t) cc_final: 0.8122 (m) REVERT: E 578 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.7839 (p) REVERT: E 579 GLU cc_start: 0.8154 (mp0) cc_final: 0.7813 (mp0) REVERT: E 684 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8122 (ttp) REVERT: D 538 LYS cc_start: 0.8496 (pptt) cc_final: 0.7929 (pttp) REVERT: D 572 ASP cc_start: 0.8836 (p0) cc_final: 0.8544 (t0) REVERT: D 579 GLU cc_start: 0.9013 (mp0) cc_final: 0.8440 (mp0) REVERT: D 611 ASP cc_start: 0.8591 (m-30) cc_final: 0.8184 (m-30) REVERT: D 614 ASP cc_start: 0.8632 (p0) cc_final: 0.8262 (p0) REVERT: A 334 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8743 (mt) REVERT: A 344 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.7300 (ttp-170) REVERT: A 522 ASP cc_start: 0.8592 (t0) cc_final: 0.8146 (t0) REVERT: A 611 ASP cc_start: 0.9117 (t0) cc_final: 0.8618 (p0) REVERT: A 660 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7806 (mp10) REVERT: A 684 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8406 (ttp) outliers start: 68 outliers final: 52 residues processed: 264 average time/residue: 0.1120 time to fit residues: 46.0046 Evaluate side-chains 273 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 556 SER Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 684 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 156 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 164 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 324 ASN ** F 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** 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 = 0.3512 r_free = 0.3512 target = 0.123256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.089217 restraints weight = 28834.961| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.58 r_work: 0.2860 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18837 Z= 0.180 Angle : 0.621 7.649 25495 Z= 0.300 Chirality : 0.044 0.311 2836 Planarity : 0.004 0.034 3229 Dihedral : 9.037 158.033 2564 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 3.27 % Allowed : 24.11 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2239 helix: 1.20 (0.20), residues: 749 sheet: -1.35 (0.29), residues: 350 loop : -1.02 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 612 TYR 0.018 0.001 TYR B 482 PHE 0.014 0.001 PHE C 444 TRP 0.021 0.001 TRP F 675 HIS 0.005 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (18837) covalent geometry : angle 0.62072 / 0.30 (25495) hydrogen bonds : bond 0.03333 / 2.16 ( 579) hydrogen bonds : angle 4.29300 / 3.05 ( 1626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 207 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.9120 (tp40) cc_final: 0.8678 (tp40) REVERT: C 335 ASP cc_start: 0.8397 (m-30) cc_final: 0.8023 (m-30) REVERT: C 460 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8431 (mt-10) REVERT: C 534 ASP cc_start: 0.8178 (m-30) cc_final: 0.7907 (m-30) REVERT: F 461 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7662 (tt) REVERT: F 462 MET cc_start: 0.8509 (tpt) cc_final: 0.8079 (tpp) REVERT: F 618 MET cc_start: 0.8630 (mtm) cc_final: 0.8172 (mmp) REVERT: E 497 CYS cc_start: 0.8933 (t) cc_final: 0.8194 (m) REVERT: E 576 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7992 (mtpt) REVERT: E 578 THR cc_start: 0.8318 (m) cc_final: 0.7879 (p) REVERT: E 579 GLU cc_start: 0.8210 (mp0) cc_final: 0.7856 (mp0) REVERT: D 371 ILE cc_start: 0.9411 (tt) cc_final: 0.9148 (tt) REVERT: D 538 LYS cc_start: 0.8477 (pptt) cc_final: 0.7953 (pttp) REVERT: D 572 ASP cc_start: 0.8893 (p0) cc_final: 0.8580 (t0) REVERT: D 579 GLU cc_start: 0.8997 (mp0) cc_final: 0.8404 (mp0) REVERT: D 611 ASP cc_start: 0.8606 (m-30) cc_final: 0.8197 (m-30) REVERT: D 614 ASP cc_start: 0.8682 (p0) cc_final: 0.8393 (p0) REVERT: A 334 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8694 (mt) REVERT: A 344 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.7333 (ttp-170) REVERT: A 522 ASP cc_start: 0.8607 (t0) cc_final: 0.8168 (t0) REVERT: A 660 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: A 684 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8557 (ttp) outliers start: 67 outliers final: 54 residues processed: 254 average time/residue: 0.1163 time to fit residues: 45.2963 Evaluate side-chains 262 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 203 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 556 SER Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 684 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 150 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 216 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 152 optimal weight: 0.0770 chunk 94 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 219 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** 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 = 0.3523 r_free = 0.3523 target = 0.124067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.090136 restraints weight = 28769.091| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.57 r_work: 0.2876 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18837 Z= 0.140 Angle : 0.605 9.412 25495 Z= 0.290 Chirality : 0.043 0.309 2836 Planarity : 0.003 0.034 3229 Dihedral : 9.011 157.828 2564 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 3.07 % Allowed : 24.30 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.18), residues: 2239 helix: 1.21 (0.20), residues: 750 sheet: -1.36 (0.29), residues: 350 loop : -1.01 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 612 TYR 0.016 0.001 TYR E 482 PHE 0.010 0.001 PHE C 444 TRP 0.023 0.001 TRP F 675 HIS 0.003 0.001 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (18837) covalent geometry : angle 0.60544 / 0.29 (25495) hydrogen bonds : bond 0.02983 / 1.94 ( 579) hydrogen bonds : angle 4.20727 / 2.99 ( 1626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.9101 (tp40) cc_final: 0.8750 (tp-100) REVERT: C 335 ASP cc_start: 0.8370 (m-30) cc_final: 0.8100 (m-30) REVERT: C 460 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8406 (mt-10) REVERT: C 534 ASP cc_start: 0.8173 (m-30) cc_final: 0.7908 (m-30) REVERT: F 462 MET cc_start: 0.8487 (tpt) cc_final: 0.8073 (tpp) REVERT: F 618 MET cc_start: 0.8598 (mtm) cc_final: 0.8169 (mmp) REVERT: E 497 CYS cc_start: 0.8917 (t) cc_final: 0.8177 (m) REVERT: E 578 THR cc_start: 0.8309 (m) cc_final: 0.7819 (p) REVERT: D 526 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: D 538 LYS cc_start: 0.8469 (pptt) cc_final: 0.7951 (pttp) REVERT: D 572 ASP cc_start: 0.8872 (p0) cc_final: 0.8585 (t0) REVERT: D 579 GLU cc_start: 0.9010 (mp0) cc_final: 0.8451 (mp0) REVERT: D 611 ASP cc_start: 0.8604 (m-30) cc_final: 0.8230 (m-30) REVERT: D 614 ASP cc_start: 0.8711 (p0) cc_final: 0.8340 (p0) REVERT: A 334 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8726 (mt) REVERT: A 344 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.7327 (ttp-170) REVERT: A 522 ASP cc_start: 0.8590 (t0) cc_final: 0.8158 (t0) REVERT: A 660 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7774 (mp10) REVERT: A 684 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8458 (ttp) outliers start: 63 outliers final: 55 residues processed: 255 average time/residue: 0.1221 time to fit residues: 47.9746 Evaluate side-chains 262 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 556 SER Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 684 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 158 optimal weight: 7.9990 chunk 140 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.0370 chunk 203 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 178 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 324 ASN E 680 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.092351 restraints weight = 28831.973| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.66 r_work: 0.2917 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18837 Z= 0.097 Angle : 0.575 8.261 25495 Z= 0.276 Chirality : 0.042 0.306 2836 Planarity : 0.003 0.034 3229 Dihedral : 8.904 158.020 2564 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.93 % Allowed : 24.35 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.18), residues: 2239 helix: 1.40 (0.20), residues: 749 sheet: -1.30 (0.29), residues: 353 loop : -0.92 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 612 TYR 0.014 0.001 TYR E 482 PHE 0.008 0.001 PHE E 561 TRP 0.020 0.001 TRP F 675 HIS 0.002 0.000 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (18837) covalent geometry : angle 0.57520 / 0.28 (25495) hydrogen bonds : bond 0.02481 / 1.62 ( 579) hydrogen bonds : angle 4.01276 / 2.85 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3580.30 seconds wall clock time: 62 minutes 16.56 seconds (3736.56 seconds total)