Starting phenix.real_space_refine on Sat Jul 4 05:09:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hwf_35056/07_2026/8hwf_35056.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwf_35056/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8hwf_35056/07_2026/8hwf_35056.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hwf_35056/07_2026/8hwf_35056.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hwf_35056/07_2026/8hwf_35056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwf_35056/07_2026/8hwf_35056.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwf_35056/07_2026/8hwf_35056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwf_35056/07_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-dev-6108/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: 3.99, per 1000 atoms: 0.22 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: 1.51 Conformation dependent library (CDL) restraints added in 793.4 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: 0.50 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: 3.09 Time building geometry restraints manager: 1.91 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.840 Find NCS groups from input model: 0.610 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.290 ------------------------------------------------------------------------------- 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= 0.361 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 0.65982 / 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 : 0.586 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: 0.1390 time to fit residues: 49.3830 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 : 0.720 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.124998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.091611 restraints weight = 28730.534| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.53 r_work: 0.2887 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18837 Z= 0.131 Angle : 0.590 7.094 25495 Z= 0.288 Chirality : 0.043 0.288 2836 Planarity : 0.004 0.065 3229 Dihedral : 9.236 157.655 2565 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.34 % Allowed : 24.16 % Favored : 73.50 % 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: -1.05 (0.18), residues: 2239 helix: 0.77 (0.20), residues: 726 sheet: -1.68 (0.29), residues: 331 loop : -1.34 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 570 TYR 0.016 0.001 TYR E 482 PHE 0.010 0.001 PHE F 630 TRP 0.008 0.001 TRP B 350 HIS 0.003 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (18837) covalent geometry : angle 0.59004 / 0.29 (25495) hydrogen bonds : bond 0.03903 / 2.52 ( 579) hydrogen bonds : angle 4.75164 / 3.38 ( 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 269 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 460 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8546 (mt-10) REVERT: F 618 MET cc_start: 0.8573 (mtm) cc_final: 0.8200 (mmp) REVERT: E 426 MET cc_start: 0.7141 (ptt) cc_final: 0.6132 (ptp) REVERT: E 578 THR cc_start: 0.8137 (m) cc_final: 0.7925 (p) REVERT: E 579 GLU cc_start: 0.8047 (mp0) cc_final: 0.7761 (mp0) REVERT: D 361 GLU cc_start: 0.8554 (pm20) cc_final: 0.8033 (pm20) REVERT: D 614 ASP cc_start: 0.8662 (p0) cc_final: 0.8391 (p0) REVERT: A 334 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8717 (mt) REVERT: A 344 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.7263 (ttp-170) REVERT: A 399 MET cc_start: 0.8486 (mtt) cc_final: 0.8259 (mtt) REVERT: A 579 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8043 (tm-30) outliers start: 48 outliers final: 25 residues processed: 258 average time/residue: 0.1389 time to fit residues: 54.4412 Evaluate side-chains 239 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 681 ILE 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: 8.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.122837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.088786 restraints weight = 29029.517| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.59 r_work: 0.2854 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18837 Z= 0.177 Angle : 0.607 11.370 25495 Z= 0.293 Chirality : 0.043 0.289 2836 Planarity : 0.004 0.056 3229 Dihedral : 9.226 157.717 2564 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 3.61 % Allowed : 23.77 % 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: -1.02 (0.18), residues: 2239 helix: 0.77 (0.20), residues: 732 sheet: -1.63 (0.29), residues: 330 loop : -1.32 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 387 TYR 0.019 0.001 TYR B 482 PHE 0.012 0.001 PHE C 444 TRP 0.008 0.001 TRP B 350 HIS 0.004 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (18837) covalent geometry : angle 0.60665 / 0.29 (25495) hydrogen bonds : bond 0.03717 / 2.41 ( 579) hydrogen bonds : angle 4.61015 / 3.29 ( 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 302 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 228 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8721 (tp40) cc_final: 0.8235 (tp40) REVERT: C 335 ASP cc_start: 0.8338 (m-30) cc_final: 0.8003 (m-30) REVERT: C 460 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8488 (mt-10) REVERT: F 525 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.8060 (m) REVERT: F 612 ARG cc_start: 0.7922 (ptm160) cc_final: 0.7617 (ptm160) REVERT: F 618 MET cc_start: 0.8551 (mtm) cc_final: 0.8156 (mmp) REVERT: E 467 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8322 (m-30) REVERT: E 578 THR cc_start: 0.8238 (m) cc_final: 0.7813 (p) REVERT: E 653 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: D 361 GLU cc_start: 0.8673 (pm20) cc_final: 0.8372 (pm20) REVERT: D 579 GLU cc_start: 0.8984 (mp0) cc_final: 0.8599 (mp0) REVERT: D 614 ASP cc_start: 0.8658 (p0) cc_final: 0.8382 (p0) REVERT: D 649 LYS cc_start: 0.9017 (mmtp) cc_final: 0.8719 (mmmm) REVERT: A 334 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8765 (mt) REVERT: A 344 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.7258 (ttp-170) REVERT: A 416 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8816 (tttt) REVERT: A 579 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7885 (tm-30) outliers start: 74 outliers final: 41 residues processed: 282 average time/residue: 0.1373 time to fit residues: 58.3036 Evaluate side-chains 250 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 525 VAL 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 467 ASP 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 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 334 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 184 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 23 optimal weight: 0.0170 chunk 20 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 49 optimal weight: 0.0970 chunk 61 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 594 ASN B 374 GLN ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 ASN ** 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 = 0.3545 r_free = 0.3545 target = 0.125682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.091692 restraints weight = 29037.249| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.62 r_work: 0.2900 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18837 Z= 0.094 Angle : 0.555 8.963 25495 Z= 0.267 Chirality : 0.042 0.288 2836 Planarity : 0.003 0.050 3229 Dihedral : 9.089 157.755 2564 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.83 % Allowed : 24.01 % Favored : 73.16 % 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: -0.79 (0.18), residues: 2239 helix: 0.95 (0.20), residues: 745 sheet: -1.54 (0.30), residues: 335 loop : -1.17 (0.18), residues: 1159 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 0.016 0.001 PHE F 630 TRP 0.007 0.001 TRP D 350 HIS 0.004 0.000 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 (18837) covalent geometry : angle 0.55538 / 0.27 (25495) hydrogen bonds : bond 0.02739 / 1.79 ( 579) hydrogen bonds : angle 4.27351 / 3.04 ( 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 290 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8573 (tp40) cc_final: 0.8037 (tp40) REVERT: C 335 ASP cc_start: 0.8075 (m-30) cc_final: 0.7699 (m-30) REVERT: C 460 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8396 (mt-10) REVERT: F 525 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7889 (m) REVERT: F 612 ARG cc_start: 0.7875 (ptm160) cc_final: 0.7569 (ptm160) REVERT: F 618 MET cc_start: 0.8563 (mtm) cc_final: 0.8189 (mmp) REVERT: E 578 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7715 (p) REVERT: E 579 GLU cc_start: 0.8173 (mp0) cc_final: 0.7861 (mp0) REVERT: E 653 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: D 361 GLU cc_start: 0.8606 (pm20) cc_final: 0.8379 (pm20) REVERT: D 538 LYS cc_start: 0.8315 (pttp) cc_final: 0.8079 (pptt) REVERT: D 611 ASP cc_start: 0.8444 (m-30) cc_final: 0.8105 (m-30) REVERT: D 614 ASP cc_start: 0.8523 (p0) cc_final: 0.8219 (p0) REVERT: D 649 LYS cc_start: 0.8943 (mmtp) cc_final: 0.8682 (mmmm) REVERT: A 334 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8735 (mt) REVERT: A 424 ASP cc_start: 0.8380 (t70) cc_final: 0.8168 (t70) REVERT: A 522 ASP cc_start: 0.8080 (t0) cc_final: 0.7783 (t0) REVERT: A 579 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7796 (tm-30) REVERT: A 660 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7713 (mp10) outliers start: 58 outliers final: 30 residues processed: 275 average time/residue: 0.1433 time to fit residues: 59.4661 Evaluate side-chains 250 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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 525 VAL 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 650 LEU Chi-restraints excluded: chain E residue 653 GLU Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain A residue 334 LEU 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: 8.9990 chunk 42 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 145 optimal weight: 9.9990 chunk 190 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 374 GLN F 324 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.091616 restraints weight = 28776.321| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.62 r_work: 0.2899 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1312 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= 0.102 Angle : 0.558 8.272 25495 Z= 0.268 Chirality : 0.042 0.288 2836 Planarity : 0.003 0.045 3229 Dihedral : 9.016 158.243 2564 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.17 % Allowed : 23.72 % 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: -0.73 (0.18), residues: 2239 helix: 0.97 (0.20), residues: 768 sheet: -1.49 (0.30), residues: 335 loop : -1.16 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 387 TYR 0.016 0.001 TYR E 482 PHE 0.009 0.001 PHE F 630 TRP 0.006 0.001 TRP B 350 HIS 0.003 0.000 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (18837) covalent geometry : angle 0.55849 / 0.27 (25495) hydrogen bonds : bond 0.02691 / 1.76 ( 579) hydrogen bonds : angle 4.15324 / 2.96 ( 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 290 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 225 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8598 (tp40) cc_final: 0.8037 (tp40) REVERT: C 335 ASP cc_start: 0.8108 (m-30) cc_final: 0.7730 (m-30) REVERT: C 529 GLN cc_start: 0.8382 (pm20) cc_final: 0.8132 (pm20) REVERT: F 525 VAL cc_start: 0.8168 (OUTLIER) cc_final: 0.7937 (m) REVERT: F 618 MET cc_start: 0.8538 (mtm) cc_final: 0.8160 (mmp) REVERT: E 576 LYS cc_start: 0.8379 (mtpt) cc_final: 0.8163 (mtpt) REVERT: E 578 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7604 (p) REVERT: E 579 GLU cc_start: 0.8140 (mp0) cc_final: 0.7826 (mp0) REVERT: E 653 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: D 572 ASP cc_start: 0.8676 (p0) cc_final: 0.8314 (t0) REVERT: D 611 ASP cc_start: 0.8450 (m-30) cc_final: 0.8143 (m-30) REVERT: D 614 ASP cc_start: 0.8512 (p0) cc_final: 0.8177 (p0) REVERT: D 649 LYS cc_start: 0.8944 (mmtp) cc_final: 0.8668 (mmmm) REVERT: A 334 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8796 (mt) REVERT: A 522 ASP cc_start: 0.8257 (t0) cc_final: 0.7921 (t0) REVERT: A 579 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7787 (tm-30) REVERT: A 660 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7748 (mp10) outliers start: 65 outliers final: 42 residues processed: 273 average time/residue: 0.1264 time to fit residues: 52.5686 Evaluate side-chains 258 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 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 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 525 VAL Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 629 HIS 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 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 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 372 ARG 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 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 594 ASN Chi-restraints excluded: chain A residue 660 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 210 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 10 optimal weight: 0.0040 chunk 163 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 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 = 0.3547 r_free = 0.3547 target = 0.125862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.092045 restraints weight = 28750.657| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.59 r_work: 0.2906 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18837 Z= 0.102 Angle : 0.559 8.797 25495 Z= 0.267 Chirality : 0.042 0.287 2836 Planarity : 0.003 0.039 3229 Dihedral : 8.962 158.400 2564 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.93 % Allowed : 24.30 % Favored : 72.77 % 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: -0.60 (0.18), residues: 2239 helix: 1.08 (0.20), residues: 769 sheet: -1.46 (0.29), residues: 353 loop : -1.07 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 387 TYR 0.015 0.001 TYR E 482 PHE 0.013 0.001 PHE E 427 TRP 0.016 0.001 TRP F 675 HIS 0.003 0.000 HIS E 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (18837) covalent geometry : angle 0.55868 / 0.27 (25495) hydrogen bonds : bond 0.02620 / 1.71 ( 579) hydrogen bonds : angle 4.09740 / 2.92 ( 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 280 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 220 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8592 (tp40) cc_final: 0.7792 (tp40) REVERT: C 335 ASP cc_start: 0.8120 (m-30) cc_final: 0.7720 (m-30) REVERT: C 399 MET cc_start: 0.9140 (mtm) cc_final: 0.8922 (mtp) REVERT: C 460 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8348 (mt-10) REVERT: C 529 GLN cc_start: 0.8453 (pm20) cc_final: 0.8183 (pm20) REVERT: F 525 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7935 (m) REVERT: F 612 ARG cc_start: 0.7811 (ptm160) cc_final: 0.7475 (ptm160) REVERT: F 618 MET cc_start: 0.8565 (mtm) cc_final: 0.8148 (mmp) REVERT: E 576 LYS cc_start: 0.8291 (mtpt) cc_final: 0.8082 (mtpt) REVERT: D 572 ASP cc_start: 0.8637 (p0) cc_final: 0.8348 (t0) REVERT: D 579 GLU cc_start: 0.8722 (mp0) cc_final: 0.8108 (mp0) REVERT: D 611 ASP cc_start: 0.8477 (m-30) cc_final: 0.8160 (m-30) REVERT: D 614 ASP cc_start: 0.8514 (p0) cc_final: 0.8174 (p0) REVERT: D 649 LYS cc_start: 0.8962 (mmtp) cc_final: 0.8750 (mmmm) REVERT: A 334 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8793 (mt) REVERT: A 344 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.7252 (ttp-170) REVERT: A 522 ASP cc_start: 0.8401 (t0) cc_final: 0.8043 (t0) REVERT: A 579 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7733 (tm-30) REVERT: A 660 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7732 (mp10) REVERT: A 684 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8262 (ttp) outliers start: 60 outliers final: 46 residues processed: 266 average time/residue: 0.1336 time to fit residues: 54.3119 Evaluate side-chains 261 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 499 THR 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 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 525 VAL 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 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 599 THR Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 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 440 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 684 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 20 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 96 optimal weight: 0.0570 chunk 42 optimal weight: 0.0050 chunk 105 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 169 optimal weight: 0.2980 chunk 117 optimal weight: 3.9990 overall best weight: 0.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN E 353 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.094002 restraints weight = 28799.722| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.60 r_work: 0.2937 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 18837 Z= 0.088 Angle : 0.556 8.798 25495 Z= 0.265 Chirality : 0.041 0.285 2836 Planarity : 0.003 0.040 3229 Dihedral : 8.882 158.669 2564 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.59 % Allowed : 24.99 % Favored : 72.43 % 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: -0.48 (0.18), residues: 2239 helix: 1.20 (0.20), residues: 773 sheet: -1.37 (0.29), residues: 353 loop : -1.02 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 387 TYR 0.014 0.001 TYR E 482 PHE 0.006 0.001 PHE B 427 TRP 0.010 0.001 TRP F 675 HIS 0.004 0.000 HIS E 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (18837) covalent geometry : angle 0.55634 / 0.26 (25495) hydrogen bonds : bond 0.02318 / 1.52 ( 579) hydrogen bonds : angle 3.95292 / 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 290 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8547 (tp40) cc_final: 0.7705 (tp40) REVERT: C 335 ASP cc_start: 0.8080 (m-30) cc_final: 0.7667 (m-30) REVERT: C 399 MET cc_start: 0.9111 (mtm) cc_final: 0.8909 (mtp) REVERT: C 460 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8359 (mt-10) REVERT: C 529 GLN cc_start: 0.8412 (pm20) cc_final: 0.8139 (pm20) REVERT: C 534 ASP cc_start: 0.7951 (m-30) cc_final: 0.7594 (m-30) REVERT: F 428 TYR cc_start: 0.8513 (m-80) cc_final: 0.8106 (m-10) REVERT: F 525 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7909 (m) REVERT: F 617 LEU cc_start: 0.8600 (tp) cc_final: 0.8275 (tp) REVERT: F 618 MET cc_start: 0.8629 (mtm) cc_final: 0.8184 (mmp) REVERT: E 497 CYS cc_start: 0.8667 (t) cc_final: 0.7957 (m) REVERT: E 570 ARG cc_start: 0.5820 (mtp85) cc_final: 0.5589 (mtm180) REVERT: E 578 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7806 (p) REVERT: E 579 GLU cc_start: 0.8027 (mp0) cc_final: 0.7697 (mp0) REVERT: D 538 LYS cc_start: 0.8347 (pptt) cc_final: 0.7959 (pttm) REVERT: D 572 ASP cc_start: 0.8599 (p0) cc_final: 0.8382 (t0) REVERT: D 579 GLU cc_start: 0.8750 (mp0) cc_final: 0.8128 (mp0) REVERT: D 611 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8169 (m-30) REVERT: D 614 ASP cc_start: 0.8461 (p0) cc_final: 0.8101 (p0) REVERT: D 649 LYS cc_start: 0.8936 (mmtp) cc_final: 0.8678 (mmmm) REVERT: A 334 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8764 (mt) REVERT: A 467 ASP cc_start: 0.8349 (m-30) cc_final: 0.8106 (m-30) REVERT: A 522 ASP cc_start: 0.8355 (t0) cc_final: 0.7889 (t0) REVERT: A 660 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: A 684 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8240 (ttp) outliers start: 53 outliers final: 31 residues processed: 276 average time/residue: 0.1269 time to fit residues: 53.2753 Evaluate side-chains 261 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 447 ASP Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 582 VAL 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 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 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 611 ASP 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 486 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 592 ILE 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: 6.9990 chunk 89 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 189 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090695 restraints weight = 28775.446| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.58 r_work: 0.2885 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18837 Z= 0.148 Angle : 0.592 7.921 25495 Z= 0.284 Chirality : 0.043 0.292 2836 Planarity : 0.003 0.039 3229 Dihedral : 8.962 158.539 2564 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.03 % Allowed : 24.69 % Favored : 72.28 % 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: -0.50 (0.18), residues: 2239 helix: 1.16 (0.20), residues: 772 sheet: -1.31 (0.30), residues: 343 loop : -1.05 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 387 TYR 0.017 0.001 TYR B 482 PHE 0.011 0.001 PHE C 444 TRP 0.019 0.001 TRP F 675 HIS 0.004 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (18837) covalent geometry : angle 0.59187 / 0.28 (25495) hydrogen bonds : bond 0.02985 / 1.94 ( 579) hydrogen bonds : angle 4.14277 / 2.94 ( 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: 62 poor density : 220 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8746 (tp40) cc_final: 0.8166 (tp40) REVERT: C 335 ASP cc_start: 0.8357 (m-30) cc_final: 0.7976 (m-30) REVERT: C 460 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8470 (mt-10) REVERT: C 529 GLN cc_start: 0.8666 (pm20) cc_final: 0.8383 (pm20) REVERT: C 534 ASP cc_start: 0.8243 (m-30) cc_final: 0.7962 (m-30) REVERT: F 428 TYR cc_start: 0.8525 (m-80) cc_final: 0.8228 (m-10) REVERT: F 461 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7614 (tt) REVERT: F 462 MET cc_start: 0.8476 (tpt) cc_final: 0.8041 (tpp) REVERT: F 525 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8030 (m) REVERT: F 617 LEU cc_start: 0.8640 (tp) cc_final: 0.8325 (tp) REVERT: F 618 MET cc_start: 0.8628 (mtm) cc_final: 0.8179 (mmp) REVERT: E 497 CYS cc_start: 0.8847 (t) cc_final: 0.8097 (m) REVERT: E 578 THR cc_start: 0.8269 (m) cc_final: 0.7856 (p) REVERT: E 579 GLU cc_start: 0.8180 (mp0) cc_final: 0.7812 (mp0) REVERT: E 637 GLU cc_start: 0.8830 (pt0) cc_final: 0.7968 (pm20) REVERT: D 538 LYS cc_start: 0.8466 (pptt) cc_final: 0.7939 (pttp) REVERT: D 572 ASP cc_start: 0.8833 (p0) cc_final: 0.8520 (t0) REVERT: D 579 GLU cc_start: 0.9019 (mp0) cc_final: 0.8437 (mp0) REVERT: D 611 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: D 614 ASP cc_start: 0.8645 (p0) cc_final: 0.8286 (p0) REVERT: D 649 LYS cc_start: 0.9019 (mmtp) cc_final: 0.8733 (mmmm) REVERT: A 334 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8752 (mt) REVERT: A 344 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.7405 (ttp-170) REVERT: A 522 ASP cc_start: 0.8579 (t0) cc_final: 0.8145 (t0) REVERT: A 611 ASP cc_start: 0.9126 (t0) cc_final: 0.8651 (p0) REVERT: A 660 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: A 684 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8407 (ttp) outliers start: 62 outliers final: 50 residues processed: 266 average time/residue: 0.1321 time to fit residues: 53.9494 Evaluate side-chains 269 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 212 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 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 581 CYS 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 525 VAL 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 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 370 SER 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 554 PHE Chi-restraints excluded: chain D residue 611 ASP 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 452 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 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: 2.9990 chunk 100 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 168 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.125806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.092138 restraints weight = 28653.241| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.57 r_work: 0.2909 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18837 Z= 0.107 Angle : 0.577 9.447 25495 Z= 0.275 Chirality : 0.042 0.283 2836 Planarity : 0.003 0.034 3229 Dihedral : 8.929 158.630 2564 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.78 % Allowed : 25.13 % Favored : 72.08 % 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: -0.37 (0.18), residues: 2239 helix: 1.35 (0.20), residues: 751 sheet: -1.26 (0.30), residues: 343 loop : -0.99 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 612 TYR 0.015 0.001 TYR E 482 PHE 0.007 0.001 PHE C 444 TRP 0.015 0.001 TRP F 675 HIS 0.003 0.000 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (18837) covalent geometry : angle 0.57676 / 0.27 (25495) hydrogen bonds : bond 0.02587 / 1.69 ( 579) hydrogen bonds : angle 4.03392 / 2.86 ( 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 278 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 221 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8730 (tp40) cc_final: 0.8167 (tp40) REVERT: C 335 ASP cc_start: 0.8349 (m-30) cc_final: 0.7974 (m-30) REVERT: C 460 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8482 (mt-10) REVERT: C 529 GLN cc_start: 0.8618 (pm20) cc_final: 0.8352 (pm20) REVERT: C 534 ASP cc_start: 0.8217 (m-30) cc_final: 0.7942 (m-30) REVERT: F 428 TYR cc_start: 0.8507 (m-80) cc_final: 0.8205 (m-10) REVERT: F 461 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7645 (tt) REVERT: F 462 MET cc_start: 0.8480 (tpt) cc_final: 0.8015 (tpp) REVERT: F 525 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7998 (m) REVERT: F 618 MET cc_start: 0.8579 (mtm) cc_final: 0.8142 (mmp) REVERT: E 497 CYS cc_start: 0.8923 (t) cc_final: 0.8200 (m) REVERT: E 578 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7829 (p) REVERT: E 579 GLU cc_start: 0.8212 (mp0) cc_final: 0.7837 (mp0) REVERT: E 680 HIS cc_start: 0.7852 (m170) cc_final: 0.7626 (m170) REVERT: D 538 LYS cc_start: 0.8469 (pptt) cc_final: 0.7960 (pttp) REVERT: D 572 ASP cc_start: 0.8815 (p0) cc_final: 0.8531 (t0) REVERT: D 579 GLU cc_start: 0.9004 (mp0) cc_final: 0.8413 (mp0) REVERT: D 611 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8299 (m-30) REVERT: D 649 LYS cc_start: 0.8994 (mmtp) cc_final: 0.8719 (mmmm) REVERT: A 334 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8754 (mt) REVERT: A 467 ASP cc_start: 0.8420 (m-30) cc_final: 0.8117 (m-30) REVERT: A 522 ASP cc_start: 0.8593 (t0) cc_final: 0.8146 (t0) REVERT: A 660 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: A 684 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8397 (ttp) outliers start: 57 outliers final: 44 residues processed: 264 average time/residue: 0.1294 time to fit residues: 52.4706 Evaluate side-chains 265 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 447 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 363 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 525 VAL 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 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 D residue 351 ILE Chi-restraints excluded: chain D residue 370 SER 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 554 PHE Chi-restraints excluded: chain D residue 611 ASP 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 385 CYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 592 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 150 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 94 optimal weight: 0.0050 chunk 129 optimal weight: 9.9990 chunk 144 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090712 restraints weight = 28870.436| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.51 r_work: 0.2895 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18837 Z= 0.148 Angle : 0.601 8.198 25495 Z= 0.288 Chirality : 0.043 0.287 2836 Planarity : 0.003 0.032 3229 Dihedral : 8.983 158.744 2564 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.78 % Allowed : 25.04 % Favored : 72.18 % 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: -0.43 (0.18), residues: 2239 helix: 1.29 (0.20), residues: 752 sheet: -1.29 (0.29), residues: 350 loop : -1.02 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 612 TYR 0.016 0.001 TYR B 482 PHE 0.011 0.001 PHE C 444 TRP 0.022 0.001 TRP F 675 HIS 0.004 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (18837) covalent geometry : angle 0.60072 / 0.29 (25495) hydrogen bonds : bond 0.03015 / 1.96 ( 579) hydrogen bonds : angle 4.17059 / 2.96 ( 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 277 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 GLN cc_start: 0.8824 (tp40) cc_final: 0.8288 (tp40) REVERT: C 335 ASP cc_start: 0.8336 (m-30) cc_final: 0.7984 (m-30) REVERT: C 460 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8473 (mt-10) REVERT: C 529 GLN cc_start: 0.8676 (pm20) cc_final: 0.8419 (pm20) REVERT: C 534 ASP cc_start: 0.8297 (m-30) cc_final: 0.8053 (m-30) REVERT: F 428 TYR cc_start: 0.8585 (m-80) cc_final: 0.8137 (m-10) REVERT: F 461 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7674 (tt) REVERT: F 462 MET cc_start: 0.8494 (tpt) cc_final: 0.8047 (tpp) REVERT: F 525 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8153 (m) REVERT: F 618 MET cc_start: 0.8603 (mtm) cc_final: 0.8256 (mmt) REVERT: E 497 CYS cc_start: 0.8868 (t) cc_final: 0.8143 (m) REVERT: E 576 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8063 (mtpt) REVERT: E 578 THR cc_start: 0.8293 (m) cc_final: 0.7865 (p) REVERT: E 579 GLU cc_start: 0.8271 (mp0) cc_final: 0.7952 (mp0) REVERT: E 637 GLU cc_start: 0.8800 (pt0) cc_final: 0.7933 (pm20) REVERT: D 538 LYS cc_start: 0.8452 (pptt) cc_final: 0.7985 (pttp) REVERT: D 572 ASP cc_start: 0.8869 (p0) cc_final: 0.8637 (t0) REVERT: D 579 GLU cc_start: 0.8950 (mp0) cc_final: 0.8469 (mp0) REVERT: D 611 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8395 (m-30) REVERT: D 649 LYS cc_start: 0.9010 (mmtp) cc_final: 0.8728 (mmmm) REVERT: A 334 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8757 (mt) REVERT: A 344 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.7433 (ttp-170) REVERT: A 522 ASP cc_start: 0.8576 (t0) cc_final: 0.8174 (t0) REVERT: A 660 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: A 684 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8316 (ttp) outliers start: 57 outliers final: 49 residues processed: 261 average time/residue: 0.1301 time to fit residues: 51.6462 Evaluate side-chains 274 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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 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 363 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 525 VAL 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 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 370 SER 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 554 PHE Chi-restraints excluded: chain D residue 611 ASP 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 536 LEU 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: 6.9990 chunk 140 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.0020 chunk 203 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 98 optimal weight: 0.0870 chunk 178 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.7568 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.126000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.092878 restraints weight = 28681.856| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.52 r_work: 0.2930 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18837 Z= 0.100 Angle : 0.576 9.676 25495 Z= 0.274 Chirality : 0.042 0.281 2836 Planarity : 0.003 0.031 3229 Dihedral : 8.904 158.825 2564 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.54 % Allowed : 25.28 % Favored : 72.18 % 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: -0.32 (0.18), residues: 2239 helix: 1.41 (0.20), residues: 750 sheet: -1.23 (0.30), residues: 343 loop : -0.96 (0.18), residues: 1146 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 0.021 0.001 PHE B 698 TRP 0.020 0.001 TRP F 675 HIS 0.003 0.000 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (18837) covalent geometry : angle 0.57631 / 0.27 (25495) hydrogen bonds : bond 0.02509 / 1.64 ( 579) hydrogen bonds : angle 4.00677 / 2.84 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4095.25 seconds wall clock time: 71 minutes 4.99 seconds (4264.99 seconds total)