Starting phenix.real_space_refine on Mon Jun 16 11:01:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwf_35056/06_2025/8hwf_35056.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwf_35056/06_2025/8hwf_35056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwf_35056/06_2025/8hwf_35056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwf_35056/06_2025/8hwf_35056.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwf_35056/06_2025/8hwf_35056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwf_35056/06_2025/8hwf_35056.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.48, per 1000 atoms: 0.62 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: 5.23 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.29 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: 5.50 Time building geometry restraints manager: 5.61 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=" 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 bond pdb=" N ASP E 534 " pdb=" CA ASP E 534 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.32e-02 5.74e+03 4.87e+00 bond pdb=" C PRO F 456 " pdb=" O PRO F 456 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.20e-02 6.94e+03 4.71e+00 bond pdb=" N GLU E 526 " pdb=" CA GLU E 526 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.27e-02 6.20e+03 4.26e+00 bond pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.25e+00 ... (remaining 18832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 24988 2.03 - 4.05: 421 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=" 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=" CB MET F 458 " pdb=" CG MET F 458 " pdb=" SD MET F 458 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C SER B 556 " pdb=" N GLU B 557 " pdb=" CA GLU B 557 " ideal model delta sigma weight residual 122.40 127.01 -4.61 1.45e+00 4.76e-01 1.01e+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: 2240 0.049 - 0.098: 500 0.098 - 0.147: 94 0.147 - 0.196: 1 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=" CA GLU B 557 " pdb=" N GLU B 557 " pdb=" C GLU B 557 " pdb=" CB GLU B 557 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-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: 0.010 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 43.010 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 0.045 18837 Z= 0.129 Angle : 0.656 10.128 25495 Z= 0.347 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (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 TRP 0.009 0.001 TRP B 350 HIS 0.004 0.000 HIS F 629 PHE 0.016 0.001 PHE C 588 TYR 0.018 0.001 TYR E 482 ARG 0.007 0.000 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.18829 ( 579) hydrogen bonds : angle 6.22316 ( 1626) covalent geometry : bond 0.00264 (18837) covalent geometry : angle 0.65558 (25495) *********************** 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 : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 387 ARG cc_start: 0.8387 (ptt90) cc_final: 0.8149 (ptt-90) REVERT: C 618 MET cc_start: 0.8642 (mtm) cc_final: 0.8248 (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: 0.6461 (tmm) REVERT: E 578 THR cc_start: 0.8001 (m) cc_final: 0.7709 (p) REVERT: D 361 GLU cc_start: 0.8478 (pm20) cc_final: 0.8267 (pm20) REVERT: D 374 GLN cc_start: 0.8829 (mt0) cc_final: 0.8574 (mt0) REVERT: A 612 ARG cc_start: 0.8598 (mtm110) cc_final: 0.7475 (ptp90) outliers start: 3 outliers final: 1 residues processed: 237 average time/residue: 0.3271 time to fit residues: 116.1907 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 : 2.249 ------------------------------------------------------------------------------- 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 186 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 173 optimal weight: 0.0060 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 200 optimal weight: 0.0030 overall best weight: 1.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.089876 restraints weight = 28704.141| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.57 r_work: 0.2873 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18837 Z= 0.146 Angle : 0.593 7.037 25495 Z= 0.289 Chirality : 0.042 0.201 2836 Planarity : 0.004 0.065 3229 Dihedral : 9.299 157.520 2565 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.78 % Allowed : 23.91 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.18), residues: 2239 helix: 0.70 (0.20), residues: 732 sheet: -1.68 (0.29), residues: 331 loop : -1.35 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 350 HIS 0.003 0.001 HIS D 680 PHE 0.011 0.001 PHE F 630 TYR 0.017 0.001 TYR E 482 ARG 0.004 0.000 ARG D 570 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 579) hydrogen bonds : angle 4.72491 ( 1626) covalent geometry : bond 0.00349 (18837) covalent geometry : angle 0.59323 (25495) *********************** 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 281 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 460 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8510 (mt-10) REVERT: F 618 MET cc_start: 0.8570 (mtm) cc_final: 0.8151 (mmp) REVERT: E 426 MET cc_start: 0.7217 (ptt) cc_final: 0.6183 (ptp) REVERT: E 578 THR cc_start: 0.8166 (m) cc_final: 0.7935 (p) REVERT: E 579 GLU cc_start: 0.8086 (mp0) cc_final: 0.7751 (mp0) REVERT: D 361 GLU cc_start: 0.8646 (pm20) cc_final: 0.8058 (pm20) REVERT: D 614 ASP cc_start: 0.8663 (p0) cc_final: 0.8398 (p0) REVERT: A 334 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8725 (mt) REVERT: A 344 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.7257 (ttp-170) REVERT: A 522 ASP cc_start: 0.8182 (t0) cc_final: 0.7950 (t0) REVERT: A 579 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7919 (tm-30) outliers start: 57 outliers final: 28 residues processed: 267 average time/residue: 0.3256 time to fit residues: 130.9860 Evaluate side-chains 243 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 2.080 ------------------------------------------------------------------------------- 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 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 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 533 THR 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 339 VAL 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 D residue 554 PHE 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 149 optimal weight: 4.9990 chunk 146 optimal weight: 0.0670 chunk 188 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 82 optimal weight: 0.1980 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 0.0770 chunk 191 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 GLN B 353 ASN B 374 GLN ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 ASN E 478 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.091186 restraints weight = 28680.052| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.58 r_work: 0.2900 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18837 Z= 0.113 Angle : 0.566 10.103 25495 Z= 0.272 Chirality : 0.041 0.207 2836 Planarity : 0.003 0.055 3229 Dihedral : 9.139 158.389 2564 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.78 % Allowed : 23.91 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.18), residues: 2239 helix: 0.85 (0.20), residues: 740 sheet: -1.60 (0.28), residues: 355 loop : -1.19 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 350 HIS 0.002 0.000 HIS B 629 PHE 0.008 0.001 PHE F 630 TYR 0.016 0.001 TYR E 482 ARG 0.006 0.000 ARG C 387 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 579) hydrogen bonds : angle 4.37729 ( 1626) covalent geometry : bond 0.00268 (18837) covalent geometry : angle 0.56611 (25495) *********************** 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 299 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 242 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8290 (m-30) cc_final: 0.8010 (m-30) REVERT: C 460 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8609 (mt-10) REVERT: F 618 MET cc_start: 0.8473 (mtm) cc_final: 0.8146 (mmp) REVERT: F 684 MET cc_start: 0.6800 (tmm) cc_final: 0.6590 (tmm) REVERT: E 535 VAL cc_start: 0.5802 (OUTLIER) cc_final: 0.5365 (t) REVERT: E 578 THR cc_start: 0.8208 (m) cc_final: 0.7746 (p) REVERT: E 579 GLU cc_start: 0.8189 (mp0) cc_final: 0.7904 (mp0) REVERT: E 606 TYR cc_start: 0.8539 (m-80) cc_final: 0.8152 (m-80) REVERT: E 653 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: D 361 GLU cc_start: 0.8719 (pm20) cc_final: 0.8511 (pm20) REVERT: D 579 GLU cc_start: 0.8954 (mp0) cc_final: 0.8622 (mp0) REVERT: D 614 ASP cc_start: 0.8640 (p0) cc_final: 0.8372 (p0) REVERT: A 334 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8790 (mt) REVERT: A 344 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.7296 (ttp-170) REVERT: A 522 ASP cc_start: 0.8272 (t0) cc_final: 0.8015 (t0) REVERT: A 570 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7913 (ttt-90) REVERT: A 579 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7932 (tm-30) outliers start: 57 outliers final: 31 residues processed: 285 average time/residue: 0.3145 time to fit residues: 134.3997 Evaluate side-chains 243 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 2.433 ------------------------------------------------------------------------------- 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 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain B residue 334 LEU 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 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain E residue 339 VAL 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 535 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 640 GLU Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 653 GLU Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain 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 344 ARG 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 63 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 1 optimal weight: 0.4980 chunk 111 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 70 optimal weight: 0.3980 chunk 138 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.123280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.089462 restraints weight = 28809.576| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.58 r_work: 0.2859 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18837 Z= 0.160 Angle : 0.585 8.284 25495 Z= 0.284 Chirality : 0.042 0.167 2836 Planarity : 0.003 0.050 3229 Dihedral : 9.154 158.753 2564 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.37 % Allowed : 24.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.18), residues: 2239 helix: 0.77 (0.20), residues: 763 sheet: -1.56 (0.29), residues: 345 loop : -1.22 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 350 HIS 0.005 0.001 HIS D 680 PHE 0.014 0.001 PHE F 630 TYR 0.017 0.001 TYR B 482 ARG 0.004 0.000 ARG C 387 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 579) hydrogen bonds : angle 4.38084 ( 1626) covalent geometry : bond 0.00386 (18837) covalent geometry : angle 0.58532 (25495) *********************** 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 287 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 218 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8397 (m-30) cc_final: 0.8062 (m-30) REVERT: C 529 GLN cc_start: 0.8602 (pm20) cc_final: 0.8358 (pm20) REVERT: F 618 MET cc_start: 0.8492 (mtm) cc_final: 0.8093 (mmp) REVERT: E 653 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: D 361 GLU cc_start: 0.8754 (pm20) cc_final: 0.8537 (pm20) REVERT: D 538 LYS cc_start: 0.8417 (pttp) cc_final: 0.8089 (pptt) REVERT: D 614 ASP cc_start: 0.8588 (p0) cc_final: 0.8300 (p0) REVERT: A 334 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8771 (mt) REVERT: A 344 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.7264 (ttp-170) REVERT: A 522 ASP cc_start: 0.8481 (t0) cc_final: 0.8206 (t0) REVERT: A 579 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7898 (tm-30) REVERT: A 660 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: A 681 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8153 (mm) outliers start: 69 outliers final: 46 residues processed: 269 average time/residue: 0.3227 time to fit residues: 129.9395 Evaluate side-chains 252 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 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 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 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 440 VAL Chi-restraints excluded: chain A residue 536 LEU 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 681 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 188 optimal weight: 0.6980 chunk 205 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 ASN F 615 ASN ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.092092 restraints weight = 28845.209| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.62 r_work: 0.2903 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18837 Z= 0.099 Angle : 0.552 8.566 25495 Z= 0.265 Chirality : 0.041 0.145 2836 Planarity : 0.003 0.045 3229 Dihedral : 8.988 158.970 2564 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.22 % Allowed : 24.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2239 helix: 0.98 (0.20), residues: 770 sheet: -1.48 (0.29), residues: 350 loop : -1.14 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 350 HIS 0.003 0.000 HIS F 629 PHE 0.007 0.001 PHE F 630 TYR 0.015 0.001 TYR E 482 ARG 0.005 0.000 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.02583 ( 579) hydrogen bonds : angle 4.08431 ( 1626) covalent geometry : bond 0.00236 (18837) covalent geometry : angle 0.55199 (25495) *********************** 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 300 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 234 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8084 (m-30) cc_final: 0.7679 (m-30) REVERT: C 460 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8362 (mt-10) REVERT: C 529 GLN cc_start: 0.8489 (pm20) cc_final: 0.8185 (pm20) REVERT: C 534 ASP cc_start: 0.7941 (m-30) cc_final: 0.7558 (m-30) REVERT: F 618 MET cc_start: 0.8525 (mtm) cc_final: 0.8111 (mmp) REVERT: E 497 CYS cc_start: 0.8843 (t) cc_final: 0.8085 (m) REVERT: E 578 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7888 (p) REVERT: E 579 GLU cc_start: 0.8220 (mp0) cc_final: 0.7910 (mp0) REVERT: E 653 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: D 426 MET cc_start: 0.8320 (mmp) cc_final: 0.8075 (mmp) REVERT: D 572 ASP cc_start: 0.8619 (p0) cc_final: 0.8341 (t0) REVERT: D 611 ASP cc_start: 0.8453 (m-30) cc_final: 0.8107 (m-30) REVERT: D 614 ASP cc_start: 0.8494 (p0) cc_final: 0.8170 (p0) REVERT: A 334 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8709 (mt) REVERT: A 344 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.7378 (ttp-170) REVERT: A 522 ASP cc_start: 0.8347 (t0) cc_final: 0.8049 (t0) REVERT: A 579 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7767 (tm-30) REVERT: A 660 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7715 (mp10) REVERT: A 684 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8262 (ttp) outliers start: 66 outliers final: 44 residues processed: 284 average time/residue: 0.3348 time to fit residues: 143.1640 Evaluate side-chains 260 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 2.130 ------------------------------------------------------------------------------- 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 342 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 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 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 671 LEU 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 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 653 GLU Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 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 592 ILE Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 684 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 30 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 324 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.089608 restraints weight = 29229.530| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.61 r_work: 0.2866 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18837 Z= 0.152 Angle : 0.586 7.058 25495 Z= 0.284 Chirality : 0.042 0.215 2836 Planarity : 0.003 0.038 3229 Dihedral : 9.043 159.396 2564 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.51 % Allowed : 24.35 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2239 helix: 1.05 (0.20), residues: 763 sheet: -1.57 (0.29), residues: 356 loop : -1.08 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 350 HIS 0.003 0.001 HIS D 680 PHE 0.011 0.001 PHE C 444 TYR 0.017 0.001 TYR B 482 ARG 0.005 0.000 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 579) hydrogen bonds : angle 4.22893 ( 1626) covalent geometry : bond 0.00365 (18837) covalent geometry : angle 0.58553 (25495) *********************** 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 278 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 206 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8119 (m-30) cc_final: 0.7711 (m-30) REVERT: C 460 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8315 (mt-10) REVERT: C 534 ASP cc_start: 0.8000 (m-30) cc_final: 0.7576 (m-30) REVERT: F 618 MET cc_start: 0.8519 (mtm) cc_final: 0.8134 (mmp) REVERT: E 344 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7423 (tpp80) REVERT: E 497 CYS cc_start: 0.8846 (t) cc_final: 0.8112 (m) REVERT: D 426 MET cc_start: 0.8400 (mmp) cc_final: 0.8163 (mmp) REVERT: D 572 ASP cc_start: 0.8713 (p0) cc_final: 0.8492 (t0) REVERT: D 614 ASP cc_start: 0.8533 (p0) cc_final: 0.8198 (p0) REVERT: A 334 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8728 (mt) REVERT: A 344 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.7407 (ttp-170) REVERT: A 399 MET cc_start: 0.8267 (mtt) cc_final: 0.7982 (mtt) REVERT: A 522 ASP cc_start: 0.8352 (t0) cc_final: 0.8015 (t0) REVERT: A 579 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7769 (tm-30) REVERT: A 660 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: A 684 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8276 (ttp) outliers start: 72 outliers final: 54 residues processed: 261 average time/residue: 0.3159 time to fit residues: 125.7232 Evaluate side-chains 256 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 198 time to evaluate : 2.395 ------------------------------------------------------------------------------- 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 659 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 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 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 671 LEU 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 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 659 ILE Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 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 452 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 219 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 180 optimal weight: 0.5980 chunk 176 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 324 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.089987 restraints weight = 28819.175| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.58 r_work: 0.2871 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18837 Z= 0.141 Angle : 0.589 9.323 25495 Z= 0.284 Chirality : 0.042 0.179 2836 Planarity : 0.003 0.037 3229 Dihedral : 9.032 159.457 2564 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.82 % Rotamer: Outliers : 3.37 % Allowed : 24.94 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.18), residues: 2239 helix: 1.08 (0.20), residues: 765 sheet: -1.54 (0.29), residues: 356 loop : -1.06 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 350 HIS 0.004 0.001 HIS D 680 PHE 0.010 0.001 PHE C 444 TYR 0.016 0.001 TYR E 482 ARG 0.007 0.000 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.02951 ( 579) hydrogen bonds : angle 4.18818 ( 1626) covalent geometry : bond 0.00341 (18837) covalent geometry : angle 0.58921 (25495) *********************** 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 281 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 212 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8408 (m-30) cc_final: 0.8010 (m-30) REVERT: C 460 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8461 (mt-10) REVERT: C 534 ASP cc_start: 0.8232 (m-30) cc_final: 0.7941 (m-30) REVERT: F 618 MET cc_start: 0.8588 (mtm) cc_final: 0.8143 (mmp) REVERT: E 344 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7591 (tpp80) REVERT: E 684 MET cc_start: 0.8580 (ttp) cc_final: 0.8379 (ttp) REVERT: D 426 MET cc_start: 0.8627 (mmp) cc_final: 0.8379 (mmp) REVERT: D 538 LYS cc_start: 0.8516 (pptt) cc_final: 0.7997 (pttp) REVERT: D 572 ASP cc_start: 0.8854 (p0) cc_final: 0.8576 (t0) REVERT: D 579 GLU cc_start: 0.9027 (mp0) cc_final: 0.8427 (mp0) REVERT: D 611 ASP cc_start: 0.8581 (m-30) cc_final: 0.8184 (m-30) REVERT: D 614 ASP cc_start: 0.8614 (p0) cc_final: 0.8278 (p0) REVERT: A 334 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8755 (mt) REVERT: A 344 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.7399 (ttp-170) REVERT: A 522 ASP cc_start: 0.8586 (t0) cc_final: 0.8160 (t0) REVERT: A 579 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7809 (tm-30) REVERT: A 660 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7736 (mp10) REVERT: A 684 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8384 (ttp) outliers start: 69 outliers final: 53 residues processed: 265 average time/residue: 0.3316 time to fit residues: 132.8437 Evaluate side-chains 258 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 201 time to evaluate : 2.088 ------------------------------------------------------------------------------- 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 342 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 671 LEU 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 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 659 ILE Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 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 104 optimal weight: 4.9990 chunk 118 optimal weight: 0.0010 chunk 46 optimal weight: 0.2980 chunk 160 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 overall best weight: 2.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3510 r_free = 0.3510 target = 0.122633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.088737 restraints weight = 28847.742| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.55 r_work: 0.2864 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18837 Z= 0.168 Angle : 0.607 9.276 25495 Z= 0.293 Chirality : 0.043 0.232 2836 Planarity : 0.003 0.037 3229 Dihedral : 9.096 159.994 2564 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.03 % Favored : 93.93 % Rotamer: Outliers : 3.61 % Allowed : 24.89 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2239 helix: 1.03 (0.20), residues: 766 sheet: -1.47 (0.28), residues: 356 loop : -1.10 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 350 HIS 0.005 0.001 HIS D 680 PHE 0.012 0.001 PHE C 444 TYR 0.018 0.001 TYR B 482 ARG 0.006 0.000 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 579) hydrogen bonds : angle 4.26778 ( 1626) covalent geometry : bond 0.00407 (18837) covalent geometry : angle 0.60710 (25495) *********************** 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 277 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 203 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8459 (m-30) cc_final: 0.8074 (m-30) REVERT: C 460 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8440 (mt-10) REVERT: C 534 ASP cc_start: 0.8241 (m-30) cc_final: 0.7949 (m-30) REVERT: F 618 MET cc_start: 0.8561 (mtm) cc_final: 0.8059 (mmp) REVERT: E 344 ARG cc_start: 0.7761 (mmm-85) cc_final: 0.7526 (tpp80) REVERT: D 538 LYS cc_start: 0.8526 (pptt) cc_final: 0.7999 (pttp) REVERT: D 572 ASP cc_start: 0.8883 (p0) cc_final: 0.8583 (t0) REVERT: D 579 GLU cc_start: 0.8955 (mp0) cc_final: 0.8386 (mp0) REVERT: D 611 ASP cc_start: 0.8615 (m-30) cc_final: 0.8219 (m-30) REVERT: D 614 ASP cc_start: 0.8667 (p0) cc_final: 0.8332 (p0) REVERT: A 334 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8786 (mt) REVERT: A 344 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.7361 (ttp-170) REVERT: A 522 ASP cc_start: 0.8589 (t0) cc_final: 0.8147 (t0) REVERT: A 579 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7847 (tm-30) REVERT: A 660 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: A 681 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8126 (mm) REVERT: A 684 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8410 (ttp) outliers start: 74 outliers final: 61 residues processed: 256 average time/residue: 0.3084 time to fit residues: 120.9312 Evaluate side-chains 268 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 659 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 447 ASP 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 534 ASP Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 671 LEU 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 497 CYS 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 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 399 MET Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 681 ILE 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 187 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 113 optimal weight: 0.3980 chunk 158 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 38 optimal weight: 0.0060 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.125796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.092159 restraints weight = 28865.461| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.56 r_work: 0.2918 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18837 Z= 0.101 Angle : 0.580 10.194 25495 Z= 0.277 Chirality : 0.041 0.213 2836 Planarity : 0.003 0.036 3229 Dihedral : 8.922 159.883 2564 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.83 % Allowed : 25.62 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2239 helix: 1.23 (0.20), residues: 767 sheet: -1.45 (0.28), residues: 366 loop : -1.01 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 350 HIS 0.002 0.000 HIS F 629 PHE 0.008 0.001 PHE F 630 TYR 0.016 0.001 TYR E 482 ARG 0.008 0.000 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.02469 ( 579) hydrogen bonds : angle 4.00535 ( 1626) covalent geometry : bond 0.00238 (18837) covalent geometry : angle 0.58002 (25495) *********************** 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 273 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8443 (m-30) cc_final: 0.8075 (m-30) REVERT: C 460 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8424 (mt-10) REVERT: C 529 GLN cc_start: 0.9017 (pm20) cc_final: 0.8810 (pm20) REVERT: C 534 ASP cc_start: 0.8253 (m-30) cc_final: 0.7988 (m-30) REVERT: F 618 MET cc_start: 0.8646 (mtm) cc_final: 0.8174 (mmt) REVERT: E 497 CYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8249 (m) REVERT: E 578 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7672 (p) REVERT: E 579 GLU cc_start: 0.8124 (mp0) cc_final: 0.7837 (mp0) REVERT: D 538 LYS cc_start: 0.8442 (pptt) cc_final: 0.7983 (pttp) REVERT: D 572 ASP cc_start: 0.8788 (p0) cc_final: 0.8552 (t0) REVERT: D 579 GLU cc_start: 0.8920 (mp0) cc_final: 0.8372 (mp0) REVERT: D 611 ASP cc_start: 0.8646 (m-30) cc_final: 0.8321 (m-30) REVERT: D 614 ASP cc_start: 0.8619 (p0) cc_final: 0.8261 (p0) REVERT: A 334 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8763 (mt) REVERT: A 399 MET cc_start: 0.8350 (mtt) cc_final: 0.8131 (mtt) REVERT: A 522 ASP cc_start: 0.8606 (t0) cc_final: 0.8165 (t0) REVERT: A 579 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7931 (tm-30) REVERT: A 660 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: A 684 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8381 (ttp) outliers start: 58 outliers final: 46 residues processed: 257 average time/residue: 0.3186 time to fit residues: 124.1211 Evaluate side-chains 256 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 2.254 ------------------------------------------------------------------------------- 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 342 THR Chi-restraints excluded: chain B residue 447 ASP 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 351 ILE Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 461 LEU 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 497 CYS Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 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 169 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 680 HIS ** 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 = 0.124975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091042 restraints weight = 29019.256| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.58 r_work: 0.2901 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18837 Z= 0.128 Angle : 0.590 10.140 25495 Z= 0.282 Chirality : 0.042 0.279 2836 Planarity : 0.003 0.036 3229 Dihedral : 8.945 160.172 2564 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.93 % Allowed : 25.43 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2239 helix: 1.25 (0.20), residues: 767 sheet: -1.44 (0.28), residues: 366 loop : -0.95 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 675 HIS 0.003 0.001 HIS D 680 PHE 0.011 0.001 PHE F 630 TYR 0.016 0.001 TYR C 482 ARG 0.008 0.000 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.02770 ( 579) hydrogen bonds : angle 4.08578 ( 1626) covalent geometry : bond 0.00309 (18837) covalent geometry : angle 0.59033 (25495) ********************** 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 266 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 206 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8195 (m-30) cc_final: 0.7799 (m-30) REVERT: C 460 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8232 (mt-10) REVERT: C 529 GLN cc_start: 0.8868 (pm20) cc_final: 0.8643 (pm20) REVERT: C 534 ASP cc_start: 0.8054 (m-30) cc_final: 0.7801 (m-30) REVERT: F 462 MET cc_start: 0.8505 (tpt) cc_final: 0.8093 (tpp) REVERT: F 618 MET cc_start: 0.8593 (mtm) cc_final: 0.8174 (mmt) REVERT: E 497 CYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8054 (m) REVERT: D 538 LYS cc_start: 0.8332 (pptt) cc_final: 0.7916 (pttp) REVERT: D 579 GLU cc_start: 0.8647 (mp0) cc_final: 0.8108 (mp0) REVERT: D 611 ASP cc_start: 0.8566 (m-30) cc_final: 0.8285 (m-30) REVERT: D 614 ASP cc_start: 0.8550 (p0) cc_final: 0.8182 (p0) REVERT: A 334 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8801 (mt) REVERT: A 399 MET cc_start: 0.8145 (mtt) cc_final: 0.7912 (mtt) REVERT: A 522 ASP cc_start: 0.8373 (t0) cc_final: 0.7915 (t0) REVERT: A 579 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7817 (tm-30) REVERT: A 681 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8032 (mm) REVERT: A 684 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8189 (ttp) outliers start: 60 outliers final: 53 residues processed: 247 average time/residue: 0.3058 time to fit residues: 115.9902 Evaluate side-chains 257 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 200 time to evaluate : 2.234 ------------------------------------------------------------------------------- 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 342 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 447 ASP 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 534 ASP Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 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 497 CYS 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 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 399 MET Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 681 ILE 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 182 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 680 HIS ** 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 = 0.3553 r_free = 0.3553 target = 0.125504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.091843 restraints weight = 28694.669| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.56 r_work: 0.2910 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1761 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= 0.114 Angle : 0.586 10.057 25495 Z= 0.280 Chirality : 0.041 0.286 2836 Planarity : 0.003 0.036 3229 Dihedral : 8.918 160.044 2564 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.78 % Allowed : 25.62 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2239 helix: 1.26 (0.20), residues: 772 sheet: -1.41 (0.28), residues: 366 loop : -0.95 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 675 HIS 0.002 0.000 HIS F 629 PHE 0.011 0.001 PHE F 630 TYR 0.015 0.001 TYR E 482 ARG 0.008 0.000 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.02638 ( 579) hydrogen bonds : angle 4.05470 ( 1626) covalent geometry : bond 0.00274 (18837) covalent geometry : angle 0.58607 (25495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9350.19 seconds wall clock time: 162 minutes 16.98 seconds (9736.98 seconds total)