Starting phenix.real_space_refine on Tue Nov 19 05:07:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwf_35056/11_2024/8hwf_35056.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwf_35056/11_2024/8hwf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwf_35056/11_2024/8hwf_35056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwf_35056/11_2024/8hwf_35056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwf_35056/11_2024/8hwf_35056.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwf_35056/11_2024/8hwf_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.36, per 1000 atoms: 0.56 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: 4.82 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: 2.11 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: 5.60 Time building geometry restraints manager: 5.56 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: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 41.240 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.880 ------------------------------------------------------------------------------- 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= 0.170 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 *********************** 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 : 2.159 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: 0.3436 time to fit residues: 120.9243 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 : 2.299 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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= 0.225 Angle : 0.593 7.036 25495 Z= 0.289 Chirality : 0.042 0.200 2836 Planarity : 0.004 0.065 3229 Dihedral : 9.298 157.519 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 *********************** 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 : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 460 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8286 (mt-10) REVERT: F 618 MET cc_start: 0.8520 (mtm) cc_final: 0.8156 (mmp) REVERT: E 426 MET cc_start: 0.6794 (ptt) cc_final: 0.5410 (ptp) REVERT: E 578 THR cc_start: 0.8164 (m) cc_final: 0.7916 (p) REVERT: E 579 GLU cc_start: 0.7824 (mp0) cc_final: 0.7544 (mp0) REVERT: D 361 GLU cc_start: 0.8505 (pm20) cc_final: 0.8040 (pm20) REVERT: D 614 ASP cc_start: 0.8667 (p0) cc_final: 0.8413 (p0) REVERT: A 334 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8787 (mt) REVERT: A 344 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.7324 (ttp-170) REVERT: A 522 ASP cc_start: 0.7965 (t0) cc_final: 0.7743 (t0) outliers start: 57 outliers final: 28 residues processed: 267 average time/residue: 0.3348 time to fit residues: 134.2794 Evaluate side-chains 242 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 2.167 ------------------------------------------------------------------------------- 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 111 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 GLN B 374 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1072 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= 0.174 Angle : 0.568 10.286 25495 Z= 0.273 Chirality : 0.041 0.210 2836 Planarity : 0.003 0.054 3229 Dihedral : 9.145 158.375 2564 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.83 % Allowed : 23.82 % Favored : 73.35 % 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: -1.54 (0.29), residues: 345 loop : -1.22 (0.18), residues: 1154 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 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8095 (m-30) cc_final: 0.7782 (m-30) REVERT: C 460 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8346 (mt-10) REVERT: F 387 ARG cc_start: 0.7644 (ptt-90) cc_final: 0.7397 (mtm180) REVERT: F 618 MET cc_start: 0.8431 (mtm) cc_final: 0.8117 (mmp) REVERT: F 684 MET cc_start: 0.6707 (tmm) cc_final: 0.6501 (tmm) REVERT: E 535 VAL cc_start: 0.5783 (OUTLIER) cc_final: 0.5352 (t) REVERT: E 578 THR cc_start: 0.8212 (m) cc_final: 0.7724 (p) REVERT: E 579 GLU cc_start: 0.7943 (mp0) cc_final: 0.7685 (mp0) REVERT: E 606 TYR cc_start: 0.8390 (m-80) cc_final: 0.8010 (m-80) REVERT: D 579 GLU cc_start: 0.8674 (mp0) cc_final: 0.8306 (mp0) REVERT: D 614 ASP cc_start: 0.8594 (p0) cc_final: 0.8334 (p0) REVERT: A 334 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8817 (mt) REVERT: A 344 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.7319 (ttp-170) REVERT: A 522 ASP cc_start: 0.8039 (t0) cc_final: 0.7830 (t0) REVERT: A 570 ARG cc_start: 0.8246 (mtp85) cc_final: 0.8022 (mtp85) outliers start: 58 outliers final: 32 residues processed: 288 average time/residue: 0.3335 time to fit residues: 143.8551 Evaluate side-chains 244 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 2.484 ------------------------------------------------------------------------------- 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 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 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 198 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 ASN B 374 GLN F 324 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1245 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= 0.233 Angle : 0.581 8.257 25495 Z= 0.281 Chirality : 0.042 0.172 2836 Planarity : 0.003 0.045 3229 Dihedral : 9.139 158.711 2564 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.42 % Allowed : 23.91 % Favored : 72.67 % 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: 0.80 (0.20), residues: 763 sheet: -1.61 (0.28), residues: 355 loop : -1.18 (0.18), residues: 1121 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 0.012 0.001 PHE F 630 TYR 0.017 0.001 TYR C 482 ARG 0.005 0.000 ARG C 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 220 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8210 (m-30) cc_final: 0.7829 (m-30) REVERT: C 529 GLN cc_start: 0.8355 (pm20) cc_final: 0.8145 (pm20) REVERT: F 387 ARG cc_start: 0.7683 (ptt-90) cc_final: 0.7440 (mtm180) REVERT: F 618 MET cc_start: 0.8454 (mtm) cc_final: 0.8129 (mmp) REVERT: D 614 ASP cc_start: 0.8578 (p0) cc_final: 0.8307 (p0) REVERT: A 334 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8803 (mt) REVERT: A 344 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.7460 (ttp-170) REVERT: A 522 ASP cc_start: 0.8211 (t0) cc_final: 0.7948 (t0) REVERT: A 660 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7738 (mp10) outliers start: 70 outliers final: 48 residues processed: 273 average time/residue: 0.3378 time to fit residues: 137.3972 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 : 2.299 ------------------------------------------------------------------------------- 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 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 659 ILE Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 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 581 CYS Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 594 ASN B 374 GLN ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18837 Z= 0.359 Angle : 0.643 8.599 25495 Z= 0.313 Chirality : 0.044 0.150 2836 Planarity : 0.004 0.042 3229 Dihedral : 9.321 159.365 2564 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.97 % Favored : 92.99 % Rotamer: Outliers : 4.05 % Allowed : 23.91 % Favored : 72.04 % 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: -0.96 (0.18), residues: 2239 helix: 0.75 (0.20), residues: 755 sheet: -1.60 (0.28), residues: 349 loop : -1.25 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 350 HIS 0.007 0.001 HIS D 680 PHE 0.015 0.001 PHE C 444 TYR 0.020 0.001 TYR C 482 ARG 0.006 0.000 ARG C 387 *********************** 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 295 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 212 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8200 (m-30) cc_final: 0.7818 (m-30) REVERT: C 460 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8307 (mt-10) REVERT: C 529 GLN cc_start: 0.8610 (pm20) cc_final: 0.8384 (pm20) REVERT: C 534 ASP cc_start: 0.7902 (m-30) cc_final: 0.7571 (m-30) REVERT: F 618 MET cc_start: 0.8425 (mtm) cc_final: 0.8016 (mmp) REVERT: D 538 LYS cc_start: 0.8444 (pptt) cc_final: 0.8054 (pttp) REVERT: D 572 ASP cc_start: 0.8805 (p0) cc_final: 0.8496 (t0) REVERT: D 611 ASP cc_start: 0.8525 (m-30) cc_final: 0.8278 (m-30) REVERT: D 614 ASP cc_start: 0.8632 (p0) cc_final: 0.8341 (p0) REVERT: A 344 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.7428 (ttp-170) REVERT: A 522 ASP cc_start: 0.8351 (t0) cc_final: 0.8060 (t0) REVERT: A 660 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7638 (mp10) REVERT: A 681 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8125 (mm) REVERT: A 684 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8556 (ttp) outliers start: 83 outliers final: 59 residues processed: 276 average time/residue: 0.3340 time to fit residues: 138.1817 Evaluate side-chains 266 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 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 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 536 LEU Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 655 LEU 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 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 609 VAL 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 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 344 ARG Chi-restraints excluded: chain A residue 440 VAL 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 681 ILE 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 71 optimal weight: 3.9990 chunk 192 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 594 ASN ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18837 Z= 0.160 Angle : 0.572 7.223 25495 Z= 0.276 Chirality : 0.041 0.197 2836 Planarity : 0.003 0.039 3229 Dihedral : 9.090 159.000 2564 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.27 % Allowed : 24.65 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.69 (0.18), residues: 2239 helix: 0.99 (0.20), residues: 763 sheet: -1.47 (0.28), residues: 376 loop : -1.10 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 350 HIS 0.003 0.000 HIS F 629 PHE 0.010 0.001 PHE E 561 TYR 0.015 0.001 TYR E 482 ARG 0.006 0.000 ARG C 387 *********************** 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 292 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8203 (m-30) cc_final: 0.7817 (m-30) REVERT: C 460 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8247 (mt-10) REVERT: C 534 ASP cc_start: 0.7924 (m-30) cc_final: 0.7583 (m-30) REVERT: F 387 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7396 (mpp-170) REVERT: F 618 MET cc_start: 0.8501 (mtm) cc_final: 0.8123 (mmp) REVERT: F 684 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6513 (tmm) REVERT: E 578 THR cc_start: 0.8312 (m) cc_final: 0.7956 (p) REVERT: E 579 GLU cc_start: 0.8108 (mp0) cc_final: 0.7850 (mp0) REVERT: D 538 LYS cc_start: 0.8423 (pptt) cc_final: 0.8060 (pttp) REVERT: D 572 ASP cc_start: 0.8646 (p0) cc_final: 0.8438 (t0) REVERT: D 579 GLU cc_start: 0.8695 (mp0) cc_final: 0.8099 (mp0) REVERT: D 611 ASP cc_start: 0.8506 (m-30) cc_final: 0.8169 (m-30) REVERT: D 614 ASP cc_start: 0.8595 (p0) cc_final: 0.8280 (p0) REVERT: A 334 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8827 (mt) REVERT: A 514 ARG cc_start: 0.8826 (mtm-85) cc_final: 0.8466 (mtm-85) REVERT: A 522 ASP cc_start: 0.8274 (t0) cc_final: 0.7866 (t0) REVERT: A 660 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: A 684 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8448 (ttp) outliers start: 67 outliers final: 47 residues processed: 275 average time/residue: 0.3397 time to fit residues: 140.1320 Evaluate side-chains 261 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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 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 447 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 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 659 ILE Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 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 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 594 ASN 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 206 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 121 optimal weight: 0.0670 chunk 156 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 overall best weight: 1.9924 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1496 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= 0.255 Angle : 0.605 9.212 25495 Z= 0.291 Chirality : 0.042 0.175 2836 Planarity : 0.003 0.041 3229 Dihedral : 9.144 159.644 2564 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.16 % Favored : 93.79 % Rotamer: Outliers : 3.90 % Allowed : 24.35 % Favored : 71.74 % 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: -0.72 (0.18), residues: 2239 helix: 0.97 (0.20), residues: 765 sheet: -1.59 (0.28), residues: 366 loop : -1.09 (0.18), residues: 1108 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 0.011 0.001 PHE C 444 TYR 0.018 0.001 TYR C 482 ARG 0.006 0.000 ARG A 612 *********************** 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 293 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 213 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8241 (m-30) cc_final: 0.7844 (m-30) REVERT: C 460 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8293 (mt-10) REVERT: C 534 ASP cc_start: 0.7973 (m-30) cc_final: 0.7637 (m-30) REVERT: F 387 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7055 (ptt-90) REVERT: F 618 MET cc_start: 0.8514 (mtm) cc_final: 0.8091 (mmp) REVERT: E 578 THR cc_start: 0.8308 (m) cc_final: 0.7960 (p) REVERT: E 579 GLU cc_start: 0.8122 (mp0) cc_final: 0.7819 (mp0) REVERT: D 538 LYS cc_start: 0.8462 (pptt) cc_final: 0.8233 (pttt) REVERT: D 579 GLU cc_start: 0.8709 (mp0) cc_final: 0.8094 (mp0) REVERT: D 611 ASP cc_start: 0.8550 (m-30) cc_final: 0.8201 (m-30) REVERT: D 614 ASP cc_start: 0.8630 (p0) cc_final: 0.8311 (p0) REVERT: A 334 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8790 (mt) REVERT: A 344 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.7437 (ttp-170) REVERT: A 399 MET cc_start: 0.8432 (mtt) cc_final: 0.8120 (mtt) REVERT: A 522 ASP cc_start: 0.8311 (t0) cc_final: 0.7900 (t0) REVERT: A 660 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7580 (mp10) REVERT: A 681 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8091 (mm) REVERT: A 684 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8442 (ttp) outliers start: 80 outliers final: 63 residues processed: 272 average time/residue: 0.3665 time to fit residues: 149.3592 Evaluate side-chains 270 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 201 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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 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 557 GLU Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 655 LEU 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 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 359 SER Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 135 optimal weight: 0.0770 chunk 145 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1631 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= 0.151 Angle : 0.566 9.263 25495 Z= 0.272 Chirality : 0.041 0.157 2836 Planarity : 0.003 0.040 3229 Dihedral : 8.957 159.739 2564 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.12 % Allowed : 25.28 % 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: -0.53 (0.18), residues: 2239 helix: 1.14 (0.20), residues: 769 sheet: -1.39 (0.29), residues: 356 loop : -1.04 (0.18), residues: 1114 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 0.014 0.001 TYR E 482 ARG 0.007 0.000 ARG A 612 *********************** 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 290 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8232 (m-30) cc_final: 0.7852 (m-30) REVERT: C 460 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8243 (mt-10) REVERT: C 534 ASP cc_start: 0.8027 (m-30) cc_final: 0.7745 (m-30) REVERT: F 387 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7281 (mpp-170) REVERT: F 618 MET cc_start: 0.8539 (mtm) cc_final: 0.8156 (mmt) REVERT: F 684 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6505 (tmm) REVERT: E 497 CYS cc_start: 0.8730 (t) cc_final: 0.8098 (m) REVERT: E 578 THR cc_start: 0.8256 (m) cc_final: 0.7743 (p) REVERT: D 538 LYS cc_start: 0.8354 (pptt) cc_final: 0.8116 (pttt) REVERT: D 579 GLU cc_start: 0.8658 (mp0) cc_final: 0.8096 (mp0) REVERT: D 611 ASP cc_start: 0.8584 (m-30) cc_final: 0.8335 (m-30) REVERT: D 614 ASP cc_start: 0.8615 (p0) cc_final: 0.8276 (p0) REVERT: A 334 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8781 (mt) REVERT: A 344 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.7375 (ttp-170) REVERT: A 399 MET cc_start: 0.8402 (mtt) cc_final: 0.8103 (mtt) REVERT: A 522 ASP cc_start: 0.8299 (t0) cc_final: 0.7919 (t0) REVERT: A 660 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7775 (mp10) REVERT: A 684 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8442 (ttp) outliers start: 64 outliers final: 45 residues processed: 271 average time/residue: 0.3545 time to fit residues: 143.0199 Evaluate side-chains 263 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain 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 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 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN 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 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 681 ILE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 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 660 GLN Chi-restraints excluded: chain A residue 684 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 0.0770 chunk 179 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- 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 353 ASN ** E 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1679 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= 0.176 Angle : 0.585 9.663 25495 Z= 0.280 Chirality : 0.041 0.234 2836 Planarity : 0.003 0.036 3229 Dihedral : 8.942 160.028 2564 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.03 % Allowed : 25.33 % 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: -0.45 (0.18), residues: 2239 helix: 1.23 (0.20), residues: 767 sheet: -1.38 (0.29), residues: 359 loop : -0.98 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 675 HIS 0.003 0.001 HIS F 629 PHE 0.011 0.001 PHE F 630 TYR 0.016 0.001 TYR E 482 ARG 0.006 0.000 ARG C 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 212 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8251 (m-30) cc_final: 0.7872 (m-30) REVERT: C 460 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8277 (mt-10) REVERT: C 534 ASP cc_start: 0.8041 (m-30) cc_final: 0.7781 (m-30) REVERT: F 462 MET cc_start: 0.8556 (tpt) cc_final: 0.8176 (tpp) REVERT: F 618 MET cc_start: 0.8544 (mtm) cc_final: 0.8155 (mmt) REVERT: F 684 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6523 (tmm) REVERT: E 344 ARG cc_start: 0.7491 (mmm-85) cc_final: 0.7265 (tpp80) REVERT: E 497 CYS cc_start: 0.8638 (t) cc_final: 0.8051 (m) REVERT: E 578 THR cc_start: 0.8148 (m) cc_final: 0.7697 (p) REVERT: D 538 LYS cc_start: 0.8342 (pptt) cc_final: 0.8113 (pttt) REVERT: D 579 GLU cc_start: 0.8658 (mp0) cc_final: 0.8095 (mp0) REVERT: D 614 ASP cc_start: 0.8616 (p0) cc_final: 0.8259 (p0) REVERT: A 334 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8781 (mt) REVERT: A 344 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.7467 (ttp-170) REVERT: A 399 MET cc_start: 0.8348 (mtt) cc_final: 0.8048 (mtt) REVERT: A 522 ASP cc_start: 0.8321 (t0) cc_final: 0.7945 (t0) REVERT: A 660 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: A 684 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8390 (ttp) outliers start: 62 outliers final: 49 residues processed: 255 average time/residue: 0.3313 time to fit residues: 127.1486 Evaluate side-chains 264 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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 447 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN 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 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 399 MET Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 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 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 209 optimal weight: 0.1980 chunk 128 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 135 optimal weight: 0.6980 chunk 107 optimal weight: 0.1980 chunk 139 optimal weight: 7.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 18837 Z= 0.144 Angle : 0.572 8.867 25495 Z= 0.274 Chirality : 0.041 0.213 2836 Planarity : 0.003 0.038 3229 Dihedral : 8.831 160.068 2564 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.34 % Allowed : 26.21 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.18), residues: 2239 helix: 1.33 (0.20), residues: 770 sheet: -1.28 (0.29), residues: 359 loop : -0.93 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 675 HIS 0.002 0.000 HIS F 629 PHE 0.010 0.001 PHE F 630 TYR 0.013 0.001 TYR C 482 ARG 0.008 0.000 ARG A 612 ********************** 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 273 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8262 (m-30) cc_final: 0.7880 (m-30) REVERT: C 460 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8301 (mt-10) REVERT: F 387 ARG cc_start: 0.7615 (mpp-170) cc_final: 0.7353 (mtm180) REVERT: F 428 TYR cc_start: 0.8465 (m-80) cc_final: 0.8061 (m-10) REVERT: F 462 MET cc_start: 0.8506 (tpt) cc_final: 0.8115 (tpp) REVERT: F 618 MET cc_start: 0.8557 (mtm) cc_final: 0.8183 (mmt) REVERT: F 684 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6435 (tmm) REVERT: E 497 CYS cc_start: 0.8634 (t) cc_final: 0.8055 (m) REVERT: D 538 LYS cc_start: 0.8270 (pptt) cc_final: 0.7973 (pttp) REVERT: D 579 GLU cc_start: 0.8651 (mp0) cc_final: 0.8102 (mp0) REVERT: D 611 ASP cc_start: 0.8600 (m-30) cc_final: 0.8363 (m-30) REVERT: A 334 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8815 (mt) REVERT: A 344 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.7584 (ttp-170) REVERT: A 467 ASP cc_start: 0.8200 (m-30) cc_final: 0.7944 (m-30) REVERT: A 522 ASP cc_start: 0.8365 (t0) cc_final: 0.7972 (t0) REVERT: A 611 ASP cc_start: 0.8942 (t0) cc_final: 0.8657 (p0) REVERT: A 660 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7792 (mp10) REVERT: A 684 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8383 (ttp) outliers start: 48 outliers final: 36 residues processed: 257 average time/residue: 0.3310 time to fit residues: 128.8728 Evaluate side-chains 251 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 499 THR 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 507 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN 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 436 TYR 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 681 ILE Chi-restraints excluded: chain D residue 399 MET 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 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 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 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 186 optimal weight: 6.9990 chunk 53 optimal weight: 0.0060 chunk 161 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- 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** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.090643 restraints weight = 28973.109| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.63 r_work: 0.2894 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1817 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= 0.223 Angle : 0.598 9.989 25495 Z= 0.287 Chirality : 0.042 0.219 2836 Planarity : 0.003 0.036 3229 Dihedral : 8.913 160.250 2564 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.59 % Allowed : 26.11 % Favored : 71.30 % 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: -0.34 (0.18), residues: 2239 helix: 1.29 (0.20), residues: 772 sheet: -1.33 (0.29), residues: 359 loop : -0.91 (0.18), residues: 1108 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 0.013 0.001 PHE F 630 TYR 0.017 0.001 TYR E 482 ARG 0.008 0.000 ARG A 612 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3812.11 seconds wall clock time: 72 minutes 8.88 seconds (4328.88 seconds total)